#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
ACADS	35	broad.mit.edu;ucsc.edu	37	12	121176678	121176678	+	Missense_Mutation	SNP	G	G	A	rs199633532		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr12:121176678G>A	ENST00000242592.4	+	8	1140	c.989G>A	c.(988-990)cGc>cAc	p.R330H	ACADS_ENST00000411593.2_Missense_Mutation_p.R326H|RP11-173P15.7_ENST00000542620.1_RNA	NM_000017.2	NP_000008.1	P16219	ACADS_HUMAN	acyl-CoA dehydrogenase, C-2 to C-3 short chain	330					butyrate catabolic process (GO:0046359)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|protein homotetramerization (GO:0051289)|response to glucocorticoid (GO:0051384)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|butyryl-CoA dehydrogenase activity (GO:0004085)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)	p.R330H(2)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			Flavin adenine dinucleotide(DB03147)	CTGACCTGGCGCGCTGCCATG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		17348	0.0		0.001	False		,,,				2504	0.0																2	Substitution - Missense(2)	prostate(1)|kidney(1)	GRCh37	CM067634	ACADS	M							46.0	52.0	50.0					12																	121176678		2203	4300	6503	SO:0001583	missense	35			M26393	CCDS9207.1	12q24.31	2012-07-13	2010-04-30		ENSG00000122971	ENSG00000122971	1.3.8.1		90	protein-coding gene	gene with protein product		606885	"""acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain"""			2565344	Standard	NM_000017		Approved	SCAD, ACAD3	uc001tza.4	P16219	OTTHUMG00000169203	ENST00000242592.4:c.989G>A	12.37:g.121176678G>A	ENSP00000242592:p.Arg330His		P78331	Missense_Mutation	SNP	ENST00000242592.4	37	CCDS9207.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357217	0.82243	.	.	ENSG00000122971	ENST00000242592;ENST00000411593	D;D	0.96619	-4.07;-4.07	4.63	4.63	0.57726	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.053187	0.64402	D	0.000001	D	0.96694	0.8921	L	0.33792	1.035	0.58432	D	0.999993	D;P;P	0.89917	1.0;0.737;0.737	D;B;B	0.80764	0.994;0.14;0.14	D	0.97682	1.0173	10	0.62326	D	0.03	.	17.5068	0.87748	0.0:0.0:1.0:0.0	.	326;330;330	E9PE82;E5KSD5;P16219	.;.;ACADS_HUMAN	H	330;326	ENSP00000242592:R330H;ENSP00000401045:R326H	ENSP00000242592:R330H	R	+	2	0	ACADS	119661061	1.000000	0.71417	0.916000	0.36221	0.916000	0.54674	7.185000	0.77714	2.125000	0.65367	0.561000	0.74099	CGC		0.642	ACADS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402861.1		NM_000017	
ACE2	59272	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	15591566	15591566	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:15591566C>A	ENST00000252519.3	-	11	1567	c.1465G>T	c.(1465-1467)Gaa>Taa	p.E489*	ACE2_ENST00000427411.1_Nonsense_Mutation_p.E489*			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	489					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.E489*(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	GGCACAGGTTCCACCACCCCA	0.433																																																	1	Substitution - Nonsense(1)	kidney(1)											155.0	131.0	139.0					X																	15591566		2203	4300	6503	SO:0001587	stop_gained	59272			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	300335	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"""			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.1465G>T	X.37:g.15591566C>A	ENSP00000252519:p.Glu489*		C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Nonsense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	C	41	8.869535	0.98984	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.169	18.91	0.92479	0.0:1.0:0.0:0.0	.	.	.	.	X	489	.	ENSP00000252519:E489X	E	-	1	0	ACE2	15501487	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.237000	0.78164	2.413000	0.81919	0.600000	0.82982	GAA		0.433	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1			
APBB1	322	hgsc.bcm.edu;ucsc.edu	37	11	6423907	6423907	+	Silent	SNP	G	G	A	rs1800424	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr11:6423907G>A	ENST00000609360.1	-	7	1252	c.1153C>T	c.(1153-1155)Ctg>Ttg	p.L385L	APBB1_ENST00000609331.1_Silent_p.L150L|APBB1_ENST00000299402.6_Silent_p.L385L|APBB1_ENST00000530885.1_Silent_p.L165L|APBB1_ENST00000608394.1_Silent_p.L126L|APBB1_ENST00000311051.3_Silent_p.L385L|APBB1_ENST00000608645.1_Silent_p.L126L|APBB1_ENST00000389906.2_Silent_p.L385L|APBB1_ENST00000608655.1_Silent_p.L165L|APBB1_ENST00000608704.1_Silent_p.L126L|APBB1_ENST00000529519.1_Intron	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	385	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		CCAGGGGCCAGCTCCTCCTCG	0.582													G|||	21	0.00419329	0.0136	0.0029	5008	,	,		16244	0.0		0.001	False		,,,				2504	0.0				GBM(147;1810 2556 5672 39622)												0								G	,	68,4334	62.3+/-99.4	0,68,2133	88.0	85.0	86.0		1153,1153	4.0	1.0	11	dbSNP_89	86	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	APBB1	NM_001164.2,NM_145689.1	,	0,68,6429	AA,AG,GG		0.0,1.5448,0.5233	,	385/711,385/709	6423907	68,12926	2201	4296	6497	SO:0001819	synonymous_variant	322			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1153C>T	11.37:g.6423907G>A			A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Silent	SNP	ENST00000609360.1	37																																																																																					0.582	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1		NM_001164	
ARHGEF11	9826	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	156909401	156909401	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr1:156909401C>A	ENST00000361409.2	-	36	4657	c.3915G>T	c.(3913-3915)agG>agT	p.R1305S	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R1345S|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.R721S	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1305					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1345S(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CAGCCAGATTCCTGTCCAGTT	0.512																																																	1	Substitution - Missense(1)	kidney(1)											74.0	79.0	77.0					1																	156909401		2203	4300	6503	SO:0001583	missense	9826			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3915G>T	1.37:g.156909401C>A	ENSP00000354644:p.Arg1305Ser		D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.698637	0.30142	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.66280	-0.2;-0.2;-0.12	4.41	3.4	0.38934	.	0.374454	0.22821	N	0.055227	T	0.29850	0.0746	N	0.24115	0.695	0.09310	N	1	P;B;P	0.36789	0.57;0.265;0.57	B;B;B	0.39217	0.294;0.05;0.217	T	0.05784	-1.0864	10	0.35671	T	0.21	-4.0454	9.1025	0.36678	0.0:0.8811:0.0:0.1189	.	721;1305;1345	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	S	1345;1305;721	ENSP00000357177:R1345S;ENSP00000354644:R1305S;ENSP00000313470:R721S	ENSP00000313470:R721S	R	-	3	2	ARHGEF11	155176025	0.487000	0.25988	0.509000	0.27700	0.693000	0.40251	0.807000	0.27140	2.243000	0.73865	0.561000	0.74099	AGG		0.512	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1		NM_198236	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149001322	149001323	+	Frame_Shift_Ins	INS	-	-	C	rs560081847		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr5:149001322_149001323insC	ENST00000333677.6	+	9	1195_1196	c.1032_1033insC	c.(1033-1035)cagfs	p.Q345fs		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	345	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GCCTGGTGTGGCAGCCACTGTG	0.594																																																	0																																										SO:0001589	frameshift_variant	389337			BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1033dupC	5.37:g.149001323_149001323dupC	ENSP00000328083:p.Gln345fs		Q6ZW51	Frame_Shift_Ins	INS	ENST00000333677.6	37	CCDS43385.1																																																																																				0.594	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1		NM_001001669	
BSN	8927	broad.mit.edu;hgsc.bcm.edu	37	3	49662433	49662433	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:49662433G>A	ENST00000296452.4	+	2	364	c.250G>A	c.(250-252)Gaa>Aaa	p.E84K		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	84					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.E84K(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGACCCCAAGGAACCCCTGGG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											43.0	48.0	47.0					3																	49662433		2203	4300	6503	SO:0001583	missense	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.250G>A	3.37:g.49662433G>A	ENSP00000296452:p.Glu84Lys		O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196315	0.58126	.	.	ENSG00000164061	ENST00000296452	T	0.15834	2.39	5.48	5.48	0.80851	.	0.117022	0.37857	N	0.001914	T	0.14141	0.0342	N	0.22421	0.69	0.35465	D	0.796827	B	0.22346	0.068	B	0.15870	0.014	T	0.11470	-1.0586	10	0.29301	T	0.29	.	18.958	0.92668	0.0:0.0:1.0:0.0	.	84	Q9UPA5	BSN_HUMAN	K	84	ENSP00000296452:E84K	ENSP00000296452:E84K	E	+	1	0	BSN	49637437	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	8.273000	0.89887	2.583000	0.87209	0.563000	0.77884	GAA		0.557	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1		NM_003458	
GCFC2	6936	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	75907426	75907426	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr2:75907426G>T	ENST00000321027.3	-	12	1838	c.1705C>A	c.(1705-1707)Ctt>Att	p.L569I	GCFC2_ENST00000541687.1_3'UTR|MRPL19_ENST00000358788.6_Intron|GCFC2_ENST00000409857.3_Missense_Mutation_p.L531I	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	569					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	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)	p.L569I(1)									GGATCCCAAAGGAATTCTACA	0.313																																																	1	Substitution - Missense(1)	kidney(1)											101.0	104.0	103.0					2																	75907426		2203	4299	6502	SO:0001583	missense	0			AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"""GC binding factor"""	189901	"""transcription factor 9 (binds GC-rich sequences)"", ""chromosome 2 open reading frame 3"""	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.1705C>A	2.37:g.75907426G>T	ENSP00000318690:p.Leu569Ile		A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	G	1.342	-0.593917	0.03771	.	.	ENSG00000005436	ENST00000321027;ENST00000409857	T;T	0.13089	2.62;2.63	5.42	0.168	0.15012	GC-rich sequence DNA-binding factor domain (1);	0.333157	0.31102	N	0.008253	T	0.02571	0.0078	N	0.00760	-1.21	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.37798	-0.9690	10	0.08599	T	0.76	-8.028	3.33	0.07080	0.137:0.0856:0.4571:0.3203	.	569	P16383	GCF_HUMAN	I	569;531	ENSP00000318690:L569I;ENSP00000386552:L531I	ENSP00000318690:L569I	L	-	1	0	C2orf3	75760934	0.526000	0.26298	0.979000	0.43373	0.904000	0.53231	0.264000	0.18497	0.433000	0.26313	-0.271000	0.10264	CTT		0.313	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2		NM_003203	
C3orf33	285315	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	155493591	155493591	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:155493591C>A	ENST00000340171.2	-	3	319	c.221G>T	c.(220-222)aGa>aTa	p.R74I	C3orf33_ENST00000534941.1_Missense_Mutation_p.R31I			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	74					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)	p.R25I(1)		breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AACATTTCTTCTTATAAATTC	0.299																																																	1	Substitution - Missense(1)	kidney(1)											95.0	94.0	94.0					3																	155493591		1800	4055	5855	SO:0001583	missense	285315			AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.221G>T	3.37:g.155493591C>A	ENSP00000342512:p.Arg74Ile		A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Missense_Mutation	SNP	ENST00000340171.2	37		.	.	.	.	.	.	.	.	.	.	C	18.35	3.603662	0.66445	.	.	ENSG00000174928	ENST00000534941;ENST00000340171;ENST00000537385	T;T	0.48836	0.8;0.8	5.45	2.36	0.29203	.	0.160773	0.53938	D	0.000048	T	0.49949	0.1587	M	0.62723	1.935	0.51767	D	0.999932	D	0.53151	0.958	P	0.51135	0.66	T	0.46512	-0.9186	10	0.72032	D	0.01	-4.332	6.4576	0.21938	0.0:0.3143:0.0:0.6857	.	74	Q6P1S2	CC033_HUMAN	I	31;74;74	ENSP00000445446:R31I;ENSP00000342512:R74I	ENSP00000342512:R74I	R	-	2	0	C3orf33	156976285	1.000000	0.71417	0.696000	0.30242	0.999000	0.98932	0.948000	0.29096	0.193000	0.20303	0.655000	0.94253	AGA		0.299	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1		NM_173657	
CACNA1S	779	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	201041938	201041938	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr1:201041938C>T	ENST00000362061.3	-	16	2398	c.2172G>A	c.(2170-2172)gaG>gaA	p.E724E	CACNA1S_ENST00000367338.3_Silent_p.E724E	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	724					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E724E(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TAGATTCAAACTCATCGATTT	0.488																																																	1	Substitution - coding silent(1)	kidney(1)											163.0	164.0	164.0					1																	201041938		2203	4300	6503	SO:0001819	synonymous_variant	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.2172G>A	1.37:g.201041938C>T			A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																				0.488	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1		NM_000069	
CACNG5	27091	hgsc.bcm.edu;ucsc.edu	37	17	64873504	64873505	+	Frame_Shift_Ins	INS	-	-	TG			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr17:64873504_64873505insTG	ENST00000533854.1	+	2	291_292	c.54_55insTG	c.(55-57)tgtfs	p.C19fs	CACNG5_ENST00000307139.3_Frame_Shift_Ins_p.C19fs|CACNG5_ENST00000169565.3_Frame_Shift_Ins_p.C19fs			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	19					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			TCTTTGCTGTCTGTGGCTTGGG	0.604																																																	0																																										SO:0001589	frameshift_variant	27091			AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.57_58dupTG	17.37:g.64873507_64873508dupTG	ENSP00000436836:p.Cys19fs		A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Frame_Shift_Ins	INS	ENST00000533854.1	37	CCDS11665.1																																																																																				0.604	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1		NM_014404, NM_145811	
