#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
ABCD3	5825	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	94953300	94953300	+	Silent	SNP	T	T	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:94953300T>C	ENST00000370214.4	+	12	1042	c.1018T>C	c.(1018-1020)Ttg>Ctg	p.L340L	ABCD3_ENST00000536817.1_Silent_p.L267L|ABCD3_ENST00000484213.1_3'UTR|ABCD3_ENST00000454898.2_Silent_p.L364L|ABCD3_ENST00000394233.2_Intron	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	340	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.L340L(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TTTCTTAGATTTGTCTCATCC	0.358																																																	1	Substitution - coding silent(1)	kidney(1)											169.0	150.0	157.0					1																	94953300		2203	4300	6503	SO:0001819	synonymous_variant	5825			M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"""ATP binding cassette transporters / subfamily D"""	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.1018T>C	1.37:g.94953300T>C		Somatic		WXS	Illumina HiSeq	Phase_I	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Silent	SNP	ENST00000370214.4	37	CCDS749.1																																																																																				0.358	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1		NM_002858	
ADAM9	8754	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	38899622	38899622	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr8:38899622T>A	ENST00000487273.2	+	12	1366	c.1288T>A	c.(1288-1290)Tgt>Agt	p.C430S		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	430	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.C430S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			AGAGTGTGACTGTGGTACTCC	0.413																																																	1	Substitution - Missense(1)	kidney(1)											96.0	92.0	93.0					8																	38899622		2203	4300	6503	SO:0001583	missense	8754			U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.1288T>A	8.37:g.38899622T>A	ENSP00000419446:p.Cys430Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	37	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897234	0.91962	.	.	ENSG00000168615	ENST00000487273	T	0.15487	2.42	6.16	6.16	0.99307	Blood coagulation inhibitor, Disintegrin (4);	0.000000	0.85682	D	0.000000	T	0.57636	0.2067	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72033	-0.4412	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	430	Q13443	ADAM9_HUMAN	S	430	ENSP00000419446:C430S	ENSP00000369249:C430S	C	+	1	0	ADAM9	39018779	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.904000	0.87408	2.367000	0.80283	0.528000	0.53228	TGT		0.413	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			
ADAMTS19	171019	hgsc.bcm.edu	37	5	128797315	128797316	+	In_Frame_Ins	INS	-	-	CCCGGC	rs3980042|rs373500239|rs142924298	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:128797315_128797316insCCCGGC	ENST00000274487.4	+	2	739_740	c.594_595insCCCGGC	c.(595-597)ccc>CCCGGCccc	p.199_199P>PGP	ADAMTS19-AS1_ENST00000502827.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	199	Pro-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.N198_P199insPG(1)		NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AGCGGCCAAATCCCGGCCCCGG	0.713														951	0.189896	0.1815	0.1254	5008	,	,		13147	0.3294		0.1083	False		,,,				2504	0.1871																1	Insertion - In frame(1)	breast(1)								443,3611		48,347,1632						-6.8	0.0		dbSNP_134	11	670,7398		63,544,3427	no	coding	ADAMTS19	NM_133638.3		111,891,5059	A1A1,A1R,RR		8.3044,10.9275,9.1817				1113,11009				SO:0001652	inframe_insertion	171019			AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.601_606dupCCCGGC	5.37:g.128797316_128797321dupCCCGGC	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Ins	INS	ENST00000274487.4	37	CCDS4146.1																																																																																				0.713	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2		NM_133638	
APOB	338	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	21225774	21225774	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr2:21225774C>T	ENST00000233242.1	-	29	12647	c.12520G>A	c.(12520-12522)Ggc>Agc	p.G4174S	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4174					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.G4174S(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTACCAAGCCATCAAACACG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											82.0	78.0	79.0					2																	21225774		2203	4300	6503	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.12520G>A	2.37:g.21225774C>T	ENSP00000233242:p.Gly4174Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	3.919	-0.018444	0.07681	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00649	5.98	5.99	-5.58	0.02512	.	1.083110	0.06948	N	0.813996	T	0.00210	0.0006	N	0.00729	-1.24	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.45948	-0.9226	10	0.02654	T	1	.	4.5665	0.12189	0.1116:0.4764:0.1136:0.2983	.	4174	P04114	APOB_HUMAN	S	4174	ENSP00000233242:G4174S	ENSP00000233242:G4174S	G	-	1	0	APOB	21079279	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.268000	0.08607	-0.433000	0.07286	-0.290000	0.09829	GGC		0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			
MPC2	25874	broad.mit.edu;hgsc.bcm.edu	37	1	167887490	167887490	+	3'UTR	SNP	A	A	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:167887490A>T	ENST00000367846.4	-	0	653				MPC2_ENST00000271373.4_3'UTR	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2						cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)										TGCTTTATCAATAACCAAATA	0.348																																																	0													171.0	151.0	157.0					1																	167887490		692	1590	2282	SO:0001624	3_prime_UTR_variant	0				CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158			24515	protein-coding gene	gene with protein product		614737	"""brain protein 44"""	BRP44		3022128, 22628558	Standard	NM_015415		Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.*71T>A	1.37:g.167887490A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K261|Q3SXR6|Q6FIF3	RNA	SNP	ENST00000367846.4	37	CCDS1266.1																																																																																				0.348	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083652.1		NM_015415	
C10orf2	56652	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	102749574	102749574	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr10:102749574C>T	ENST00000311916.2	+	2	1602	c.1417C>T	c.(1417-1419)Cac>Tac	p.H473Y	C10orf2_ENST00000473656.1_3'UTR|MRPL43_ENST00000318325.2_5'Flank|MRPL43_ENST00000370236.1_5'Flank|MRPL43_ENST00000370242.4_5'Flank|MRPL43_ENST00000477279.1_5'Flank|MRPL43_ENST00000370234.4_5'Flank|MRPL43_ENST00000299179.5_5'Flank|C10orf2_ENST00000370228.1_Missense_Mutation_p.H473Y|MRPL43_ENST00000493646.1_5'Flank|MRPL43_ENST00000318364.8_5'Flank|MRPL43_ENST00000342071.1_5'Flank|MRPL43_ENST00000370241.3_5'Flank	NM_001163813.1|NM_021830.4	NP_001157285.1|NP_068602.2	Q96RR1	PEO1_HUMAN	chromosome 10 open reading frame 2	473	SF4 helicase. {ECO:0000255|PROSITE- ProRule:PRU00596}.				cell death (GO:0008219)|DNA unwinding involved in DNA replication (GO:0006268)|mitochondrial DNA replication (GO:0006264)|protein hexamerization (GO:0034214)|protein homooligomerization (GO:0051260)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial nucleoid (GO:0042645)	5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.H473Y(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|stomach(1)	24		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)		CAAATATGATCACTGGGCTGA	0.532																																																	1	Substitution - Missense(1)	kidney(1)											137.0	134.0	135.0					10																	102749574		2203	4300	6503	SO:0001583	missense	56652			AF292004	CCDS7506.1, CCDS53570.1	10q24	2013-05-13			ENSG00000107815	ENSG00000107815			1160	protein-coding gene	gene with protein product	"""twinkle"", ""T7 helicase-related protein with intramitochondrial nucleoid localization"""	606075	"""infantile onset spinocerebellar ataxia (autosomal recessive)"""	IOSCA		11431692, 10645945, 16135556	Standard	NM_021830		Approved	PEO, PEO1, TWINKLE, FLJ21832, TWINL	uc001ksf.2	Q96RR1	OTTHUMG00000018917	ENST00000311916.2:c.1417C>T	10.37:g.102749574C>T	ENSP00000309595:p.His473Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B2CQL2|Q6MZX2|Q6PJP5|Q96RR0	Missense_Mutation	SNP	ENST00000311916.2	37	CCDS7506.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.488527	0.01018	.	.	ENSG00000107815	ENST00000311916;ENST00000370228	D;D	0.94232	-3.38;-3.38	6.04	4.18	0.49190	Circadian clock protein KaiC/DNA repair protein RadA (1);DNA helicase, DnaB-like, C-terminal (1);	0.351848	0.35207	N	0.003378	D	0.82879	0.5133	N	0.03608	-0.345	0.26361	N	0.977045	B;B	0.11235	0.004;0.0	B;B	0.15870	0.014;0.0	T	0.73142	-0.4076	10	0.35671	T	0.21	-33.1849	11.1615	0.48518	0.0713:0.1328:0.7959:0.0	.	473;473	Q96RR1-2;Q96RR1	.;PEO1_HUMAN	Y	473	ENSP00000309595:H473Y;ENSP00000359248:H473Y	ENSP00000309595:H473Y	H	+	1	0	C10orf2	102739564	0.999000	0.42202	0.934000	0.37439	0.426000	0.31534	2.692000	0.47018	1.565000	0.49641	-0.344000	0.07964	CAC		0.532	C10orf2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049886.1		NM_021830	
SMG8	55181	hgsc.bcm.edu;ucsc.edu	37	17	57292221	57292225	+	Frame_Shift_Del	DEL	CCCTT	CCCTT	-	rs141773415		TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	CCCTT	CCCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr17:57292221_57292225delCCCTT	ENST00000543872.2	+	5	3098_3102	c.2834_2838delCCCTT	c.(2833-2838)acccttfs	p.TL945fs	SMG8_ENST00000300917.5_Frame_Shift_Del_p.TL945fs|CTD-2510F5.6_ENST00000577660.1_Frame_Shift_Del_p.TL64fs			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	945					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CAAGAAATCACCCTTCCACCTGATG	0.424																																																	0																																										SO:0001589	frameshift_variant	0			AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2834_2838delCCCTT	17.37:g.57292221_57292225delCCCTT	ENSP00000438748:p.Thr945fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Frame_Shift_Del	DEL	ENST00000543872.2	37	CCDS11615.1																																																																																				0.424	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2		NM_018149	