CD27	939	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	6554632	6554632	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr12:6554632C>A	ENST00000266557.3	+	2	408	c.179C>A	c.(178-180)gCt>gAt	p.A60D	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA|CD27_ENST00000541233.1_3'UTR	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	60					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)	p.A60D(1)		kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						AGAAAGGCTGCTCAGTGTGAT	0.582																																																	1	Substitution - Missense(1)	kidney(1)											148.0	121.0	130.0					12																	6554632		2203	4300	6503	SO:0001583	missense	939			M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11922	protein-coding gene	gene with protein product		186711	"""tumor necrosis factor receptor superfamily, member 7"""	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.179C>A	12.37:g.6554632C>A	ENSP00000266557:p.Ala60Asp		B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.194283	0.78902	.	.	ENSG00000139193	ENST00000266557	D	0.94184	-3.37	4.54	4.54	0.55810	TNFR/CD27/30/40/95 cysteine-rich region (2);	1.218180	0.05882	N	0.626604	D	0.92028	0.7474	L	0.32530	0.975	0.09310	N	0.999997	P	0.43231	0.801	P	0.45829	0.494	D	0.84241	0.0472	10	0.54805	T	0.06	-0.3705	12.6495	0.56753	0.0:1.0:0.0:0.0	.	60	P26842	CD27_HUMAN	D	60	ENSP00000266557:A60D	ENSP00000266557:A60D	A	+	2	0	CD27	6424893	0.025000	0.19082	0.032000	0.17829	0.507000	0.33981	1.977000	0.40589	2.359000	0.80004	0.563000	0.77884	GCT		0.582	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1			
COL19A1	1310	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	70878567	70878567	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr6:70878567C>T	ENST00000322773.4	+	40	2664	c.2562C>T	c.(2560-2562)ggC>ggT	p.G854G	COL19A1_ENST00000393344.1_Silent_p.G476G	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	854	Collagen-like 9.|Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.G854G(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GCGATCCTGGCCCAGTGGTAT	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											147.0	139.0	142.0					6																	70878567		2203	4300	6503	SO:0001819	synonymous_variant	1310				CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2562C>T	6.37:g.70878567C>T			Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																				0.388	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			
COL4A5	1287	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	107938641	107938641	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:107938641G>A	ENST00000361603.2	+	50	5192	c.4948G>A	c.(4948-4950)Gca>Aca	p.A1650T	COL4A5_ENST00000328300.6_Missense_Mutation_p.A1656T	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1650	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.		Missing (in APSX). {ECO:0000269|PubMed:7853788}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.A1650T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CTTTTGGCTGGCAACTGTAGA	0.453									Alport syndrome with Diffuse Leiomyomatosis																																								1	Substitution - Missense(1)	kidney(1)											122.0	106.0	111.0					X																	107938641		2203	4300	6503	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4948G>A	X.37:g.107938641G>A	ENSP00000354505:p.Ala1650Thr		Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Nonsense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893988	0.91889	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.94046	-3.34;-3.34	5.44	5.44	0.79542	C-type lectin fold (1);	0.058040	0.64402	D	0.000002	D	0.93612	0.7960	N	0.25094	0.71	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	D	0.92186	0.5755	10	0.22109	T	0.4	.	18.3768	0.90438	0.0:0.0:1.0:0.0	.	1653;1650	E7EVY4;P29400	.;CO4A5_HUMAN	T	1656;1650;1656	ENSP00000331902:A1656T;ENSP00000354505:A1650T	ENSP00000331902:A1656T	A	+	1	0	COL4A5	107825297	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.062000	0.89475	2.280000	0.76307	0.600000	0.82982	GCA		0.453	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			
CSAG1	158511	hgsc.bcm.edu;ucsc.edu	37	X	151908814	151908814	+	Frame_Shift_Del	DEL	G	G	-	rs186409993		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:151908814delG	ENST00000370287.3	+	4	381	c.53delG	c.(52-54)cggfs	p.R18fs	CSAG1_ENST00000452779.2_Frame_Shift_Del_p.R18fs|CSAG1_ENST00000370291.2_Frame_Shift_Del_p.R18fs	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	18										central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGAAGCTCGGGGAGACCAG	0.512																																																	0													184.0	178.0	180.0					X																	151908814		2203	4300	6503	SO:0001589	frameshift_variant	158511			AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.53delG	X.37:g.151908814delG	ENSP00000359310:p.Arg18fs		A6NE22	Frame_Shift_Del	DEL	ENST00000370287.3	37	CCDS14711.1																																																																																				0.512	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2		NM_153479	
CSMD1	64478	broad.mit.edu	37	8	3245041	3245041	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr8:3245041C>T	ENST00000520002.1	-	19	3315	c.2760G>A	c.(2758-2760)tgG>tgA	p.W920*	CSMD1_ENST00000537824.1_Nonsense_Mutation_p.W919*|CSMD1_ENST00000602723.1_Nonsense_Mutation_p.W920*|CSMD1_ENST00000400186.3_Nonsense_Mutation_p.W920*|CSMD1_ENST00000539096.1_Nonsense_Mutation_p.W919*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.W919*|CSMD1_ENST00000602557.1_Nonsense_Mutation_p.W920*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	920	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.W648*(1)|p.W919*(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AGGCGTGGTTCCACTGGTGGT	0.587																																																	2	Substitution - Nonsense(2)	kidney(2)											41.0	47.0	45.0					8																	3245041		2109	4225	6334	SO:0001587	stop_gained	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2760G>A	8.37:g.3245041C>T	ENSP00000430733:p.Trp920*		Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	45|45	12.038172|12.038172	0.99630|0.99630	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|.	.|.	.|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|.	0.46288|.	0.1385|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40478|.	-0.9561|.	3|.	.|0.02654	.|T	.|1	.|.	18.5306|18.5306	0.90990|0.90990	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	K|X	400|920;920;782;919;919;919	.|.	.|ENSP00000320445:W782X	E|W	-|-	1|3	0|0	CSMD1|CSMD1	3232448|3232448	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.903000|0.903000	0.53119|0.53119	7.635000|7.635000	0.83286|0.83286	2.374000|2.374000	0.81015|0.81015	0.650000|0.650000	0.86243|0.86243	GAA|TGG		0.587	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2		NM_033225	
DDX3X	1654	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	41202084	41202084	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:41202084G>C	ENST00000399959.2	+	6	1393	c.538G>C	c.(538-540)Gaa>Caa	p.E180Q	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000542215.1_Missense_Mutation_p.E224Q|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000457138.2_Missense_Mutation_p.E164Q	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	180	Interaction with GSK3B.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)	p.E180Q(1)		NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						TCCACATATTGAAAGTGTGAG	0.378										HNSCC(61;0.18)																																							1	Substitution - Missense(1)	kidney(1)											98.0	84.0	88.0					X																	41202084		1927	4126	6053	SO:0001583	missense	1654			U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"""DEAD-boxes"""	2745	protein-coding gene	gene with protein product		300160	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"""	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.538G>C	X.37:g.41202084G>C	ENSP00000382840:p.Glu180Gln		A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049745	0.75846	.	.	ENSG00000215301	ENST00000399959;ENST00000457138;ENST00000542215	T;T;T	0.42513	2.07;2.06;0.97	5.54	5.54	0.83059	RNA helicase, DEAD-box type, Q motif (1);	0.048477	0.85682	D	0.000000	T	0.39118	0.1066	L	0.47716	1.5	0.80722	D	1	B;B;B;B;B	0.24651	0.108;0.04;0.065;0.041;0.041	B;B;B;B;B	0.23275	0.045;0.004;0.007;0.026;0.016	T	0.16100	-1.0414	10	0.20519	T	0.43	-8.0209	18.5081	0.90905	0.0:0.0:1.0:0.0	.	180;164;180;192;180	B4DLU5;B4E3E8;B5BTY4;Q59GX6;O00571	.;.;.;.;DDX3X_HUMAN	Q	180;164;224	ENSP00000382840:E180Q;ENSP00000392494:E164Q;ENSP00000439799:E224Q	ENSP00000382840:E180Q	E	+	1	0	DDX3X	41087028	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.313000	0.78055	0.600000	0.82982	GAA		0.378	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1		NM_024005	
DACH2	117154	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	85906058	85906058	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:85906058G>C	ENST00000373125.4	+	4	660	c.660G>C	c.(658-660)atG>atC	p.M220I	DACH2_ENST00000508860.1_Missense_Mutation_p.M53I|DACH2_ENST00000373131.1_Missense_Mutation_p.M207I|DACH2_ENST00000510272.1_Start_Codon_SNP_p.M1I	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	220					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.M220I(1)|p.M207I(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						CTGCAGCGATGGCTGAGGCGA	0.368																																																	2	Substitution - Missense(2)	kidney(2)											75.0	59.0	64.0					X																	85906058		2203	4300	6503	SO:0001583	missense	117154			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.660G>C	X.37:g.85906058G>C	ENSP00000362217:p.Met220Ile		B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.694737	0.48202	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297	D;D	0.81821	-1.54;-1.53	4.69	4.69	0.59074	.	0.064313	0.64402	D	0.000007	T	0.68659	0.3025	N	0.19112	0.55	0.26410	N	0.976276	B;B;B	0.27971	0.196;0.013;0.049	B;B;B	0.27076	0.032;0.076;0.074	T	0.54912	-0.8222	10	0.19147	T	0.46	.	16.9482	0.86236	0.0:0.0:1.0:0.0	.	86;207;220	Q1RMF5;Q96NX9-2;Q96NX9	.;.;DACH2_HUMAN	I	220;207;220;53;1;53	ENSP00000362223:M207I;ENSP00000362217:M220I	ENSP00000345134:M220I	M	+	3	0	DACH2	85792714	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	6.936000	0.75892	1.918000	0.55548	0.513000	0.50165	ATG		0.368	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1		NM_053281	
DHX35	60625	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	37650496	37650496	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr20:37650496G>T	ENST00000252011.3	+	16	1544	c.1511G>T	c.(1510-1512)tGt>tTt	p.C504F	DHX35_ENST00000373325.2_Missense_Mutation_p.C504F|DHX35_ENST00000373323.4_Missense_Mutation_p.C473F	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	504					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.C504F(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				AACTTCGGCTGTTCTCAGGAA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											176.0	175.0	175.0					20																	37650496		2203	4300	6503	SO:0001583	missense	60625			AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1511G>T	20.37:g.37650496G>T	ENSP00000252011:p.Cys504Phe		A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	37	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451008	0.84209	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321	T;T;T	0.39229	1.09;1.09;1.09	6.07	6.07	0.98685	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	D	0.83376	0.5241	H	0.99916	4.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90811	0.4701	10	0.87932	D	0	.	20.239	0.98366	0.0:0.0:1.0:0.0	.	473;504	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	F	504;504;473;10	ENSP00000362422:C504F;ENSP00000252011:C504F;ENSP00000362420:C473F	ENSP00000252011:C504F	C	+	2	0	DHX35	37083910	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.922000	0.92789	2.884000	0.98904	0.655000	0.94253	TGT		0.433	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2		NM_021931	
DMKN	93099	broad.mit.edu	37	19	35991482	35991482	+	Splice_Site	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr19:35991482C>T	ENST00000339686.3	-	12	1416	c.1240G>A	c.(1240-1242)Ggt>Agt	p.G414S	DMKN_ENST00000467637.1_Splice_Site_p.G139S|DMKN_ENST00000602781.1_Splice_Site_p.G127S|DMKN_ENST00000462126.1_5'UTR|DMKN_ENST00000402589.2_Splice_Site_p.G127S|DMKN_ENST00000414866.2_Splice_Site_p.G127S|DMKN_ENST00000436012.1_Splice_Site_p.G110S|DMKN_ENST00000472252.2_Splice_Site_p.G61S|DMKN_ENST00000419602.1_Splice_Site_p.G403S|DMKN_ENST00000443640.1_Splice_Site_p.G177S|DMKN_ENST00000429837.1_Splice_Site_p.G373S|DMKN_ENST00000480502.1_Splice_Site_p.G108S|DMKN_ENST00000408915.2_Splice_Site_p.G28S|DMKN_ENST00000492341.2_Splice_Site_p.G61S	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	414						extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G414S(1)|p.G403S(1)		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)			GCGTCCGCACCCTGAAAGGAA	0.617																																																	2	Substitution - Missense(2)	kidney(2)											70.0	47.0	55.0					19																	35991482		2203	4300	6503	SO:0001630	splice_region_variant	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.1240-1G>A	19.37:g.35991482C>T			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|C	16.88|16.88	3.243376|3.243376	0.58995|0.58995	.|.	.|.	ENSG00000161249|ENSG00000161249	ENST00000434389|ENST00000408915;ENST00000402589;ENST00000339686;ENST00000436012;ENST00000414866;ENST00000429837;ENST00000419602;ENST00000443640	.|T;T;T;T;T;T;T;T	.|0.73258	.|-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	3.96|3.96	2.9|2.9	0.33743|0.33743	.|.	0.338596|0.338596	0.21477|0.21477	N|N	0.073882|0.073882	T|T	0.78780|0.78780	0.4337|0.4337	L|L	0.59436|0.59436	1.845|1.845	0.20196|0.20196	N|N	0.999921|0.999921	.|P;P;D;D;D;D;D;D;P;P;P;P	.|0.89917	.|0.94;0.484;1.0;1.0;1.0;1.0;0.999;0.996;0.94;0.873;0.543;0.551	.|P;B;D;D;D;D;D;P;P;B;B;B	.|0.91635	.|0.51;0.241;0.999;0.998;0.998;0.998;0.962;0.848;0.51;0.318;0.125;0.134	T|T	0.67256|0.67256	-0.5716|-0.5716	6|10	.|0.87932	.|D	.|0	-2.4712|-2.4712	9.1623|9.1623	0.37030|0.37030	0.2165:0.7835:0.0:0.0|0.2165:0.7835:0.0:0.0	.|.	.|110;61;70;70;90;108;403;373;414;127;177;28	.|B4E3D1;B7ZB10;Q6E0U4-12;Q6E0U4-11;Q6E0U4-10;Q6E0U4-9;C9J4P6;Q6E0U4-4;Q6E0U4;Q6E0U4-8;C9IYI1;Q6E0U4-15	.|.;.;.;.;.;.;.;.;DMKN_HUMAN;.;.;.	E|S	124|28;127;414;110;127;373;403;177	.|ENSP00000386225:G28S;ENSP00000384509:G127S;ENSP00000342012:G414S;ENSP00000412075:G110S;ENSP00000392222:G127S;ENSP00000405503:G373S;ENSP00000391036:G403S;ENSP00000406864:G177S	.|ENSP00000342012:G414S	G|G	-|-	2|1	0|0	DMKN|DMKN	40683322|40683322	0.971000|0.971000	0.33674|0.33674	0.023000|0.023000	0.16930|0.16930	0.102000|0.102000	0.19082|0.19082	3.095000|3.095000	0.50235|0.50235	1.001000|1.001000	0.39076|0.39076	0.436000|0.436000	0.28706|0.28706	GGG|GGT		0.617	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2		NM_033317	Missense_Mutation