CACNA1D	776	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	53844188	53844188	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr3:53844188C>A	ENST00000350061.5	+	47	6566	c.6055C>A	c.(6055-6057)Ctg>Atg	p.L2019M	CACNA1D_ENST00000288139.4_Missense_Mutation_p.L2039M|CACNA1D_ENST00000422281.2_Missense_Mutation_p.L1995M|CACNA1D_ENST00000544977.1_3'UTR	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2019					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.L2039M(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTGCCGTCCCTGCACCGCAG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											56.0	55.0	56.0					3																	53844188		2203	4300	6503	SO:0001583	missense	776			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6055C>A	3.37:g.53844188C>A	ENSP00000288133:p.Leu2019Met	Somatic		WXS	Illumina HiSeq	Phase_I	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	37	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146377	0.57044	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.34	4.45	0.53987	.	0.209202	0.29900	N	0.010915	T	0.47801	0.1465	L	0.57536	1.79	0.80722	D	1	B;B;P;B	0.40909	0.319;0.107;0.732;0.264	B;B;B;B	0.40165	0.066;0.027;0.321;0.045	T	0.43988	-0.9357	10	0.35671	T	0.21	.	10.3675	0.44033	0.0:0.8316:0.0:0.1684	.	1995;1712;2019;2039	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	M	2019;2039;1995;1712	ENSP00000288133:L2019M;ENSP00000288139:L2039M;ENSP00000409174:L1995M;ENSP00000418014:L1712M	ENSP00000288139:L2039M	L	+	1	2	CACNA1D	53819228	0.965000	0.33210	1.000000	0.80357	0.775000	0.43874	1.204000	0.32296	2.672000	0.90937	0.557000	0.71058	CTG		0.627	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1		NM_000720	
CATSPERG	57828	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38853135	38853135	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr19:38853135C>A	ENST00000409235.3	+	19	2392	c.2277C>A	c.(2275-2277)ttC>ttA	p.F759L	CATSPERG_ENST00000410018.1_Missense_Mutation_p.F719L|AC005625.1_ENST00000590304.1_RNA|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	759					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.F399L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						AGCGCATTTTCCTGGACAAGG	0.607																																																	1	Substitution - Missense(1)	kidney(1)											66.0	63.0	64.0					19																	38853135		2203	4300	6503	SO:0001583	missense	57828			AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.2277C>A	19.37:g.38853135C>A	ENSP00000386962:p.Phe759Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	C	16.28	3.079438	0.55753	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	T;T	0.32753	1.44;1.44	4.61	3.57	0.40892	.	0.260548	0.27482	N	0.019179	T	0.44705	0.1306	M	0.67953	2.075	0.80722	D	1	D;D	0.63880	0.987;0.993	P;P	0.57720	0.722;0.826	T	0.39396	-0.9616	10	0.66056	D	0.02	-31.5841	8.8883	0.35418	0.0:0.894:0.0:0.106	.	759;719	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	L	719;759;759	ENSP00000387057:F719L;ENSP00000386962:F759L	ENSP00000386962:F759L	F	+	3	2	CATSPERG	43544975	1.000000	0.71417	0.995000	0.50966	0.419000	0.31324	2.335000	0.43929	0.933000	0.37291	-0.448000	0.05591	TTC		0.607	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1		NM_021185	
CD300LG	146894	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	41931245	41931246	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr17:41931245_41931246GC>TA	ENST00000317310.4	+	4	593_594	c.552_553GC>TA	c.(550-555)ttGCca>ttTAca	p.184_185LP>FT	CD300LG_ENST00000586233.1_Intron|CD300LG_ENST00000293396.8_Intron|CD300LG_ENST00000539718.1_Missense_Mutation_p.184_185LP>FT|CD300LG_ENST00000377203.4_Missense_Mutation_p.150_151LP>FT	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	184					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L184F(1)|p.P185T(1)|p.L184>?(1)		central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CCCCTCCATTGCCAGGGACTTC	0.619																																																	3	Substitution - Missense(2)|Complex(1)	kidney(3)																																								SO:0001583	missense	146894			BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		Exception_encountered	17.37:g.41931245_41931246delinsTA	ENSP00000321005:p.L184_P185delinsFT	Somatic		WXS	Illumina HiSeq	Phase_I	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Missense_Mutation	SNP	ENST00000317310.4	37	CCDS11470.1																																																																																				0.619	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1		NM_145273	
CD74	972	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	149792311	149792311	+	Start_Codon_SNP	SNP	A	A	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:149792311A>T	ENST00000009530.7	-	1	3	c.2T>A	c.(1-3)aTg>aAg	p.M1K	CD74_ENST00000524315.1_Start_Codon_SNP_p.M1K|CD74_ENST00000353334.6_Start_Codon_SNP_p.M1K|CD74_ENST00000377795.3_Start_Codon_SNP_p.M1K			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	1					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)	p.M1K(2)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCCTGTGCATCTGGGACCC	0.577			T	ROS1	NSCLC																																			Dom	yes		5	5q32	972	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""		E	2	Substitution - Missense(2)	kidney(2)											135.0	136.0	136.0					5																	149792311		2203	4300	6503	SO:0001582	initiator_codon_variant	972				CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.2T>A	5.37:g.149792311A>T	ENSP00000009530:p.Met1Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Missense_Mutation	SNP	ENST00000009530.7	37	CCDS47309.1	.	.	.	.	.	.	.	.	.	.	A	9.057	0.993429	0.19043	.	.	ENSG00000019582	ENST00000377795;ENST00000353334;ENST00000524315;ENST00000009530	T	0.58060	0.36	5.88	-6.3	0.02007	.	.	.	.	.	T	0.37785	0.1016	.	.	.	0.22648	N	0.998897	B;B;B;B	0.17268	0.002;0.021;0.008;0.002	B;B;B;B	0.15484	0.002;0.013;0.013;0.004	T	0.42015	-0.9476	8	0.87932	D	0	9.36	9.8147	0.40844	0.6123:0.0:0.2888:0.099	.	1;1;1;1	A9YLN4;P04233-3;P04233-2;P04233	.;.;.;HG2A_HUMAN	K	1	ENSP00000009530:M1K	ENSP00000009530:M1K	M	-	2	0	CD74	149772504	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-1.133000	0.03232	-1.020000	0.03354	-0.912000	0.02778	ATG		0.577	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374178.1		NM_004355	Missense_Mutation
CDK6	1021	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	92252376	92252376	+	Silent	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr7:92252376A>G	ENST00000265734.4	-	6	1083	c.672T>C	c.(670-672)gaT>gaC	p.D224D	CDK6_ENST00000424848.2_Silent_p.D224D	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.D224D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			GTTGATCAACATCTGAACTTC	0.299			T	MLLT10	ALL																																			Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	1	Substitution - coding silent(1)	kidney(1)											51.0	52.0	52.0					7																	92252376		2198	4296	6494	SO:0001819	synonymous_variant	1021				CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"""Cyclin-dependent kinases"""	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.672T>C	7.37:g.92252376A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A4D1G0	Silent	SNP	ENST00000265734.4	37	CCDS5628.1																																																																																				0.299	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2			
CEP164	22897	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	117265695	117265695	+	Silent	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr11:117265695C>T	ENST00000278935.3	+	22	2967	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	940	Glu-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.A940A(1)		breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		ATGTCAAGGCCAGATTGGCTC	0.512																																																	1	Substitution - coding silent(1)	kidney(1)											137.0	139.0	138.0					11																	117265695		2201	4296	6497	SO:0001819	synonymous_variant	22897			AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.2820C>T	11.37:g.117265695C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Silent	SNP	ENST00000278935.3	37	CCDS31683.1																																																																																				0.512	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1		NM_014956	
CLSPN	63967	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	36230187	36230187	+	Missense_Mutation	SNP	T	T	A	rs201606744		TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:36230187T>A	ENST00000318121.3	-	3	319	c.262A>T	c.(262-264)Aat>Tat	p.N88Y	CLSPN_ENST00000373220.3_Missense_Mutation_p.N88Y|CLSPN_ENST00000251195.5_Missense_Mutation_p.N88Y|CLSPN_ENST00000520551.1_Missense_Mutation_p.N88Y	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	88					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.N88Y(2)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTCTCTTTATTTTCCTCCTCG	0.373																																																	2	Substitution - Missense(2)	kidney(2)											77.0	80.0	79.0					1																	36230187		2201	4300	6501	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.262A>T	1.37:g.36230187T>A	ENSP00000312995:p.Asn88Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.253626	0.59212	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551;ENST00000544356	T;T;T;T	0.24908	1.84;1.85;1.83;1.84	6.03	0.9	0.19278	.	0.581949	0.18576	N	0.137182	T	0.29556	0.0737	L	0.43152	1.355	0.21445	N	0.999689	P;D	0.57571	0.955;0.98	P;P	0.53593	0.66;0.73	T	0.09796	-1.0658	10	0.62326	D	0.03	-5.332	8.509	0.33206	0.0:0.4713:0.0:0.5287	.	88;88	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Y	88	ENSP00000251195:N88Y;ENSP00000312995:N88Y;ENSP00000362317:N88Y;ENSP00000428848:N88Y	ENSP00000251195:N88Y	N	-	1	0	CLSPN	36002774	0.951000	0.32395	0.866000	0.34008	0.952000	0.60782	0.043000	0.13971	0.125000	0.18397	0.533000	0.62120	AAT		0.373	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1		NM_022111	
CXorf21	80231	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	30578381	30578381	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chrX:30578381T>C	ENST00000378962.3	-	3	414	c.92A>G	c.(91-93)aAg>aGg	p.K31R		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	31								p.K31R(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						CTCCTCTTCCTTTTCCCCAGC	0.458																																																	1	Substitution - Missense(1)	kidney(1)											95.0	80.0	85.0					X																	30578381		2202	4300	6502	SO:0001583	missense	80231			BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.92A>G	X.37:g.30578381T>C	ENSP00000368245:p.Lys31Arg	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000378962.3	37	CCDS14224.1	.	.	.	.	.	.	.	.	.	.	T	5.388	0.256885	0.10185	.	.	ENSG00000120280	ENST00000378962	.	.	.	5.0	1.23	0.21249	.	0.518270	0.19077	N	0.123349	T	0.28499	0.0705	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20371	-1.0277	9	0.13853	T	0.58	-8.3278	4.4701	0.11708	0.1629:0.4105:0.0:0.4266	.	31	Q9HAI6	CX021_HUMAN	R	31	.	ENSP00000368245:K31R	K	-	2	0	CXorf21	30488302	0.081000	0.21417	0.003000	0.11579	0.388000	0.30384	0.471000	0.22100	0.248000	0.21435	-0.443000	0.05667	AAG		0.458	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1		NM_025159	