DMXL2	23312	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	51778458	51778458	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr15:51778458G>T	ENST00000251076.5	-	23	5581	c.5294C>A	c.(5293-5295)tCa>tAa	p.S1765*	DMXL2_ENST00000449909.3_Nonsense_Mutation_p.S1129*|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Nonsense_Mutation_p.S1765*	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1765						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.S1765*(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ATAAGTGGATGAAGTCTCAAA	0.353																																																	1	Substitution - Nonsense(1)	kidney(1)											84.0	86.0	85.0					15																	51778458		2196	4293	6489	SO:0001587	stop_gained	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.5294C>A	15.37:g.51778458G>T	ENSP00000251076:p.Ser1765*		B2RTR3|B7ZMH3|F5GWF1|O94938	Nonsense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	42	9.625105	0.99223	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1041	0.97884	0.0:0.0:1.0:0.0	.	.	.	.	X	1765;1765;1129	.	ENSP00000251076:S1765X	S	-	2	0	DMXL2	49565750	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.602000	0.98312	2.826000	0.97356	0.655000	0.94253	TCA		0.353	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2		NM_015263	
DMXL2	23312	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	51778460	51778460	+	Silent	SNP	A	A	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr15:51778460A>G	ENST00000251076.5	-	23	5579	c.5292T>C	c.(5290-5292)acT>acC	p.T1764T	DMXL2_ENST00000449909.3_Silent_p.T1128T|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Silent_p.T1764T	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1764						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.T1764T(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AAGTGGATGAAGTCTCAAATT	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											83.0	86.0	85.0					15																	51778460		2196	4293	6489	SO:0001819	synonymous_variant	23312			AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.5292T>C	15.37:g.51778460A>G			B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																				0.348	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2		NM_015263	
DNAH9	1770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	11648186	11648186	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr17:11648186C>T	ENST00000262442.4	+	31	6252	c.6184C>T	c.(6184-6186)Cct>Tct	p.P2062S	DNAH9_ENST00000454412.2_Missense_Mutation_p.P2062S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2062					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.P2062S(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAGGAGACCCTGACCGGCC	0.572																																																	1	Substitution - Missense(1)	kidney(1)											65.0	58.0	60.0					17																	11648186		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6184C>T	17.37:g.11648186C>T	ENSP00000262442:p.Pro2062Ser		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710263	0.89018	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.15372	2.43;2.43	5.46	5.46	0.80206	.	1.880920	0.02181	N	0.060493	T	0.33527	0.0866	M	0.64260	1.97	0.80722	D	1	B	0.34226	0.443	B	0.38327	0.271	T	0.31888	-0.9927	10	0.44086	T	0.13	.	19.3688	0.94475	0.0:1.0:0.0:0.0	.	2062	Q9NYC9	DYH9_HUMAN	S	2062;2062;644	ENSP00000262442:P2062S;ENSP00000414874:P2062S	ENSP00000262442:P2062S	P	+	1	0	DNAH9	11588911	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.910000	0.69931	2.565000	0.86533	0.650000	0.86243	CCT		0.572	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
EBLN2	55096	hgsc.bcm.edu	37	3	73111481	73111481	+	Missense_Mutation	SNP	C	C	A	rs3832186|rs201649088	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:73111481C>A	ENST00000533473.1	+	1	672	c.249C>A	c.(247-249)aaC>aaA	p.N83K	PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	83										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						CTGGGAAAAACAGACAGTATC	0.478																																																	0													34.0	34.0	34.0					3																	73111481		1942	4138	6080	SO:0001583	missense	55096				CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.249C>A	3.37:g.73111481C>A	ENSP00000432104:p.Asn83Lys		Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	C	4.916	0.170168	0.09339	.	.	ENSG00000255423	ENST00000533473	.	.	.	0.458	0.458	0.16670	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.16854	0.0405	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.23368	-1.0190	7	0.31617	T	0.26	.	.	.	.	.	83	Q6P2I7	EBLN2_HUMAN	K	83	.	ENSP00000432104:N83K	N	+	3	2	EBLN2	73194171	0.047000	0.20315	0.005000	0.12908	0.005000	0.04900	0.305000	0.19254	0.482000	0.27582	0.484000	0.47621	AAC		0.478	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1		NM_018029	
EDC4	23644	broad.mit.edu	37	16	67917881	67917881	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr16:67917881C>A	ENST00000358933.5	+	29	4275	c.4036C>A	c.(4036-4038)Cac>Aac	p.H1346N	NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1346					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.H1346N(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		GGCCGTGATGCACCTGGACCA	0.637											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					2	Substitution - Missense(2)	endometrium(1)|kidney(1)											66.0	59.0	61.0					16																	67917881		2198	4300	6498	SO:0001583	missense	23644			U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.4036C>A	16.37:g.67917881C>A	ENSP00000351811:p.His1346Asn	1103	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	37	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625078	0.46840	.	.	ENSG00000038358	ENST00000358933	.	.	.	5.24	5.24	0.73138	.	0.043316	0.85682	D	0.000000	T	0.40815	0.1132	N	0.12569	0.235	0.45962	D	0.998783	B	0.06786	0.001	B	0.06405	0.002	T	0.24297	-1.0164	9	0.15499	T	0.54	-16.5403	18.7721	0.91896	0.0:1.0:0.0:0.0	.	1346	Q6P2E9	EDC4_HUMAN	N	1346	.	ENSP00000351811:H1346N	H	+	1	0	EDC4	66475382	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.627000	0.61276	2.622000	0.88805	0.655000	0.94253	CAC		0.637	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2		NM_014329	
OTULIN	90268	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	14693052	14693052	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr5:14693052C>T	ENST00000284274.4	+	7	1032	c.954C>T	c.(952-954)gtC>gtT	p.V318V		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		318	OTU.				canonical Wnt signaling pathway (GO:0060070)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|protein linear deubiquitination (GO:1990108)|sprouting angiogenesis (GO:0002040)	cytoplasm (GO:0005737)|LUBAC complex (GO:0071797)	cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)	p.V318V(1)		breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	14	Lung NSC(4;0.00696)					TCATCACAGTCTACCCCACCG	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											106.0	113.0	111.0					5																	14693052		2095	4219	6314	SO:0001819	synonymous_variant	90268																														ENST00000284274.4:c.954C>T	5.37:g.14693052C>T			D3DTD3|Q8NAS0|Q96IA3	Silent	SNP	ENST00000284274.4	37	CCDS43302.1																																																																																				0.542	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1			
FEM1B	10116	broad.mit.edu;ucsc.edu	37	15	68582835	68582835	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr15:68582835A>T	ENST00000306917.4	+	2	1754	c.1139A>T	c.(1138-1140)aAc>aTc	p.N380I		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	380					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)	p.N380I(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						GGTAACAGGAACACCCACAAG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											83.0	79.0	81.0					15																	68582835		2200	4298	6498	SO:0001583	missense	10116				CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"""Ankyrin repeat domain containing"""	3649	protein-coding gene	gene with protein product		613539	"""FEM-1 (C. elegans) homolog b"""			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1139A>T	15.37:g.68582835A>T	ENSP00000307298:p.Asn380Ile		O43146	Missense_Mutation	SNP	ENST00000306917.4	37	CCDS10228.1	.	.	.	.	.	.	.	.	.	.	A	15.57	2.873714	0.51695	.	.	ENSG00000169018	ENST00000306917	T	0.38560	1.13	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.30603	0.0770	L	0.31207	0.915	0.80722	D	1	P	0.42941	0.794	B	0.35931	0.214	T	0.06789	-1.0807	10	0.30078	T	0.28	-41.5039	15.3634	0.74499	1.0:0.0:0.0:0.0	.	380	Q9UK73	FEM1B_HUMAN	I	380	ENSP00000307298:N380I	ENSP00000307298:N380I	N	+	2	0	FEM1B	66369889	1.000000	0.71417	0.963000	0.40424	0.956000	0.61745	9.264000	0.95635	2.220000	0.72140	0.397000	0.26171	AAC		0.408	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1			
GBF1	8729	hgsc.bcm.edu;ucsc.edu	37	10	104118423	104118423	+	Silent	SNP	G	G	T	rs142955445	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr10:104118423G>T	ENST00000369983.3	+	10	1208	c.948G>T	c.(946-948)ggG>ggT	p.G316G		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	316					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GCTCTCCAGGGTACAGCACAG	0.522																																																	0													99.0	95.0	97.0					10																	104118423		2203	4300	6503	SO:0001819	synonymous_variant	8729			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.948G>T	10.37:g.104118423G>T			Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																				0.522	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			
GMCL1	64395	broad.mit.edu	37	2	70057234	70057234	+	Silent	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr2:70057234G>A	ENST00000282570.3	+	1	461	c.210G>A	c.(208-210)gaG>gaA	p.E70E	GMCL1_ENST00000468386.2_3'UTR	NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	70					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)		p.E70E(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						AGACGGACGAGGATGAGGAGG	0.682																																																	1	Substitution - coding silent(1)	kidney(1)											18.0	18.0	18.0					2																	70057234		2188	4290	6478	SO:0001819	synonymous_variant	64395			AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"""BTB/POZ domain containing"""	23843	protein-coding gene	gene with protein product	"""spermatogenesis associated 29"""		"""germ cell-less homolog 1 (Drosophila)"""				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.210G>A	2.37:g.70057234G>A			Q9H826|Q9H8V7|Q9H927	Silent	SNP	ENST00000282570.3	37	CCDS1895.1																																																																																				0.682	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2		NM_178439	
GPR98	84059	broad.mit.edu;ucsc.edu	37	5	90281200	90281200	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr5:90281200C>A	ENST00000405460.2	+	85	18109	c.18013C>A	c.(18013-18015)Cac>Aac	p.H6005N	GPR98_ENST00000425867.2_Missense_Mutation_p.H1666N	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6005					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.H6005N(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAATGATGAGCACACAGAGAG	0.403																																																	1	Substitution - Missense(1)	kidney(1)											302.0	289.0	293.0					5																	90281200		1990	4170	6160	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.18013C>A	5.37:g.90281200C>A	ENSP00000384582:p.His6005Asn		O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023449	0.75390	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.41758	0.99;0.99	5.7	5.7	0.88788	GPCR, family 2-like (1);	0.049849	0.85682	D	0.000000	T	0.36276	0.0961	L	0.28115	0.83	0.80722	D	1	P;P;P	0.46784	0.817;0.884;0.782	B;P;B	0.45794	0.372;0.493;0.255	T	0.04678	-1.0934	9	.	.	.	.	14.641	0.68726	0.1456:0.8544:0.0:0.0	.	1666;6005;1666	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	N	6005;6005;1666	ENSP00000384582:H6005N;ENSP00000392618:H1666N	.	H	+	1	0	GPR98	90316956	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.654000	0.67974	2.690000	0.91761	0.557000	0.71058	CAC		0.403	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2		NM_032119	
HOOK1	51361	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	60325915	60325915	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr1:60325915G>C	ENST00000371208.3	+	15	1704	c.1447G>C	c.(1447-1449)Ggc>Cgc	p.G483R	HOOK1_ENST00000465876.1_3'UTR|HOOK1_ENST00000395561.2_Missense_Mutation_p.G441R	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	483	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)	p.G483R(1)		biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					ACAGCAAGAAGGCTCTGAGAA	0.373																																																	1	Substitution - Missense(1)	kidney(1)											124.0	130.0	128.0					1																	60325915		2203	4300	6503	SO:0001583	missense	51361			AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"""hook homolog 1 (Drosophila)"""			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1447G>C	1.37:g.60325915G>C	ENSP00000360252:p.Gly483Arg		A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Missense_Mutation	SNP	ENST00000371208.3	37	CCDS612.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950635	0.92660	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.21191	2.02;2.02	4.95	4.95	0.65309	.	0.112626	0.64402	D	0.000007	T	0.38692	0.1050	M	0.62088	1.915	0.80722	D	1	D	0.59357	0.985	P	0.58266	0.836	T	0.03545	-1.1026	10	0.18276	T	0.48	.	18.7375	0.91761	0.0:0.0:1.0:0.0	.	483	Q9UJC3	HOOK1_HUMAN	R	483;441	ENSP00000360252:G483R;ENSP00000378928:G441R	ENSP00000360252:G483R	G	+	1	0	HOOK1	60098503	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	8.484000	0.90445	2.733000	0.93635	0.655000	0.94253	GGC		0.373	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1		NM_015888	