DCAF13	25879	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	104438314	104438314	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr8:104438314A>G	ENST00000297579.5	+	4	1142	c.865A>G	c.(865-867)Aaa>Gaa	p.K289E	DCAF13_ENST00000519682.1_Missense_Mutation_p.K133E|DCAF13_ENST00000521999.1_3'UTR|DCAF13_ENST00000521971.1_Missense_Mutation_p.K97E	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	137					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.K289E(1)		NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GAAGCAGTGGAAAATGGATGG	0.348																																																	1	Substitution - Missense(1)	kidney(1)											77.0	79.0	78.0					8																	104438314		2203	4300	6503	SO:0001583	missense	25879			AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.865A>G	8.37:g.104438314A>G	ENSP00000297579:p.Lys289Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.790738	0.50102	.	.	ENSG00000164934	ENST00000297579;ENST00000521971;ENST00000519682	T;T;T	0.60299	0.2;5.03;0.2	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.152104	0.64402	D	0.000011	T	0.44329	0.1288	N	0.25245	0.725	0.58432	D	0.999999	B;B	0.20368	0.003;0.044	B;B	0.24974	0.017;0.057	T	0.37911	-0.9685	10	0.44086	T	0.13	-25.3125	11.0094	0.47654	0.861:0.0:0.0:0.1389	.	137;137	B3KME9;Q9NV06	.;DCA13_HUMAN	E	289;97;133	ENSP00000297579:K289E;ENSP00000430883:K97E;ENSP00000430411:K133E	ENSP00000297579:K289E	K	+	1	0	DCAF13	104507490	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.839000	0.62810	2.147000	0.66899	0.533000	0.62120	AAA		0.348	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2		NM_015420	
DCTD	1635	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	183836682	183836682	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr4:183836682C>T	ENST00000438320.2	-	2	330	c.40G>A	c.(40-42)Gaa>Aaa	p.E14K	DCTD_ENST00000513383.1_5'UTR|DCTD_ENST00000510370.1_Missense_Mutation_p.E14K|DCTD_ENST00000357067.3_Missense_Mutation_p.E25K	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	14					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)	p.E14K(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	TCTGGCCATTCCAAATAGTCG	0.403																																																	1	Substitution - Missense(1)	kidney(1)											126.0	139.0	135.0					4																	183836682		2203	4300	6503	SO:0001583	missense	1635			L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.40G>A	4.37:g.183836682C>T	ENSP00000398194:p.Glu14Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Missense_Mutation	SNP	ENST00000438320.2	37	CCDS3831.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883453	0.72410	.	.	ENSG00000129187	ENST00000357067;ENST00000438320;ENST00000510370;ENST00000503182;ENST00000510307;ENST00000512766;ENST00000514754;ENST00000503820;ENST00000503988;ENST00000508994	T;T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	4.7	3.85	0.44370	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.048716	0.85682	D	0.000000	T	0.25975	0.0633	N	0.05414	-0.055	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.004	T	0.07347	-1.0777	10	0.62326	D	0.03	-29.3648	15.2677	0.73675	0.0:0.8591:0.1409:0.0	.	25;14	P32321-2;P32321	.;DCTD_HUMAN	K	25;14;14;14;14;14;14;14;14;14	ENSP00000349576:E25K;ENSP00000398194:E14K;ENSP00000424017:E14K;ENSP00000422662:E14K;ENSP00000424050:E14K;ENSP00000423182:E14K;ENSP00000423894:E14K;ENSP00000421792:E14K;ENSP00000422729:E14K	ENSP00000349576:E25K	E	-	1	0	DCTD	184073676	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	5.565000	0.67365	1.317000	0.45149	0.655000	0.94253	GAA		0.403	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2			
ERP44	23071	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	102822388	102822388	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr9:102822388delT	ENST00000262455.6	-	2	323	c.124delA	c.(124-126)attfs	p.I42fs		NM_015051.1	NP_055866.1	Q9BS26	ERP44_HUMAN	endoplasmic reticulum protein 44	42	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|glycoprotein metabolic process (GO:0009100)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)	19						TTACTTAAAATTTCATCTATA	0.249																																																	0													23.0	25.0	24.0					9																	102822388		2156	4247	6403	SO:0001589	frameshift_variant	23071			AB011145	CCDS35082.1	9q22.33	2011-10-19	2009-02-23	2009-02-23	ENSG00000023318	ENSG00000023318		"""Protein disulfide isomerases"""	18311	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 10"""	609170	"""thioredoxin domain containing 4 (endoplasmic reticulum)"""	TXNDC4		11847130	Standard	NM_015051		Approved	KIAA0573, PDIA10	uc004bam.3	Q9BS26	OTTHUMG00000020363	ENST00000262455.6:c.124delA	9.37:g.102822388delT	ENSP00000262455:p.Ile42fs	Somatic		WXS	Illumina HiSeq	Phase_I	O60319|Q4VXC1|Q5VWZ7|Q6UW14|Q8WX67	Frame_Shift_Del	DEL	ENST00000262455.6	37	CCDS35082.1																																																																																				0.249	ERP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053402.1		XM_088476	
FOXP2	93986	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	114282567	114282567	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr7:114282567C>T	ENST00000393494.2	+	7	1157	c.878C>T	c.(877-879)aCt>aTt	p.T293I	FOXP2_ENST00000393489.3_Missense_Mutation_p.T201I|FOXP2_ENST00000350908.4_Missense_Mutation_p.T293I|FOXP2_ENST00000390668.3_Missense_Mutation_p.T317I|FOXP2_ENST00000403559.4_Missense_Mutation_p.T310I|FOXP2_ENST00000408937.3_Missense_Mutation_p.T318I|FOXP2_ENST00000378237.3_Missense_Mutation_p.T293I|FOXP2_ENST00000360232.4_Missense_Mutation_p.T293I|FOXP2_ENST00000393498.2_Missense_Mutation_p.T272I|FOXP2_ENST00000393491.3_Missense_Mutation_p.T201I|FOXP2_ENST00000393500.3_Missense_Mutation_p.T218I			O15409	FOXP2_HUMAN	forkhead box P2	293				DLTTNNSSSTTSSNT -> EEFPVQGPAAVCAGL (in Ref. 10; AAB91439). {ECO:0000305}.	camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T318I(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						GACCTCACTACTAACAATTCC	0.443																																																	1	Substitution - Missense(1)	kidney(1)											240.0	209.0	220.0					7																	114282567		2203	4300	6503	SO:0001583	missense	93986			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.878C>T	7.37:g.114282567C>T	ENSP00000377132:p.Thr293Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.686127	0.88639	.	.	ENSG00000128573	ENST00000393500;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000393489;ENST00000360232;ENST00000393495;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T;T	0.37235	1.21;1.32;1.21;1.21;1.32;1.32;1.32;1.32;1.21;1.32	4.86	4.86	0.63082	.	0.090253	0.85682	D	0.000000	T	0.60077	0.2241	M	0.65975	2.015	0.80722	D	1	D;D;D;P;D;D;D	0.69078	0.995;0.995;0.984;0.936;0.997;0.995;0.997	D;D;D;P;D;D;D	0.75484	0.969;0.969;0.969;0.55;0.986;0.969;0.986	T	0.64170	-0.6470	10	0.72032	D	0.01	.	18.3604	0.90372	0.0:1.0:0.0:0.0	.	292;310;201;293;317;293;318	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4	.;.;.;.;.;FOXP2_HUMAN;.	I	218;293;318;310;293;270;293;201;293;150;317;201	ENSP00000377137:T218I;ENSP00000377132:T293I;ENSP00000386200:T318I;ENSP00000385069:T310I;ENSP00000265436:T293I;ENSP00000367482:T293I;ENSP00000377129:T201I;ENSP00000353367:T293I;ENSP00000375084:T317I;ENSP00000377130:T201I	ENSP00000265436:T293I	T	+	2	0	FOXP2	114069803	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.442000	0.80503	2.410000	0.81850	0.460000	0.39030	ACT		0.443	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1		NM_014491	
IL12RB2	3595	hgsc.bcm.edu;ucsc.edu	37	1	67845752	67845761	+	Frame_Shift_Del	DEL	CTGACAGCTG	CTGACAGCTG	-			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	CTGACAGCTG	CTGACAGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:67845752_67845761delCTGACAGCTG	ENST00000262345.1	+	13	2441_2450	c.1801_1810delCTGACAGCTG	c.(1801-1812)ctgacagctgctfs	p.LTAA601fs	IL12RB2_ENST00000541374.1_Frame_Shift_Del_p.LTAA601fs|IL12RB2_ENST00000465396.1_3'UTR|IL12RB2_ENST00000371000.1_Frame_Shift_Del_p.LTAA601fs|IL12RB2_ENST00000544434.1_Frame_Shift_Del_p.LTAA515fs	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	601	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						GATGACAGCTCTGACAGCTGCTGGTGAAAG	0.481																																																	0																																										SO:0001589	frameshift_variant	3595			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1801_1810delCTGACAGCTG	1.37:g.67845752_67845761delCTGACAGCTG	ENSP00000262345:p.Leu601fs	Somatic		WXS	Illumina HiSeq	Phase_I	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Frame_Shift_Del	DEL	ENST00000262345.1	37	CCDS638.1																																																																																				0.481	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2		NM_001559	
ISG20L2	81875	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	156697247	156697247	+	Silent	SNP	C	C	T	rs61742814	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:156697247C>T	ENST00000313146.6	-	1	980	c.198G>A	c.(196-198)acG>acA	p.T66T	ISG20L2_ENST00000472824.2_5'Flank|RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|ISG20L2_ENST00000368219.1_Silent_p.T66T|RRNAD1_ENST00000368216.4_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	66					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)	p.T66T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGCCATCGACCGTAGGAGTTT	0.512													C|||	3	0.000599042	0.0	0.0	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0031																1	Substitution - coding silent(1)	kidney(1)											66.0	74.0	72.0					1																	156697247		2203	4300	6503	SO:0001819	synonymous_variant	81875			AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.198G>A	1.37:g.156697247C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DVC6|Q64KA2	Silent	SNP	ENST00000313146.6	37	CCDS1153.1																																																																																				0.512	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1		NM_030980	
LAMA1	284217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	6983136	6983136	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr18:6983136C>A	ENST00000389658.3	-	40	5851	c.5758G>T	c.(5758-5760)Gcc>Tcc	p.A1920S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1920	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A1920S(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GCATCTCTGGCCAGTTCCTCC	0.498																																																	1	Substitution - Missense(1)	kidney(1)											110.0	102.0	105.0					18																	6983136		2203	4300	6503	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5758G>T	18.37:g.6983136C>A	ENSP00000374309:p.Ala1920Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.105685	0.56291	.	.	ENSG00000101680	ENST00000389658	T	0.28895	1.59	5.87	5.87	0.94306	.	0.134719	0.48767	D	0.000177	T	0.49304	0.1549	L	0.52759	1.655	0.34916	D	0.747927	D	0.89917	1.0	D	0.68353	0.957	T	0.57100	-0.7869	10	0.51188	T	0.08	.	15.7747	0.78204	0.1368:0.8632:0.0:0.0	.	1920	P25391	LAMA1_HUMAN	S	1920	ENSP00000374309:A1920S	ENSP00000374309:A1920S	A	-	1	0	LAMA1	6973136	1.000000	0.71417	0.499000	0.27577	0.137000	0.21094	3.906000	0.56340	2.774000	0.95407	0.650000	0.86243	GCC		0.498	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1		NM_005559	