HOXB13	10481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	46805408	46805408	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr17:46805408C>A	ENST00000290295.7	-	1	1132	c.548G>T	c.(547-549)tGt>tTt	p.C183F	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	183					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)	p.C183F(1)		endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						TCCCTGGCAACACATCTGGCT	0.577																																																	1	Substitution - Missense(1)	kidney(1)											78.0	72.0	74.0					17																	46805408		2203	4300	6503	SO:0001583	missense	10481			U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"""Homeoboxes / ANTP class : HOXL subclass"""	5112	protein-coding gene	gene with protein product		604607	"""homeo box B13"""			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.548G>T	17.37:g.46805408C>A	ENSP00000290295:p.Cys183Phe		B2R878|Q96QM4|Q99810	Missense_Mutation	SNP	ENST00000290295.7	37	CCDS11536.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077063	0.36662	.	.	ENSG00000159184	ENST00000290295	D	0.91124	-2.79	5.06	5.06	0.68205	.	0.054757	0.85682	D	0.000000	D	0.86335	0.5908	L	0.53249	1.67	0.45995	D	0.998802	P	0.40731	0.728	B	0.35114	0.196	D	0.86746	0.1957	10	0.56958	D	0.05	.	10.7018	0.45931	0.0:0.9132:0.0:0.0868	.	183	Q92826	HXB13_HUMAN	F	183	ENSP00000290295:C183F	ENSP00000290295:C183F	C	-	2	0	HOXB13	44160407	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.847000	0.48270	2.648000	0.89879	0.561000	0.74099	TGT		0.577	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3		NM_006361	
IGF2R	3482	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	160509177	160509177	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr6:160509177G>T	ENST00000356956.1	+	42	6466	c.6318G>T	c.(6316-6318)aaG>aaT	p.K2106N		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2106					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.K2106N(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CTGCATTCAAGAGGTCAGGAG	0.522											OREG0017769	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											79.0	69.0	72.0					6																	160509177		2203	4300	6503	SO:0001583	missense	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6318G>T	6.37:g.160509177G>T	ENSP00000349437:p.Lys2106Asn	1809	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	1.097	-0.662342	0.03454	.	.	ENSG00000197081	ENST00000356956	T	0.29397	1.57	5.0	-1.84	0.07809	Mannose-6-phosphate receptor, binding (1);	1.022190	0.07744	N	0.947400	T	0.05502	0.0145	N	0.25647	0.755	0.35145	D	0.769253	B	0.02656	0.0	B	0.09377	0.004	T	0.43540	-0.9385	10	0.19147	T	0.46	-10.7121	2.0642	0.03599	0.1372:0.302:0.2699:0.291	.	2106	P11717	MPRI_HUMAN	N	2106	ENSP00000349437:K2106N	ENSP00000349437:K2106N	K	+	3	2	IGF2R	160429167	0.000000	0.05858	0.704000	0.30370	0.217000	0.24651	-0.672000	0.05244	-0.374000	0.07967	-0.140000	0.14226	AAG		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1		NM_000876	
IL1RAPL2	26280	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	104961379	104961379	+	Silent	SNP	C	C	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:104961379C>G	ENST00000372582.1	+	7	1548	c.792C>G	c.(790-792)ccC>ccG	p.P264P	IL1RAPL2_ENST00000344799.4_Silent_p.P264P	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	264	Ig-like C2-type 3.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.P264P(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGAACATCCCCTGCAAAGCAT	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											140.0	135.0	137.0					X																	104961379		2203	4300	6503	SO:0001819	synonymous_variant	26280			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.792C>G	X.37:g.104961379C>G			Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	37	CCDS14517.1																																																																																				0.433	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1		NM_017416	
ITGAX	3687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	31388553	31388553	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr16:31388553C>T	ENST00000268296.4	+	23	2877	c.2756C>T	c.(2755-2757)cCg>cTg	p.P919L	ITGAX_ENST00000562522.1_Missense_Mutation_p.P919L	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	919					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.P919L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CTGGAGCTCCCGGTGAAGTAT	0.502																																																	1	Substitution - Missense(1)	kidney(1)											108.0	112.0	110.0					16																	31388553		2197	4300	6497	SO:0001583	missense	3687			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2756C>T	16.37:g.31388553C>T	ENSP00000268296:p.Pro919Leu		Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.694286	0.30052	.	.	ENSG00000140678	ENST00000268296	T	0.48522	0.81	4.37	3.38	0.38709	Integrin alpha-2 (1);	.	.	.	.	T	0.67618	0.2912	M	0.82193	2.58	0.25820	N	0.984298	D;D	0.89917	1.0;1.0	D;D	0.74348	0.966;0.983	T	0.57370	-0.7823	9	0.72032	D	0.01	.	9.1048	0.36692	0.0:0.8882:0.0:0.1118	.	919;104	P20702;Q8TES5	ITAX_HUMAN;.	L	919	ENSP00000268296:P919L	ENSP00000268296:P919L	P	+	2	0	ITGAX	31296054	0.256000	0.24012	0.291000	0.24904	0.013000	0.08279	2.424000	0.44714	1.123000	0.41961	0.390000	0.25778	CCG		0.502	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2		NM_000887	
ITSN1	6453	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	35144369	35144369	+	Silent	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr21:35144369G>C	ENST00000381318.3	+	12	1335	c.1047G>C	c.(1045-1047)acG>acC	p.T349T	ITSN1_ENST00000399338.4_Silent_p.T349T|ITSN1_ENST00000399352.1_Silent_p.T349T|ITSN1_ENST00000381285.4_Silent_p.T349T|ITSN1_ENST00000399326.3_Silent_p.T349T|ITSN1_ENST00000399355.2_Silent_p.T349T|ITSN1_ENST00000399353.1_Silent_p.T312T|ITSN1_ENST00000437442.2_Silent_p.T349T|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399349.1_Silent_p.T349T|ITSN1_ENST00000399367.3_Silent_p.T349T|ITSN1_ENST00000379960.5_Silent_p.T349T|ITSN1_ENST00000381291.4_Silent_p.T349T|ITSN1_ENST00000488166.1_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	349	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T349T(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CTGAAGTAACGTTTGAAGATA	0.443																																																	1	Substitution - coding silent(1)	kidney(1)											63.0	64.0	64.0					21																	35144369		2203	4300	6503	SO:0001819	synonymous_variant	6453			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1047G>C	21.37:g.35144369G>C			A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Silent	SNP	ENST00000381318.3	37	CCDS33545.1																																																																																				0.443	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4		NM_003024	
JAKMIP3	282973	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	133961488	133961488	+	Silent	SNP	C	C	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr10:133961488C>G	ENST00000298622.4	+	13	1920	c.1782C>G	c.(1780-1782)ctC>ctG	p.L594L	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	594						Golgi apparatus (GO:0005794)		p.L594L(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AGGCTCGGCTCAGACACGAGG	0.552																																																	1	Substitution - coding silent(1)	kidney(1)											112.0	90.0	97.0					10																	133961488		2201	4292	6493	SO:0001819	synonymous_variant	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1782C>G	10.37:g.133961488C>G			A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																				0.552	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3		NM_194303	
KBTBD4	55709	broad.mit.edu;hgsc.bcm.edu	37	11	47599123	47599123	+	Silent	SNP	T	T	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr11:47599123T>C	ENST00000526005.1	-	2	582	c.429A>G	c.(427-429)caA>caG	p.Q143Q	NDUFS3_ENST00000534208.1_5'Flank|NDUFS3_ENST00000528192.1_5'Flank|RNU5E-10P_ENST00000363506.1_RNA|KBTBD4_ENST00000450908.1_5'Flank|KBTBD4_ENST00000533290.1_Silent_p.Q168Q|NDUFS3_ENST00000263774.4_5'Flank|KBTBD4_ENST00000525720.1_Silent_p.Q192Q|KBTBD4_ENST00000395288.2_Silent_p.Q143Q|NDUFS3_ENST00000529276.1_5'Flank|KBTBD4_ENST00000430070.2_Silent_p.Q159Q|NDUFS3_ENST00000533507.1_Intron|NDUFS3_ENST00000534716.2_5'Flank			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	143								p.Q143Q(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						AGTTTCCCACTTGCACTGTGC	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											173.0	171.0	172.0					11																	47599123		2201	4298	6499	SO:0001819	synonymous_variant	55709			AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"""BTB/POZ domain containing"""	23761	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 4"""	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.429A>G	11.37:g.47599123T>C			D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Silent	SNP	ENST00000526005.1	37	CCDS7940.1	.	.	.	.	.	.	.	.	.	.	T	9.227	1.034777	0.19590	.	.	ENSG00000123444	ENST00000359900	.	.	.	5.54	-1.7	0.08159	.	.	.	.	.	T	0.62282	0.2415	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62544	-0.6832	5	0.87932	D	0	-7.0581	9.3245	0.37984	0.0:0.683:0.0953:0.2217	.	.	.	.	R	158	.	ENSP00000352971:K158R	K	-	2	0	KBTBD4	47555699	0.720000	0.27996	0.983000	0.44433	0.979000	0.70002	-0.083000	0.11286	-0.643000	0.05473	0.379000	0.24179	AAG		0.537	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1		NM_016506	
KLF10	7071	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	103664082	103664082	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr8:103664082C>A	ENST00000285407.6	-	3	778	c.478G>T	c.(478-480)Gct>Tct	p.A160S	KLF10_ENST00000395884.3_Missense_Mutation_p.A149S	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	160					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A160S(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGGCATCAGCTGTATGACGA	0.473											OREG0018913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Esophageal Squamous(16;495 519 2144 16528 44005)												1	Substitution - Missense(1)	kidney(1)											114.0	117.0	116.0					8																	103664082		2203	4300	6503	SO:0001583	missense	7071			U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11810	protein-coding gene	gene with protein product		601878	"""TGFB inducible early growth response"""	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.478G>T	8.37:g.103664082C>A	ENSP00000285407:p.Ala160Ser	1375	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Missense_Mutation	SNP	ENST00000285407.6	37	CCDS6294.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561584	0.86335	.	.	ENSG00000155090	ENST00000285407;ENST00000395884	T;T	0.18338	2.22;2.3	6.02	6.02	0.97574	.	0.065623	0.64402	D	0.000006	T	0.42245	0.1194	M	0.70275	2.135	0.58432	D	0.999996	D;D	0.71674	0.998;0.998	P;P	0.62089	0.898;0.898	T	0.04767	-1.0928	10	0.51188	T	0.08	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	160;149	Q13118;O75411	KLF10_HUMAN;.	S	160;149	ENSP00000285407:A160S;ENSP00000379222:A149S	ENSP00000285407:A160S	A	-	1	0	KLF10	103733258	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	6.772000	0.75001	2.865000	0.98341	0.655000	0.94253	GCT		0.473	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			
KRT5	3852	broad.mit.edu;hgsc.bcm.edu	37	12	52910988	52910988	+	Missense_Mutation	SNP	C	C	T	rs200072843		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr12:52910988C>T	ENST00000252242.4	-	6	1511	c.1121G>A	c.(1120-1122)cGg>cAg	p.R374Q		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	374	Coil 2.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.R374Q(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATCGCCATGCCGGCCAGCTGT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		19071	0.0		0.001	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											95.0	90.0	92.0					12																	52910988		2203	4300	6503	SO:0001583	missense	3852				CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1121G>A	12.37:g.52910988C>T	ENSP00000252242:p.Arg374Gln		Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.15	2.150228	0.37923	.	.	ENSG00000186081	ENST00000252242;ENST00000456000	T	0.74947	-0.89	5.63	3.79	0.43588	Filament (1);	0.000000	0.53938	D	0.000052	T	0.61388	0.2343	L	0.46819	1.47	0.09310	N	1	P	0.47034	0.889	B	0.37508	0.252	T	0.52019	-0.8631	10	0.25751	T	0.34	.	8.8377	0.35121	0.0:0.6935:0.0:0.3065	.	374	P13647	K2C5_HUMAN	Q	374;339	ENSP00000252242:R374Q	ENSP00000252242:R374Q	R	-	2	0	KRT5	51197255	0.031000	0.19500	0.568000	0.28447	0.996000	0.88848	0.623000	0.24447	0.712000	0.32039	0.655000	0.94253	CGG		0.498	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			
LOC441666	441666	broad.mit.edu	37	10	42833154	42833154	+	RNA	SNP	T	T	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr10:42833154T>C	ENST00000609841.1	-	0	749					NR_024380.1																						TTGTAGGTTGTATCTCCAGTA	0.338																																																	0																																												441666																															10.37:g.42833154T>C				RNA	SNP	ENST00000609841.1	37																																																																																					0.338	RP11-313J2.1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472483.1			
LOC81691	81691	broad.mit.edu;ucsc.edu	37	16	20824600	20824600	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr16:20824600G>A	ENST00000261377.6	+	3	436	c.227G>A	c.(226-228)gGc>gAc	p.G76D	AC004381.6_ENST00000567297.1_3'UTR|AC004381.6_ENST00000564274.1_Missense_Mutation_p.G76D|ERI2_ENST00000564349.1_Intron|AC004381.6_ENST00000348433.6_Missense_Mutation_p.G76D	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2												p.G76D(1)									GCAGTTCTGGGCAAATCCAAT	0.383																																																	1	Substitution - Missense(1)	kidney(1)											67.0	65.0	66.0					16																	20824600		2201	4300	6501	SO:0001583	missense	81691																														ENST00000261377.6:c.227G>A	16.37:g.20824600G>A	ENSP00000261377:p.Gly76Asp			Missense_Mutation	SNP	ENST00000261377.6	37	CCDS10591.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969240	0.74246	.	.	ENSG00000005189	ENST00000348433;ENST00000261377	T;T	0.72835	-0.69;-0.45	5.56	4.6	0.57074	.	0.164767	0.53938	D	0.000049	T	0.82079	0.4959	M	0.65498	2.005	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.99	D	0.83404	0.0024	10	0.56958	D	0.05	-8.2324	14.4042	0.67071	0.0:0.1476:0.8524:0.0	.	76;76	Q96IC2-2;Q96IC2	.;REXON_HUMAN	D	76	ENSP00000261378:G76D;ENSP00000261377:G76D	ENSP00000261377:G76D	G	+	2	0	AC004381.6	20732101	1.000000	0.71417	0.983000	0.44433	0.976000	0.68499	5.392000	0.66272	1.325000	0.45301	0.561000	0.74099	GGC		0.383	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			
MAMLD1	10046	broad.mit.edu	37	X	149639327	149639327	+	Silent	SNP	G	G	A	rs374561693		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:149639327G>A	ENST00000370401.2	+	4	1792	c.1482G>A	c.(1480-1482)caG>caA	p.Q494Q	MAMLD1_ENST00000262858.5_Silent_p.Q494Q|MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000432680.2_Silent_p.Q469Q|MAMLD1_ENST00000426613.2_Silent_p.Q469Q			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	494	Poly-Gln.				male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					GCcagcaacagcagcagcagc	0.532																																																	3	Substitution - coding silent(3)	kidney(3)											42.0	41.0	41.0					X																	149639327		2203	4300	6503	SO:0001819	synonymous_variant	10046			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1482G>A	X.37:g.149639327G>A			B2RCQ4|B4DG93|B9EGA5	Silent	SNP	ENST00000370401.2	37	CCDS14693.2																																																																																				0.532	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2		NM_005491	