KMT2A	4297	hgsc.bcm.edu;ucsc.edu	37	11	118372561	118372561	+	Nonsense_Mutation	SNP	T	T	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr11:118372561T>A	ENST00000389506.5	+	26	6485	c.6485T>A	c.(6484-6486)tTg>tAg	p.L2162*	KMT2A_ENST00000534358.1_Nonsense_Mutation_p.L2165*|KMT2A_ENST00000354520.4_Nonsense_Mutation_p.L2124*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2162					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGTCGACCGTTGCCTTCTGCA	0.438																																																	0													79.0	79.0	79.0					11																	118372561		2200	4296	6496	SO:0001587	stop_gained	4297			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.6485T>A	11.37:g.118372561T>A	ENSP00000374157:p.Leu2162*	Somatic		WXS	Illumina HiSeq	Phase_I	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	T	46	12.721034	0.99691	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	.	.	.	5.53	5.53	0.82687	.	0.136740	0.49916	D	0.000129	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6946	0.62569	0.0:0.0:0.0:1.0	.	.	.	.	X	2165;2162;2124;1072	.	ENSP00000346516:L2124X	L	+	2	0	MLL	117877771	1.000000	0.71417	0.965000	0.40720	0.589000	0.36550	5.534000	0.67167	2.219000	0.72066	0.482000	0.46254	TTG		0.438	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2		NM_005933	
MOXD1	26002	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	132643865	132643865	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr6:132643865T>C	ENST00000367963.3	-	8	1376	c.1258A>G	c.(1258-1260)Aat>Gat	p.N420D	MOXD1_ENST00000336749.3_Missense_Mutation_p.N352D|MOXD1_ENST00000489128.1_5'UTR	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	420						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.N420D(1)|p.N352D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TCCTGGAAATTGAAGTCAAAA	0.383																																																	2	Substitution - Missense(2)	kidney(2)											118.0	121.0	120.0					6																	132643865		2203	4300	6503	SO:0001583	missense	26002			AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1258A>G	6.37:g.132643865T>C	ENSP00000356940:p.Asn420Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245859	0.80024	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.76839	-1.05;-1.05	5.78	5.78	0.91487	PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	L	0.49571	1.57	0.80722	D	1	P;D	0.71674	0.867;0.998	P;D	0.80764	0.874;0.994	T	0.80379	-0.1407	10	0.36615	T	0.2	-31.5304	16.1008	0.81169	0.0:0.0:0.0:1.0	.	420;352	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	D	420;352	ENSP00000356940:N420D;ENSP00000336998:N352D	ENSP00000336998:N352D	N	-	1	0	MOXD1	132685558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.742000	0.74843	2.206000	0.71126	0.533000	0.62120	AAT		0.383	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1		NM_015529	
PARP4	143	broad.mit.edu;hgsc.bcm.edu	37	13	25008976	25008976	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr13:25008976G>T	ENST00000381989.3	-	31	4408	c.4303C>A	c.(4303-4305)Ccc>Acc	p.P1435T		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1435					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.P1435T(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TGAAGCTGGGGAGAATCCAGC	0.512																																																	1	Substitution - Missense(1)	kidney(1)											26.0	28.0	27.0					13																	25008976		2203	4299	6502	SO:0001583	missense	143			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.4303C>A	13.37:g.25008976G>T	ENSP00000371419:p.Pro1435Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	g	7.101	0.574150	0.13623	.	.	ENSG00000102699	ENST00000381989	T	0.01933	4.55	2.78	0.935	0.19483	.	.	.	.	.	T	0.01730	0.0055	N	0.24115	0.695	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.46748	-0.9169	9	0.62326	D	0.03	-1.0482	3.4596	0.07528	0.1461:0.0:0.6068:0.2471	.	1435	Q9UKK3	PARP4_HUMAN	T	1435	ENSP00000371419:P1435T	ENSP00000371419:P1435T	P	-	1	0	PARP4	23906976	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-0.176000	0.09811	0.058000	0.16222	0.462000	0.41574	CCC		0.512	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1		NM_006437	
PAX1	5075	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	21689243	21689243	+	Missense_Mutation	SNP	G	G	A	rs202103929	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr20:21689243G>A	ENST00000398485.2	+	3	1018	c.964G>A	c.(964-966)Gac>Aac	p.D322N	PAX1_ENST00000444366.2_Missense_Mutation_p.D298N|PAX1_ENST00000460221.1_3'UTR	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	322					bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D322N(1)|p.D228N(1)		autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						CAAGATGGAAGACTGGGCCGG	0.602													G|||	2	0.000399361	0.0	0.0029	5008	,	,		17560	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)											56.0	65.0	62.0					20																	21689243		2203	4300	6503	SO:0001583	missense	5075				CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"""Paired boxes"""	8615	protein-coding gene	gene with protein product		167411	"""paired box gene 1"""			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.964G>A	20.37:g.21689243G>A	ENSP00000381499:p.Asp322Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	37	CCDS13146.