MPP1	4354	broad.mit.edu;ucsc.edu	37	X	154010064	154010064	+	Silent	SNP	C	C	A	rs147268060		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:154010064C>A	ENST00000369534.3	-	10	1107	c.960G>T	c.(958-960)ccG>ccT	p.P320P	MPP1_ENST00000393531.1_Silent_p.P300P|MPP1_ENST00000413259.3_Silent_p.P290P|MPP1_ENST00000462825.1_5'Flank	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	320	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|Interaction with MPP5.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.P320P(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TCTTCCTTGGCGGCCGTGTTG	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											181.0	151.0	161.0					X																	154010064		2203	4300	6503	SO:0001819	synonymous_variant	4354				CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"""membrane protein, palmitoylated 1 (55kD)"""	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.960G>T	X.37:g.154010064C>A			B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Silent	SNP	ENST00000369534.3	37	CCDS14762.1																																																																																				0.507	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3		NM_002436	
MS4A14	84689	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60183100	60183100	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr11:60183100A>C	ENST00000300187.6	+	5	936	c.659A>C	c.(658-660)cAa>cCa	p.Q220P	MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.Q108P|MS4A14_ENST00000531783.1_Missense_Mutation_p.Q253P|MS4A14_ENST00000395005.2_Missense_Mutation_p.Q203P	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	220						integral component of membrane (GO:0016021)		p.Q220P(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						TTAGTCTCCCAACCAGGTAAT	0.398																																																	1	Substitution - Missense(1)	kidney(1)											96.0	97.0	96.0					11																	60183100		2203	4300	6503	SO:0001583	missense	84689			AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.659A>C	11.37:g.60183100A>C	ENSP00000300187:p.Gln220Pro		E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853180	0.32699	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.12147	4.31;4.31;4.31;2.71	3.63	-0.249	0.13011	.	5.378320	0.00397	N	0.000041	T	0.11281	0.0275	L	0.36672	1.1	0.09310	N	1	B;B	0.24768	0.091;0.111	B;B	0.23150	0.026;0.044	T	0.32295	-0.9912	10	0.72032	D	0.01	-0.2242	0.9413	0.01356	0.495:0.1999:0.112:0.193	.	203;220	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	P	108;220;203;253	ENSP00000437222:Q108P;ENSP00000300187:Q220P;ENSP00000378453:Q203P;ENSP00000433761:Q253P	ENSP00000300187:Q220P	Q	+	2	0	MS4A14	59939676	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.323000	0.19593	-0.058000	0.13177	-0.297000	0.09499	CAA		0.398	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			
MUC4	4585	hgsc.bcm.edu	37	3	195508442	195508537	+	In_Frame_Del	DEL	CTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	CTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	-	rs568124972|rs545603027|rs200820395|rs535230509|rs200195189|rs574066429|rs201933946|rs374619108|rs200683272|rs76305071|rs568102602|rs553845624|rs566110482|rs146135943|rs201164988|rs71187746|rs141064104|rs199896372|rs368202391|rs62282476|rs541132330|rs150322486|rs201319965|rs148923966|rs537438050|rs549411987|rs531526881|rs540026448|rs534369822|rs80085168|rs202097189|rs201298940|rs549350827|rs113686997|rs201195860|rs543837546	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	CTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	CTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:195508442_195508537delCTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	ENST00000463781.3	-	2	10373_10468	c.9914_10009delTATCCACAGGTCACGCCACTCCTCTTCTTGTCACCGACGCTTCCTCAGCATCCACAGGTCACGCCACCCCTCTTCATGTCACCAGCCCTTCCTCAG	c.(9913-10011)gtatccacaggtcacgccactcctcttcttgtcaccgacgcttcctcagcatccacaggtcacgccacccctcttcatgtcaccagcccttcctcagca>gca	p.VSTGHATPLLVTDASSASTGHATPLHVTSPSS3305del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.VSTGHATPLLVTDASSASTGHATPLHVTSPSS3305del	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.D3317E(2)|p.H3325Q(2)|p.A3310T(2)|p.H3309D(2)|p.V3305A(1)|p.D3317N(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)|p.L3314P(1)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.S3317R(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)		CCTGTGGATGCTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATACTGAGGAAGT	0.574																																																	14	Substitution - Missense(12)|Deletion - In frame(2)	stomach(11)|lung(2)|kidney(1)																																								SO:0001651	inframe_deletion	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.9914_10009delTATCCACAGGTCACGCCACTCCTCTTCTTGTCACCGACGCTTCCTCAGCATCCACAGGTCACGCCACCCCTCTTCATGTCACCAGCCCTTCCTCAG	3.37:g.195508442_195508537delCTGAGGAAGGGCTGGTGACATGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGCGTCGGTGACAAGAAGAGGAGTGGCGTGACCTGTGGATA	ENSP00000417498:p.Val3305_Ser3336del		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.574	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515413	195515413	+	Missense_Mutation	SNP	C	C	T	rs55868431	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:195515413C>T	ENST00000463781.3	-	2	3497	c.3038G>A	c.(3037-3039)aGc>aAc	p.S1013N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1013N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				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.S1013_T1028delSPSSVSTGHTTPLPVT(4)		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)		TGAGGAAGGGCTGGTGACAGG	0.572													.|||	808	0.161342	0.152	0.1124	5008	,	,		17298	0.2321		0.1352	False		,,,				2504	0.1626																4	Deletion - In frame(4)	stomach(4)											55.0	29.0	37.0					3																	195515413		688	1591	2279	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.3038G>A	3.37:g.195515413C>T	ENSP00000417498:p.Ser1013Asn		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	.	.	.	.	.	.	.	.	.	.	-	4.515	0.095618	0.08681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.42;1.41	0.814	-1.63	0.08345	.	.	.	.	.	T	0.14960	0.0361	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.11329	0.006	T	0.15809	-1.0424	8	.	.	.	.	3.4557	0.07514	0.0:0.2084:0.4437:0.3479	rs55868431	1013	E7ESK3	.	N	1013	ENSP00000417498:S1013N;ENSP00000420243:S1013N	.	S	-	2	0	MUC4	196999808	.	.	0.000000	0.03702	0.010000	0.07245	.	.	-3.282000	0.00197	-2.088000	0.00374	AGC		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYCBP2	23077	broad.mit.edu;ucsc.edu	37	13	77629761	77629761	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr13:77629761A>G	ENST00000544440.2	-	80	13482	c.13465T>C	c.(13465-13467)Ttt>Ctt	p.F4489L	MYCBP2_ENST00000357337.6_Missense_Mutation_p.F4489L|MYCBP2_ENST00000407578.2_Missense_Mutation_p.F4527L					MYC binding protein 2, E3 ubiquitin protein ligase									p.F4489L(1)|p.F4527L(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCATTATAAAACCTCACACCA	0.348																																																	2	Substitution - Missense(2)	kidney(2)											129.0	100.0	110.0					13																	77629761		2203	4300	6503	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.13465T>C	13.37:g.77629761A>G	ENSP00000444596:p.Phe4489Leu			Missense_Mutation	SNP	ENST00000544440.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.059042|4.059042	0.76074|0.76074	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440|ENST00000429715	T;T;T|.	0.32988|.	1.43;1.43;1.43|.	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69851|0.69851	0.3157|0.3157	L|L	0.58810|0.58810	1.83|1.83	0.80722|0.80722	D|D	1|1	P|.	0.49447|.	0.924|.	P|.	0.60682|.	0.878|.	T|T	0.68949|0.68949	-0.5274|-0.5274	10|5	0.72032|.	D|.	0.01|.	.|.	15.0607|15.0607	0.71951|0.71951	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	4489|.	O75592|.	MYCB2_HUMAN|.	L|A	4489;4527;4489|909	ENSP00000349892:F4489L;ENSP00000384288:F4527L;ENSP00000444596:F4489L|.	ENSP00000349892:F4489L|.	F|V	-|-	1|2	0|0	MYCBP2|MYCBP2	76527762|76527762	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.753000|8.753000	0.91637|0.91637	2.130000|2.130000	0.65690|0.65690	0.533000|0.533000	0.62120|0.62120	TTT|GTT		0.348	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1		NM_015057	
MYOM1	8736	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	3135721	3135721	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr18:3135721G>A	ENST00000356443.4	-	15	2366	c.2033C>T	c.(2032-2034)gCa>gTa	p.A678V	MYOM1_ENST00000261606.7_Missense_Mutation_p.A678V|MYOM1_ENST00000400569.3_Missense_Mutation_p.A678V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	678	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.A678V(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TTCTGTTCCTGCCTCACACTG	0.512																																																	1	Substitution - Missense(1)	kidney(1)											38.0	41.0	40.0					18																	3135721		1972	4170	6142	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2033C>T	18.37:g.3135721G>A	ENSP00000348821:p.Ala678Val		Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	4.539	0.100076	0.08731	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.56275	0.47;0.47;0.47	5.76	3.96	0.45880	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.394958	0.28273	N	0.015943	T	0.26846	0.0657	N	0.03084	-0.415	0.21675	N	0.999592	B;B	0.10296	0.002;0.003	B;B	0.15052	0.007;0.012	T	0.14420	-1.0473	10	0.12766	T	0.61	.	11.9356	0.52872	0.1423:0.0:0.8577:0.0	.	678;678	P52179-2;P52179	.;MYOM1_HUMAN	V	678	ENSP00000348821:A678V;ENSP00000383413:A678V;ENSP00000261606:A678V	ENSP00000261606:A678V	A	-	2	0	MYOM1	3125721	0.999000	0.42202	0.007000	0.13788	0.992000	0.81027	4.717000	0.61923	0.876000	0.35872	0.650000	0.86243	GCA		0.512	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2		NM_003803	
EPB41L4A	64097	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	111496807	111496807	+	IGR	SNP	A	A	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr5:111496807A>G	ENST00000261486.5	-	0	4707				EPB41L4A_ENST00000507810.1_Intron|SNORA13_ENST00000458790.1_RNA|EPB41L4A-AS1_ENST00000413221.2_lincRNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ATTTGTGTTTACATCATCGAC	0.542																																																	0													35.0	34.0	34.0					5																	111496807		692	1591	2283	SO:0001628	intergenic_variant	0			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902		5.37:g.111496807A>G			A4FUI6	RNA	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																				0.542	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			
NOS2	4843	broad.mit.edu	37	17	26091141	26091141	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr17:26091141G>C	ENST00000313735.6	-	21	2691	c.2458C>G	c.(2458-2460)Ccc>Gcc	p.P820A		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	820	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.P820A(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GAGCAGGGGGGCAGCCTCTTG	0.607																																																	1	Substitution - Missense(1)	kidney(1)											18.0	21.0	20.0					17																	26091141		2203	4295	6498	SO:0001583	missense	4843			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2458C>G	17.37:g.26091141G>C	ENSP00000327251:p.Pro820Ala		A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315220	0.81358	.	.	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.65916	-0.18	5.23	4.26	0.50523	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.062767	0.64402	D	0.000005	T	0.79528	0.4461	M	0.80508	2.5	0.52099	D	0.999948	D	0.89917	1.0	D	0.97110	1.0	T	0.82806	-0.0275	10	0.87932	D	0	.	14.5569	0.68106	0.0:0.1475:0.8525:0.0	.	820	P35228	NOS2_HUMAN	A	820;781	ENSP00000327251:P820A	ENSP00000327251:P820A	P	-	1	0	NOS2	23115268	1.000000	0.71417	0.995000	0.50966	0.948000	0.59901	8.012000	0.88631	1.198000	0.43158	0.462000	0.41574	CCC		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1		NM_000625	
OR2B3	442184	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	29054173	29054173	+	Silent	SNP	A	A	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr6:29054173A>G	ENST00000377173.2	-	1	917	c.853T>C	c.(853-855)Ttg>Ctg	p.L285L		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L285L(1)		breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						AGGGAGTTCAACATGGATGTG	0.403																																																	1	Substitution - coding silent(1)	kidney(1)											92.0	84.0	87.0					6																	29054173		2203	4300	6503	SO:0001819	synonymous_variant	442184				CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"""GPCR / Class A : Olfactory receptors"""	8238	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 3 pseudogene"""	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.853T>C	6.37:g.29054173A>G			B0UYQ1|Q5ST41|Q96R13	Silent	SNP	ENST00000377173.2	37	CCDS34358.1																																																																																				0.403	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			
POU2F1	5451	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	167365627	167365627	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr1:167365627G>T	ENST00000541643.3	+	11	1185	c.1023G>T	c.(1021-1023)aaG>aaT	p.K341N	POU2F1_ENST00000367866.2_Missense_Mutation_p.K364N|POU2F1_ENST00000420254.3_Missense_Mutation_p.K341N|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367862.5_Missense_Mutation_p.K353N|POU2F1_ENST00000429375.2_Missense_Mutation_p.K301N			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	341	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K364N(1)|p.K341N(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						ACATGTGCAAGTTGAAGCCAC	0.388																																																	2	Substitution - Missense(2)	kidney(2)											148.0	139.0	142.0					1																	167365627		2203	4300	6503	SO:0001583	missense	5451			BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.1023G>T	1.37:g.167365627G>T	ENSP00000441285:p.Lys341Asn		B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	37		.	.	.	.	.	.	.	.	.	.	G	17.07	3.296029	0.60086	.	.	ENSG00000143190	ENST00000367866;ENST00000429375;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	D;D;D;D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07;-2.07;-2.07;-2.07	6.17	2.3	0.28687	POU-specific (3);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.89836	0.6830	M	0.87827	2.91	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;0.993;0.995;0.996	D	0.89748	0.3938	10	0.87932	D	0	.	10.2806	0.43537	0.2625:0.0:0.7375:0.0	.	301;341;353;339;341	B4E029;P14859-4;P14859-2;P14859-3;P14859	.;.;.;.;PO2F1_HUMAN	N	364;301;339;341;341;353;249	ENSP00000356840:K364N;ENSP00000401217:K301N;ENSP00000356839:K339N;ENSP00000414660:K341N;ENSP00000441285:K341N;ENSP00000356836:K353N;ENSP00000415993:K249N	ENSP00000356836:K353N	K	+	3	2	POU2F1	165632251	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.165000	0.31822	0.190000	0.20209	0.655000	0.94253	AAG		0.388	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_002697	
PPP1R9A	55607	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	94540664	94540664	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr7:94540664C>T	ENST00000433881.1	+	2	1771	c.1239C>T	c.(1237-1239)gaC>gaT	p.D413D	PPP1R9A_ENST00000424654.1_Silent_p.D413D|PPP1R9A_ENST00000289495.5_Silent_p.D413D|PPP1R9A_ENST00000340694.4_Silent_p.D413D|PPP1R9A_ENST00000456331.2_Silent_p.D413D|PPP1R9A_ENST00000433360.1_Silent_p.D413D			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	413					actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)		p.D413D(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			ATAATTCAGACTGGGGAGAGA	0.423										HNSCC(28;0.073)																																							2	Substitution - coding silent(2)	kidney(2)											63.0	58.0	60.0					7																	94540664		2203	4300	6503	SO:0001819	synonymous_variant	55607			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1239C>T	7.37:g.94540664C>T			A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Silent	SNP	ENST00000433881.1	37	CCDS34683.1																																																																																				0.423	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1		NM_001166160	
PSMB7	5695	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	127177673	127177673	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr9:127177673A>T	ENST00000259457.3	-	1	45	c.32T>A	c.(31-33)gTt>gAt	p.V11D	PSMB7_ENST00000536392.1_Missense_Mutation_p.V11D|PSMB7_ENST00000498485.1_5'Flank	NM_002799.3	NP_002790.1	Q99436	PSB7_HUMAN	proteasome (prosome, macropain) subunit, beta type, 7	11					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)	p.V11D(1)		breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)	5						GAAGCCTCCAACTGGTGGAGC	0.612											OREG0019476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											44.0	44.0	44.0					9																	127177673		2203	4300	6503	SO:0001583	missense	5695			AJ420455	CCDS6855.1	9q34.11-q34.12	2008-02-05			ENSG00000136930	ENSG00000136930		"""Proteasome (prosome, macropain) subunits"""	9544	protein-coding gene	gene with protein product		604030				8811196	Standard	NM_002799		Approved	Z	uc004boj.4	Q99436	OTTHUMG00000021042	ENST00000259457.3:c.32T>A	9.37:g.127177673A>T	ENSP00000259457:p.Val11Asp	1555	B4E0P1|Q5TBG6|Q96AG8|Q9BWA7	Missense_Mutation	SNP	ENST00000259457.3	37	CCDS6855.1	.	.	.	.	.	.	.	.	.	.	A	7.198	0.592922	0.13875	.	.	ENSG00000136930	ENST00000259457;ENST00000536392;ENST00000441097	T;T;T	0.34859	1.34;1.34;1.34	6.17	5.04	0.67666	.	0.414071	0.27080	N	0.021033	T	0.27524	0.0676	L	0.46614	1.455	0.51767	D	0.999939	B;B	0.24533	0.105;0.0	B;B	0.26202	0.067;0.001	T	0.06972	-1.0797	10	0.12103	T	0.63	-10.809	6.7231	0.23340	0.7701:0.1528:0.0771:0.0	.	11;11	B4E0P1;Q99436	.;PSB7_HUMAN	D	11	ENSP00000259457:V11D;ENSP00000440247:V11D;ENSP00000393157:V11D	ENSP00000259457:V11D	V	-	2	0	PSMB7	126217494	0.004000	0.15560	0.950000	0.38849	0.328000	0.28507	0.357000	0.20199	1.159000	0.42565	0.533000	0.62120	GTT		0.612	PSMB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055525.1		NM_002799	
RIN2	54453	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	19977395	19977395	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr20:19977395G>A	ENST00000255006.6	+	11	2569	c.2420G>A	c.(2419-2421)cGa>cAa	p.R807Q	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Missense_Mutation_p.R325Q	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	758	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)	p.R807Q(1)|p.R758Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CAAGCAGCGCGACTGCTCAGC	0.522																																																	2	Substitution - Missense(2)	kidney(2)											75.0	85.0	82.0					20																	19977395		2044	4193	6237	SO:0001583	missense	54453			AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.2420G>A	20.37:g.19977395G>A	ENSP00000255006:p.Arg807Gln		Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030441	0.35797	.	.	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.25250	2.87;1.81	5.69	4.72	0.59763	Vacuolar sorting protein 9, subgroup (1);	0.423022	0.24745	N	0.035959	T	0.22399	0.0540	L	0.45228	1.405	0.22305	N	0.999218	B;B	0.21071	0.002;0.051	B;B	0.15052	0.002;0.012	T	0.11867	-1.0570	9	.	.	.	-8.5931	13.3243	0.60450	0.0794:0.0:0.9206:0.0	.	325;758	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	Q	807;325	ENSP00000255006:R807Q;ENSP00000391239:R325Q	.	R	+	2	0	RIN2	19925395	0.392000	0.25229	0.002000	0.10522	0.137000	0.21094	3.272000	0.51616	1.350000	0.45770	0.655000	0.94253	CGA		0.522	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			
SACS	26278	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	23907922	23907922	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr13:23907922G>C	ENST00000382292.3	-	9	10366	c.10093C>G	c.(10093-10095)Cta>Gta	p.L3365V	SACS_ENST00000402364.1_Missense_Mutation_p.L2615V|SACS_ENST00000382298.3_Missense_Mutation_p.L3365V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3365					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.L3365V(1)|p.L3218V(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATATAATGTAGAGCCTTCAAG	0.353																																																	2	Substitution - Missense(2)	kidney(2)											76.0	75.0	75.0					13																	23907922		2203	4299	6502	SO:0001583	missense	26278			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10093C>G	13.37:g.23907922G>C	ENSP00000371729:p.Leu3365Val		O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.583138	0.00872	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.89810	-2.41;-2.57;-2.41	5.94	-2.84	0.05751	.	0.597847	0.17164	N	0.184532	T	0.72518	0.3470	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.58679	-0.7594	10	0.21540	T	0.41	.	7.3338	0.26599	0.1225:0.113:0.646:0.1185	.	3365	Q9NZJ4	SACS_HUMAN	V	3365;2615;3365	ENSP00000371729:L3365V;ENSP00000385844:L2615V;ENSP00000371735:L3365V	ENSP00000371729:L3365V	L	-	1	2	SACS	22805922	0.059000	0.20769	0.388000	0.26195	0.990000	0.78478	-0.074000	0.11450	-0.412000	0.07519	-0.367000	0.07326	CTA		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3		NM_014363	
SAG	6295	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	234235795	234235795	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr2:234235795C>T	ENST00000409110.1	+	7	694	c.464C>T	c.(463-465)gCa>gTa	p.A155V	SAG_ENST00000449594.2_Missense_Mutation_p.A21V	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	155					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)	p.A155V(2)		cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		GAGGTCAAAGCATTCGCCACA	0.592																																																	2	Substitution - Missense(2)	kidney(2)											115.0	118.0	117.0					2																	234235795		2092	4223	6315	SO:0001583	missense	6295				CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.464C>T	2.37:g.234235795C>T	ENSP00000386444:p.Ala155Val		A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067344	0.36470	.	.	ENSG00000130561	ENST00000252857;ENST00000447536;ENST00000409110;ENST00000449594	T;T;T	0.18174	2.56;2.56;2.23	3.96	3.96	0.45880	Arrestin, N-terminal (1);Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);	0.157173	0.56097	D	0.000028	T	0.13114	0.0318	L	0.36672	1.1	0.80722	D	1	B;P	0.34892	0.089;0.474	B;B	0.26770	0.02;0.073	T	0.09684	-1.0663	10	0.37606	T	0.19	-7.7945	14.7721	0.69688	0.0:1.0:0.0:0.0	.	21;155	B7Z7L5;P10523	.;ARRS_HUMAN	V	155;155;155;21	ENSP00000408937:A155V;ENSP00000386444:A155V;ENSP00000392889:A21V	ENSP00000252857:A155V	A	+	2	0	SAG	233900534	1.000000	0.71417	0.934000	0.37439	0.157000	0.22087	6.723000	0.74742	2.204000	0.70986	0.555000	0.69702	GCA		0.592	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1		NM_000541	
SEMA3E	9723	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	82997339	82997339	+	Nonsense_Mutation	SNP	T	T	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr7:82997339T>A	ENST00000307792.3	-	17	2358	c.1891A>T	c.(1891-1893)Aga>Tga	p.R631*	SEMA3E_ENST00000427262.1_Nonsense_Mutation_p.R571*	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	631	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R631*(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TTAACCACTCTGTCATCTGTC	0.403																																																	1	Substitution - Nonsense(1)	kidney(1)											111.0	107.0	109.0					7																	82997339		2203	4300	6503	SO:0001587	stop_gained	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1891A>T	7.37:g.82997339T>A	ENSP00000303212:p.Arg631*		B4E1P1|Q75M94|Q75M97	Nonsense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	T	38	6.706643	0.97776	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	.	.	.	5.77	1.87	0.25490	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2243	0.65848	0.0:0.0:0.4796:0.5204	.	.	.	.	X	631;571;631	.	ENSP00000303212:R631X	R	-	1	2	SEMA3E	82835275	0.998000	0.40836	0.998000	0.56505	0.969000	0.65631	2.360000	0.44151	0.075000	0.16796	0.477000	0.44152	AGA		0.403	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1		NM_012431	
SLC26A1	10861	broad.mit.edu	37	4	983003	983003	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr4:983003delT	ENST00000361661.2	-	4	2101	c.1724delA	c.(1723-1725)gagfs	p.E575fs	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000509744.1_Intron|SLC26A1_ENST00000398520.2_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Frame_Shift_Del_p.E575fs|IDUA_ENST00000453894.1_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	575	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TGAGCCCCCCTCCTTCCTCCT	0.692																																																	0													18.0	21.0	20.0					4																	983003		2191	4288	6479	SO:0001589	frameshift_variant	10861			AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.1724delA	4.37:g.983003delT	ENSP00000354721:p.Glu575fs		A8K9N2|Q7Z5R3|Q96BK0	Frame_Shift_Del	DEL	ENST00000361661.2	37	CCDS33934.1																																																																																				0.692	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1		NM_022042, NM_134425	
SLC26A4	5172	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	107334908	107334908	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr7:107334908C>T	ENST00000265715.3	+	11	1548	c.1324C>T	c.(1324-1326)Ctg>Ttg	p.L442L	SLC26A4_ENST00000480841.1_3'UTR|SLC26A4_ENST00000541474.1_Intron|SLC26A4_ENST00000543100.1_Silent_p.L11L|SLC26A4_ENST00000544569.1_Silent_p.L29L	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	442					chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.L442L(1)		central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GGGGAAGCTTCTGGAACCCTT	0.463									Pendred syndrome																																								1	Substitution - coding silent(1)	kidney(1)											183.0	163.0	170.0					7																	107334908		2203	4300	6503	SO:0001819	synonymous_variant	5172	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"""Solute carriers"""	8818	protein-coding gene	gene with protein product	"""pendrin"""	605646	"""solute carrier family 26, member 4"""	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1324C>T	7.37:g.107334908C>T			B7Z266|O43170	Silent	SNP	ENST00000265715.3	37	CCDS5746.1																																																																																				0.463	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1		NM_000441	
SOX5	6660	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	23998950	23998950	+	Nonsense_Mutation	SNP	T	T	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr12:23998950T>A	ENST00000451604.2	-	3	549	c.448A>T	c.(448-450)Aaa>Taa	p.K150*	SOX5_ENST00000537393.1_Nonsense_Mutation_p.K115*|SOX5_ENST00000545921.1_Nonsense_Mutation_p.K140*|SOX5_ENST00000309359.1_Nonsense_Mutation_p.K137*|SOX5_ENST00000546136.1_Nonsense_Mutation_p.K137*|SOX5_ENST00000541536.1_Nonsense_Mutation_p.K137*|SOX5_ENST00000381381.2_Nonsense_Mutation_p.K137*|SOX5_ENST00000541847.1_Nonsense_Mutation_p.K140*|SOX5_ENST00000441133.2_Nonsense_Mutation_p.K115*			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	150					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.K150*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TCTTCCATTTTCCTCTGCTTC	0.458																																																	1	Substitution - Nonsense(1)	kidney(1)											118.0	108.0	111.0					12																	23998950		2203	4300	6503	SO:0001587	stop_gained	6660			AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.448A>T	12.37:g.23998950T>A	ENSP00000398273:p.Lys150*		B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Nonsense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	T	36	5.960560	0.97145	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921;ENST00000541847;ENST00000441133;ENST00000538083	.	.	.	5.79	5.79	0.91817	.	0.144833	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1299	0.81422	0.0:0.0:0.0:1.0	.	.	.	.	X	137;137;137;150;102;115;137;140;140;115;137	.	ENSP00000308927:K137X	K	-	1	0	SOX5	23890217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.684000	0.84104	2.215000	0.71742	0.528000	0.53228	AAA		0.458	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2		NM_006940	
SPRED1	161742	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	38591742	38591742	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr15:38591742C>G	ENST00000299084.4	+	2	1061	c.201C>G	c.(199-201)gaC>gaG	p.D67E	SPRED1_ENST00000561205.1_3'UTR	NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	67	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.D67E(1)		kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GACTCAGGGACAAAATGGTAA	0.368									Legius syndrome																												Melanoma(196;2146 2959 7698 16532)												1	Substitution - Missense(1)	kidney(1)											77.0	69.0	72.0					15																	38591742		2200	4297	6497	SO:0001583	missense	161742	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 147"""	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.201C>G	15.37:g.38591742C>G	ENSP00000299084:p.Asp67Glu		B2RPJ8|Q05D53|Q8N256	Missense_Mutation	SNP	ENST00000299084.4	37	CCDS32193.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.832720	0.71258	.	.	ENSG00000166068	ENST00000299084	D	0.88431	-2.38	5.72	5.72	0.89469	EVH1 (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	M	0.80422	2.495	0.58432	D	0.999998	D	0.64830	0.994	D	0.71870	0.975	D	0.93108	0.6514	10	0.87932	D	0	-25.2534	7.49	0.27456	0.0:0.8033:0.0:0.1967	.	67	Q7Z699	SPRE1_HUMAN	E	67	ENSP00000299084:D67E	ENSP00000299084:D67E	D	+	3	2	SPRED1	36379034	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.797000	0.55514	2.709000	0.92574	0.655000	0.94253	GAC		0.368	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1			
STAG2	10735	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	123197875	123197875	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:123197875C>T	ENST00000371160.1	+	20	2289	c.1999C>T	c.(1999-2001)Cgg>Tgg	p.R667W	STAG2_ENST00000371145.3_Missense_Mutation_p.R667W|STAG2_ENST00000354548.5_Missense_Mutation_p.R598W|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.R667W|STAG2_ENST00000371157.3_Missense_Mutation_p.R667W|STAG2_ENST00000371144.3_Missense_Mutation_p.R667W	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	667					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R667W(2)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TAAATTTAACCGGCTTCTTGA	0.348																																																	2	Substitution - Missense(2)	kidney(2)											37.0	34.0	35.0					X																	123197875		2203	4298	6501	SO:0001583	missense	10735			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1999C>T	X.37:g.123197875C>T	ENSP00000360202:p.Arg667Trp		B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474231	0.63737	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	5.5	2.46	0.29980	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	L	0.36672	1.1	0.40359	D	0.979225	D;D	0.69078	0.997;0.995	D;P	0.63957	0.92;0.834	T	0.48768	-0.9006	10	0.72032	D	0.01	-21.5834	14.3481	0.66680	0.6187:0.3813:0.0:0.0	.	667;667	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	W	667;598;667;667;667;667	ENSP00000218089:R667W;ENSP00000346555:R598W;ENSP00000360202:R667W;ENSP00000360199:R667W;ENSP00000360187:R667W;ENSP00000360186:R667W	ENSP00000218089:R667W	R	+	1	2	STAG2	123025556	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.018000	0.30002	0.422000	0.26005	-0.222000	0.12452	CGG		0.348	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2		NM_006603	
STRN4	29888	broad.mit.edu;ucsc.edu	37	19	47228597	47228597	+	Silent	SNP	C	C	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr19:47228597C>G	ENST00000263280.6	-	11	1513	c.1464G>C	c.(1462-1464)cgG>cgC	p.R488R	STRN4_ENST00000539396.1_Silent_p.R369R|STRN4_ENST00000594357.2_5'UTR|STRN4_ENST00000391910.3_Silent_p.R495R	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	488						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.R488R(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		ACCTGTGAGCCCGGAAAGCAT	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											210.0	197.0	201.0					19																	47228597		2203	4300	6503	SO:0001819	synonymous_variant	29888			AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"""WD repeat domain containing"""	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.1464G>C	19.37:g.47228597C>G			A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Silent	SNP	ENST00000263280.6	37	CCDS12690.1																																																																																				0.607	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2			
STT3A	3703	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	125479362	125479362	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr11:125479362C>A	ENST00000529196.1	+	11	1201	c.995C>A	c.(994-996)tCg>tAg	p.S332*	STT3A_ENST00000531491.1_Nonsense_Mutation_p.S240*|STT3A_ENST00000392708.4_Nonsense_Mutation_p.S332*			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	332					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.S332*(1)		NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		CGTTTCTACTCGCTGCTGGAT	0.453																																																	1	Substitution - Nonsense(1)	kidney(1)											200.0	189.0	193.0					11																	125479362		2201	4299	6500	SO:0001587	stop_gained	3703			BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.995C>A	11.37:g.125479362C>A	ENSP00000436962:p.Ser332*		B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Nonsense_Mutation	SNP	ENST00000529196.1	37	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	C	39	7.881100	0.98539	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	.	.	.	5.62	5.62	0.85841	.	0.173195	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8117	19.2822	0.94055	0.0:1.0:0.0:0.0	.	.	.	.	X	332;332;240	.	ENSP00000376472:S332X	S	+	2	0	STT3A	124984572	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	7.610000	0.82949	2.656000	0.90262	0.453000	0.30009	TCG		0.453	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1		NM_152713	
STXBP5	134957	broad.mit.edu	37	6	147588238	147588238	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr6:147588238T>C	ENST00000321680.6	+	7	649	c.649T>C	c.(649-651)Tct>Cct	p.S217P	STXBP5_ENST00000367480.3_Missense_Mutation_p.S217P|STXBP5_ENST00000367481.3_Missense_Mutation_p.S217P|STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000546097.1_Missense_Mutation_p.S217P	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	217					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)	p.S217P(2)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGGCTTTGAATCTGGAACAGT	0.313																																																	2	Substitution - Missense(2)	kidney(2)											194.0	200.0	198.0					6																	147588238		2203	4299	6502	SO:0001583	missense	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.649T>C	6.37:g.147588238T>C	ENSP00000321826:p.Ser217Pro		Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.460387	0.63401	.	.	ENSG00000164506	ENST00000367481;ENST00000546097;ENST00000321680;ENST00000367480	T;T;T;T	0.67523	1.51;4.93;1.51;-0.27	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.108661	0.64402	D	0.000004	T	0.68274	0.2983	M	0.73962	2.25	0.80722	D	1	D;D	0.57899	0.969;0.981	P;P	0.51016	0.656;0.536	T	0.71755	-0.4497	10	0.46703	T	0.11	.	16.0637	0.80856	0.0:0.0:0.0:1.0	.	217;217	Q5T5C0-2;Q5T5C0	.;STXB5_HUMAN	P	217	ENSP00000356451:S217P;ENSP00000441479:S217P;ENSP00000321826:S217P;ENSP00000356450:S217P	ENSP00000321826:S217P	S	+	1	0	STXBP5	147629931	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.586000	0.82596	2.197000	0.70478	0.533000	0.62120	TCT		0.313	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			
TCF12	6938	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	57489997	57489998	+	Missense_Mutation	DNP	AA	AA	GG			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr15:57489997_57489998AA>GG	ENST00000267811.5	+	8	857_858	c.553_554AA>GG	c.(553-555)AAg>GGg	p.K185G	TCF12_ENST00000557843.1_Missense_Mutation_p.K185G|TCF12_ENST00000452095.2_Missense_Mutation_p.K181G|TCF12_ENST00000333725.5_Missense_Mutation_p.K185G|TCF12_ENST00000438423.2_Missense_Mutation_p.K185G	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	185					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)	p.K185R(2)|p.K185E(2)|p.K181E(1)|p.K181R(1)	TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		AAAAGTCAGAAAGGTGCCTCCT	0.351			T	TEC	extraskeletal myxoid chondrosarcoma																																			Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	6	Substitution - Missense(6)	kidney(6)																																								SO:0001583	missense	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	Exception_encountered	15.37:g.57489997_57489998delinsGG	ENSP00000267811:p.Lys185Gly		Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																				0.351	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3		NM_003205	
TFDP3	51270	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	132351937	132351937	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chrX:132351937C>T	ENST00000310125.4	-	1	439	c.351G>A	c.(349-351)aaG>aaA	p.K117K		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	117					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K57K(1)|p.K117K(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					TCTCCCAGACCTTCATGGAAA	0.592																																																	2	Substitution - coding silent(2)	kidney(2)											97.0	93.0	94.0					X																	132351937		2203	4300	6503	SO:0001819	synonymous_variant	51270			AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.351G>A	X.37:g.132351937C>T			Q6DK49|Q9NZ54	Silent	SNP	ENST00000310125.4	37	CCDS14636.2																																																																																				0.592	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1		NM_016521	
TJP2	9414	hgsc.bcm.edu;ucsc.edu	37	9	71842779	71842780	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr9:71842779_71842780insA	ENST00000377245.4	+	8	1517_1518	c.1309_1310insA	c.(1309-1311)gaafs	p.E437fs	TJP2_ENST00000535702.1_Frame_Shift_Ins_p.E441fs|TJP2_ENST00000348208.4_Frame_Shift_Ins_p.E437fs|TJP2_ENST00000539225.1_Frame_Shift_Ins_p.E468fs|TJP2_ENST00000265384.7_Frame_Shift_Ins_p.E437fs|TJP2_ENST00000453658.2_Frame_Shift_Ins_p.E414fs	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	437					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GAAGCTGAAGGAAAGGCCAAGG	0.351																																																	0																																										SO:0001589	frameshift_variant	9414			L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1312dupA	9.37:g.71842782_71842782dupA	ENSP00000366453:p.Glu437fs		A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Frame_Shift_Ins	INS	ENST00000377245.4	37	CCDS6627.1																																																																																				0.351	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2		NM_201629	
TSC2	7249	broad.mit.edu	37	16	2131631	2131631	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr16:2131631C>A	ENST00000219476.3	+	31	4276	c.3646C>A	c.(3646-3648)Ctc>Atc	p.L1216I	TSC2_ENST00000353929.4_Missense_Mutation_p.L1173I|TSC2_ENST00000401874.2_Missense_Mutation_p.L1172I|TSC2_ENST00000350773.4_Missense_Mutation_p.L1216I|TSC2_ENST00000568454.1_Missense_Mutation_p.L1183I|TSC2_ENST00000439673.2_Missense_Mutation_p.L1136I|TSC2_ENST00000382538.6_Missense_Mutation_p.L1124I	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1216					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)	p.L1216I(2)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GGAGAACCCGCTCAGCCCTTT	0.637			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																														yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	2	Substitution - Missense(2)	kidney(2)											90.0	76.0	81.0					16																	2131631		2198	4297	6495	SO:0001583	missense	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.3646C>A	16.37:g.2131631C>A	ENSP00000219476:p.Leu1216Ile		A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036471	0.54896	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.89050	-2.33;-2.39;-2.46;-2.43;-2.32	4.7	4.7	0.59300	.	0.067492	0.64402	D	0.000008	D	0.93148	0.7818	L	0.57536	1.79	0.51233	D	0.999919	D;D;D;D;D;D	0.65815	0.983;0.99;0.995;0.99;0.993;0.982	P;P;D;P;D;D	0.77557	0.771;0.885;0.953;0.885;0.99;0.952	D	0.93360	0.6726	10	0.51188	T	0.08	-26.78	17.6634	0.88198	0.0:1.0:0.0:0.0	.	1124;1136;1216;1172;1172;1216	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	I	1216;1173;1173;1136;1124;1216	ENSP00000219476:L1216I;ENSP00000248099:L1173I;ENSP00000399232:L1136I;ENSP00000371978:L1124I;ENSP00000344383:L1216I	ENSP00000219476:L1216I	L	+	1	0	TSC2	2071632	1.000000	0.71417	0.944000	0.38274	0.977000	0.68977	5.939000	0.70179	2.174000	0.68829	0.561000	0.74099	CTC		0.637	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2		NM_000548	
TSEN2	80746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	12545142	12545142	+	Silent	SNP	C	C	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:12545142C>T	ENST00000284995.6	+	5	1077	c.690C>T	c.(688-690)ctC>ctT	p.L230L	TSEN2_ENST00000402228.3_Silent_p.L230L|TSEN2_ENST00000314571.7_Silent_p.L230L|TSEN2_ENST00000454502.2_Intron|RNU6-404P_ENST00000515968.1_RNA|TSEN2_ENST00000415684.1_Silent_p.L230L|TSEN2_ENST00000444864.1_Silent_p.L230L|TSEN2_ENST00000383797.5_Silent_p.L230L	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	230					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)	p.L230L(1)		central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						CTCTCATCCTCCAGCGTGGCC	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											52.0	47.0	49.0					3																	12545142		2203	4300	6503	SO:0001819	synonymous_variant	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.690C>T	3.37:g.12545142C>T			B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Silent	SNP	ENST00000284995.6	37	CCDS2611.1																																																																																				0.587	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1		NM_025265	
TTC21B	79809	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	166731270	166731270	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr2:166731270G>T	ENST00000243344.7	-	29	4083	c.3946C>A	c.(3946-3948)Cct>Act	p.P1316T	TTC21B_ENST00000536175.1_Missense_Mutation_p.P254T	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1316					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)		p.P1316T(1)		breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						TATTTTCAAGGTCTTAAAGAC	0.348																																																	1	Substitution - Missense(1)	kidney(1)											65.0	64.0	64.0					2																	166731270		2203	4300	6503	SO:0001583	missense	79809			AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.3946C>A	2.37:g.166731270G>T	ENSP00000243344:p.Pro1316Thr		A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261220	0.59431	.	.	ENSG00000123607	ENST00000536175;ENST00000243344	T;D	0.83335	-1.23;-1.71	5.61	2.39	0.29439	.	0.229728	0.44902	D	0.000418	T	0.72637	0.3485	L	0.45744	1.44	0.28185	N	0.927999	B	0.02656	0.0	B	0.08055	0.003	T	0.65425	-0.6171	10	0.72032	D	0.01	.	3.2791	0.06908	0.0817:0.3119:0.3123:0.2941	.	1316	Q7Z4L5	TT21B_HUMAN	T	254;1316	ENSP00000438692:P254T;ENSP00000243344:P1316T	ENSP00000243344:P1316T	P	-	1	0	TTC21B	166439516	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	1.387000	0.34430	1.367000	0.46095	0.650000	0.86243	CCT		0.348	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1		NM_024753	
UBE2Q1	55585	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	154527220	154527220	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr1:154527220C>A	ENST00000292211.4	-	4	658	c.579G>T	c.(577-579)gaG>gaT	p.E193D	UBE2Q1_ENST00000497453.1_5'UTR|UBE2Q1-AS1_ENST00000441613.1_RNA	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	193					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)	p.E193D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCTCAGGCATCTCCTCATCTT	0.527																																																	1	Substitution - Missense(1)	kidney(1)											70.0	62.0	65.0					1																	154527220		2203	4300	6503	SO:0001583	missense	55585			AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"""Ubiquitin-conjugating enzymes E2"""	15698	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2Q (putative)"""	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.579G>T	1.37:g.154527220C>A	ENSP00000292211:p.Glu193Asp		B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Missense_Mutation	SNP	ENST00000292211.4	37	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936424	0.52972	.	.	ENSG00000160714	ENST00000292211	.	.	.	5.14	4.24	0.50183	.	0.120680	0.53938	D	0.000044	T	0.14056	0.0340	N	0.11131	0.1	0.39994	D	0.975079	B	0.11235	0.004	B	0.08055	0.003	T	0.08722	-1.0708	9	0.19147	T	0.46	-22.947	9.3142	0.37924	0.0:0.904:0.0:0.096	.	193	Q7Z7E8	UB2Q1_HUMAN	D	193	.	ENSP00000292211:E193D	E	-	3	2	UBE2Q1	152793844	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.953000	0.40352	1.395000	0.46643	0.557000	0.71058	GAG		0.527	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1		NM_017582	
FLJ35934	400579	broad.mit.edu	37	17	18315107	18315108	+	lincRNA	INS	-	-	CT	rs113907775|rs71283274	byFrequency	TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr17:18315107_18315108insCT	ENST00000577684.1	+	0	635_636																											gccctcttctcctcactgtctt	0.604														1367	0.272963	0.4153	0.2911	5008	,	,		21384	0.0724		0.3091	False		,,,				2504	0.2372																0																																												0																															17.37:g.18315108_18315109dupCT				RNA	INS	ENST00000577684.1	37																																																																																					0.604	RP1-37N7.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000447480.1			
PLEKHD1	400224	broad.mit.edu;ucsc.edu	37	14	69992827	69992827	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr14:69992827T>C	ENST00000322564.7	+	9	1123	c.911T>C	c.(910-912)cTg>cCg	p.L304P		NM_001161498.1	NP_001154970.1	A6NEE1	PLHD1_HUMAN	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	304								p.L304P(1)|p.L134P(1)		breast(1)|endometrium(1)|kidney(2)	4						GAGAAGCTCCTGGCAGAGAAG	0.592																																																	2	Substitution - Missense(2)	kidney(2)											37.0	44.0	42.0					14																	69992827		692	1591	2283	SO:0001583	missense	0			AK126770	CCDS53903.1	14q24.1	2013-01-10	2011-05-04		ENSG00000175985	ENSG00000175985		"""Pleckstrin homology (PH) domain containing"""	20148	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family D (with M protein repeats) member 1"""				Standard	NM_001161498		Approved	UPF0639	uc010ttf.1	A6NEE1		ENST00000322564.7:c.911T>C	14.37:g.69992827T>C	ENSP00000317175:p.Leu304Pro		B9EJC2	Missense_Mutation	SNP	ENST00000322564.7	37	CCDS53903.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.390689	0.62066	.	.	ENSG00000175985	ENST00000322564	T	0.78003	-1.14	5.56	5.56	0.83823	.	0.102055	0.42172	D	0.000754	T	0.66528	0.2798	N	0.19112	0.55	0.52099	D	0.999944	D	0.56968	0.978	P	0.46110	0.504	T	0.66052	-0.6019	9	.	.	.	-13.6283	11.1339	0.48362	0.1377:0.0:0.0:0.8623	.	304	B9EJC2	.	P	304	ENSP00000317175:L304P	.	L	+	2	0	PLEKHD1	69062580	0.998000	0.40836	0.987000	0.45799	0.945000	0.59286	3.136000	0.50554	2.241000	0.73720	0.533000	0.62120	CTG		0.592	PLEKHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412451.2		NM_001161498	
URB1	9875	broad.mit.edu;ucsc.edu	37	21	33697561	33697561	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr21:33697561G>A	ENST00000382751.3	-	31	5214	c.5099C>T	c.(5098-5100)gCa>gTa	p.A1700V		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1700						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.A1700V(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						TTGGAACCGTGCGCCCTCCAA	0.612																																																	2	Substitution - Missense(2)	kidney(2)											73.0	63.0	66.0					21																	33697561		692	1591	2283	SO:0001583	missense	9875			AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.5099C>T	21.37:g.33697561G>A	ENSP00000372199:p.Ala1700Val		D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.109204	0.77096	.	.	ENSG00000142207	ENST00000382751	T	0.31510	1.49	5.15	5.15	0.70609	.	0.046367	0.85682	D	0.000000	T	0.51907	0.1702	M	0.61703	1.905	0.80722	D	1	D	0.63046	0.992	P	0.60473	0.875	T	0.54111	-0.8342	10	0.72032	D	0.01	-16.7543	19.0055	0.92849	0.0:0.0:1.0:0.0	.	1700	O60287	NPA1P_HUMAN	V	1700	ENSP00000372199:A1700V	ENSP00000372199:A1700V	A	-	2	0	URB1	32619432	1.000000	0.71417	0.806000	0.32338	0.112000	0.19704	9.743000	0.98849	2.555000	0.86185	0.655000	0.94253	GCA		0.612	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2			
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188268	10188268	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:10188268delG	ENST00000256474.2	+	2	1251	c.411delG	c.(409-411)gtgfs	p.V137fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	137	Involved in binding to CCT complex.				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)			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)		AATTATTTGTGCCATCTCTCA	0.423		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"""	0													218.0	202.0	207.0					3																	10188268		2203	4300	6503	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.411delG	3.37:g.10188268delG	ENSP00000256474:p.Val137fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.423	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WASL	8976	broad.mit.edu	37	7	123332841	123332841	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr7:123332841G>C	ENST00000223023.4	-	9	1239	c.907C>G	c.(907-909)Cct>Gct	p.P303A		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	303	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)	p.P303A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCCTagcaggaggaggagga	0.617																																																	1	Substitution - Missense(1)	kidney(1)											46.0	50.0	49.0					7																	123332841		2203	4300	6503	SO:0001583	missense	8976			D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.907C>G	7.37:g.123332841G>C	ENSP00000223023:p.Pro303Ala		A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416432	0.25552	.	.	ENSG00000106299	ENST00000223023	D	0.91945	-2.94	5.39	5.39	0.77823	Wiscott-Aldrich syndrome, C-terminal (1);	0.112290	0.64402	D	0.000008	D	0.95338	0.8487	M	0.63169	1.94	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.94398	0.7620	10	0.39692	T	0.17	-8.9232	19.209	0.93747	0.0:0.0:1.0:0.0	.	303	O00401	WASL_HUMAN	A	303	ENSP00000223023:P303A	ENSP00000223023:P303A	P	-	1	0	WASL	123120077	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.853000	0.62911	2.528000	0.85240	0.644000	0.83932	CCT		0.617	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1		NM_003941	
CFAP44	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	A	C	rs79365690|rs370566069		TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr3:113049451A>C	ENST00000393845.2	-	26	3746	c.3680T>G	c.(3679-3681)gTt>gGt	p.V1227G	WDR52_ENST00000308346.6_5'Flank	NM_001164496.1	NP_001157968.1												p.V375G(5)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TTCCTCAACAACAGCCACTTT	0.408																																																	5	Substitution - Missense(5)	kidney(5)																																								SO:0001583	missense	55779																														ENST00000393845.2:c.3680T>G	3.37:g.113049451A>C	ENSP00000377428:p.Val1227Gly			Missense_Mutation	SNP	ENST00000393845.2	37	CCDS54624.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.22|14.22	2.469473|2.469473	0.43839|0.43839	.|.	.|.	ENSG00000206530|ENSG00000206530	ENST00000465636|ENST00000393845	.|T	.|0.11821	.|2.74	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.643254	.|0.11770	.|U	.|0.531195	T|T	0.27349|0.27349	0.0671|0.0671	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	.|D	.|0.57899	.|0.981	.|P	.|0.56563	.|0.801	T|T	0.01169|0.01169	-1.1430|-1.1430	5|10	.|0.87932	.|D	.|0	-19.8203|-19.8203	8.8767|8.8767	0.35350|0.35350	0.854:0.0:0.146:0.0|0.854:0.0:0.146:0.0	.|.	.|1227	.|Q96MT7-2	.|.	W|G	363|1227	.|ENSP00000377428:V1227G	.|ENSP00000377428:V1227G	C|V	-|-	3|2	2|0	WDR52|WDR52	114532141|114532141	0.947000|0.947000	0.32204|0.32204	0.873000|0.873000	0.34254|0.34254	0.340000|0.340000	0.28889|0.28889	3.859000|3.859000	0.55987|0.55987	2.081000|2.081000	0.62600|0.62600	0.459000|0.459000	0.35465|0.35465	TGT|GTT		0.408	WDR52-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
WDR75	84128	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	190324065	190324065	+	Silent	SNP	G	G	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr2:190324065G>A	ENST00000314761.4	+	8	753	c.693G>A	c.(691-693)agG>agA	p.R231R		NM_032168.1	NP_115544.1	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	231						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R231R(1)		breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			CCAATAGGAGGAATTTTTATG	0.318																																																	1	Substitution - coding silent(1)	kidney(1)											100.0	103.0	102.0					2																	190324065		2203	4300	6503	SO:0001819	synonymous_variant	84128			AK091546	CCDS2298.1	2q32.2	2013-01-09			ENSG00000115368	ENSG00000115368		"""WD repeat domain containing"""	25725	protein-coding gene	gene with protein product	"""UTP17, small subunit (SSU) processome component, homolog (yeast)"""					17699751	Standard	NM_032168		Approved	FLJ12519, NET16, UTP17	uc002uql.1	Q8IWA0	OTTHUMG00000132660	ENST00000314761.4:c.693G>A	2.37:g.190324065G>A			Q96J10|Q9H8U8|Q9H9U5|Q9H9V8|Q9UIX2	Silent	SNP	ENST00000314761.4	37	CCDS2298.1																																																																																				0.318	WDR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255913.1		NM_032168	
ZKSCAN3	80317	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	28329175	28329175	+	Silent	SNP	A	A	G			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr6:28329175A>G	ENST00000377255.3	+	4	774	c.477A>G	c.(475-477)caA>caG	p.Q159Q	ZKSCAN3_ENST00000252211.2_Silent_p.Q159Q|ZKSCAN3_ENST00000341464.5_Silent_p.Q11Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	159					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q159Q(1)		kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						CAGGGTCACAAAGTAGCCAAT	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											110.0	96.0	101.0					6																	28329175		2203	4300	6503	SO:0001819	synonymous_variant	80317			U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.477A>G	6.37:g.28329175A>G			B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Silent	SNP	ENST00000377255.3	37	CCDS4650.1																																																																																				0.433	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3		NM_024493	
ZNF765	91661	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	53910951	53910951	+	Splice_Site	SNP	A	A	T			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr19:53910951A>T	ENST00000396408.3	+	4	260	c.143A>T	c.(142-144)gAt>gTt	p.D48V	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	48	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D48V(1)		endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		TACTTTTTAGATATCTCTTCC	0.338																																																	1	Substitution - Missense(1)	kidney(1)											44.0	44.0	44.0					19																	53910951		2160	4283	6443	SO:0001630	splice_region_variant	91661			BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"""Zinc fingers, C2H2-type"", ""-"""	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.143-1A>T	19.37:g.53910951A>T			A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.567657	0.28003	.	.	ENSG00000196417	ENST00000396408	T	0.01871	4.59	0.998	-0.887	0.10587	Krueppel-associated box (4);	.	.	.	.	T	0.03434	0.0099	L	0.34521	1.04	0.25467	N	0.987861	P	0.49447	0.924	P	0.55749	0.783	T	0.41466	-0.9507	8	.	.	.	.	3.2847	0.06927	0.6605:0.0:0.3395:0.0	.	48	Q7L2R6	ZN765_HUMAN	V	48	ENSP00000379689:D48V	.	D	+	2	0	ZNF765	58602763	0.000000	0.05858	0.003000	0.11579	0.069000	0.16628	0.033000	0.13754	-0.469000	0.06911	0.147000	0.16070	GAT		0.338	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1		NM_138372	Missense_Mutation
ZSWIM6	57688	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	60827477	60827477	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5709-01A-11D-1534-10	TCGA-B0-5709-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	bfeaecbe-7148-4642-b69a-b908a248f328	3eddc24f-dc63-45e6-b4db-f40af3af4d35	g.chr5:60827477T>A	ENST00000252744.5	+	9	2170	c.2170T>A	c.(2170-2172)Tct>Act	p.S724T		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	724					neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)	p.S724T(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						GCAGCTCATTTCTAAGCTTCA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											100.0	84.0	89.0					5																	60827477		692	1591	2283	SO:0001583	missense	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.2170T>A	5.37:g.60827477T>A	ENSP00000252744:p.Ser724Thr			Missense_Mutation	SNP	ENST00000252744.5	37	CCDS47215.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.346878	0.61183	.	.	ENSG00000130449	ENST00000252744	T	0.45276	0.9	5.83	4.65	0.58169	.	0.112347	0.64402	D	0.000008	T	0.31231	0.0790	L	0.27053	0.805	0.33461	D	0.584975	B	0.17038	0.02	B	0.21708	0.036	T	0.33574	-0.9863	10	0.27082	T	0.32	-4.7219	13.1851	0.59675	0.0:0.0:0.1333:0.8667	.	724	Q9HCJ5	ZSWM6_HUMAN	T	724	ENSP00000252744:S724T	ENSP00000252744:S724T	S	+	1	0	ZSWIM6	60863234	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.126000	0.64721	1.017000	0.39495	0.533000	0.62120	TCT		0.463	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1		NM_020928	