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	24.1	4.498082	0.85069	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.98419	-4.49;-4.92	5.3	5.3	0.74995	.	0.107994	0.64402	D	0.000008	D	0.98302	0.9437	M	0.75447	2.3	0.58432	D	0.999996	B;B;D	0.59767	0.2;0.321;0.986	B;B;P	0.53266	0.089;0.105;0.722	D	0.98465	1.0598	10	0.44086	T	0.13	.	18.5491	0.91057	0.0:0.0:1.0:0.0	.	298;228;322	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	N	322;298	ENSP00000381499:D322N;ENSP00000410355:D298N	ENSP00000381499:D322N	D	+	1	0	PAX1	21637243	1.000000	0.71417	1.000000	0.80357	0.372000	0.29890	9.277000	0.95755	2.474000	0.83562	0.455000	0.32223	GAC		0.602	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52668655	52668655	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr3:52668655G>A	ENST00000296302.7	-	11	1265	c.1264C>T	c.(1264-1266)Cag>Tag	p.Q422*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Q422*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Q422*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Q390*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Q422*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Q422*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Q422*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Q422*			Q86U86	PB1_HUMAN	polybromo 1	422	Bromo 3. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Q422*(2)|p.Q390*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTAATTTGCTGGTAATAATCA	0.363			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											156.0	178.0	171.0					3																	52668655		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1264C>T	3.37:g.52668655G>A	ENSP00000296302:p.Gln422*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	38	6.808166	0.97853	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.68	5.68	0.88126	.	0.130229	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-41.2192	19.7907	0.96456	0.0:0.0:1.0:0.0	.	.	.	.	X	390;422;422;422;422;422;422;422;422;366	.	ENSP00000296302:Q422X	Q	-	1	0	PBRM1	52643695	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.686000	0.91538	0.491000	0.48974	CAG		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PIK3R4	30849	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	130454821	130454821	+	Silent	SNP	T	T	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr3:130454821T>C	ENST00000356763.3	-	3	1316	c.759A>G	c.(757-759)acA>acG	p.T253T		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T253T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						GTACACCTTCTGTAAAAAGCT	0.318																																																	1	Substitution - coding silent(1)	kidney(1)											102.0	109.0	107.0					3																	130454821		2203	4299	6502	SO:0001819	synonymous_variant	30849			Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"""WD repeat domain containing"""	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.759A>G	3.37:g.130454821T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q2TBF4	Silent	SNP	ENST00000356763.3	37	CCDS3067.1																																																																																				0.318	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1		NM_014602	
PLA2G16	11145	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	63357820	63357820	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr11:63357820C>T	ENST00000323646.5	-	3	493	c.139G>A	c.(139-141)Gca>Aca	p.A47T	PLA2G16_ENST00000394613.3_5'UTR|PLA2G16_ENST00000415826.1_Missense_Mutation_p.A47T	NM_007069.3	NP_009000.2	P53816	HRSL3_HUMAN	phospholipase A2, group XVI	47					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|negative regulation of cell cycle (GO:0045786)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	1-acyl-2-lysophosphatidylserine acylhydrolase activity (GO:0052740)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phosphatidylserine 1-acylhydrolase activity (GO:0052739)|phospholipase A2 activity (GO:0004623)	p.A47T(1)		kidney(2)|lung(1)|ovary(1)|skin(1)	5						ACACTGGCTGCACCAGCTCCT	0.582																																																	1	Substitution - Missense(1)	kidney(1)											116.0	83.0	94.0					11																	63357820		2201	4298	6499	SO:0001583	missense	11145			X92814	CCDS8047.1	11q12.3	2014-03-14	2008-09-19	2008-09-19	ENSG00000176485	ENSG00000176485	3.1.1.4		17825	protein-coding gene	gene with protein product	"""adipose-specific PLA2"""	613867	"""HRAS-like suppressor 3"""	HRASLS3		9771974, 18614531	Standard	NM_007069		Approved	HREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA	uc009you.1	P53816	OTTHUMG00000167852	ENST00000323646.5:c.139G>A	11.37:g.63357820C>T	ENSP00000320337:p.Ala47Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7Q4|B7XAK5|Q3SYI3|Q9HDD1	Missense_Mutation	SNP	ENST00000323646.5	37	CCDS8047.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.440034	0.43326	.	.	ENSG00000176485	ENST00000323646;ENST00000415826	T;T	0.22539	1.95;1.95	5.58	3.71	0.42584	.	0.249831	0.39341	N	0.001399	T	0.12008	0.0292	N	0.24115	0.695	0.09310	N	1	B;B	0.18610	0.029;0.006	B;B	0.24394	0.053;0.021	T	0.32719	-0.9896	10	0.16420	T	0.52	-0.5815	6.24	0.20785	0.0:0.6823:0.1519:0.1658	.	78;47	Q3MI98;P53816	.;PAG16_HUMAN	T	47	ENSP00000320337:A47T;ENSP00000389124:A47T	ENSP00000320337:A47T	A	-	1	0	PLA2G16	63114396	0.000000	0.05858	0.003000	0.11579	0.023000	0.10783	0.030000	0.13688	0.720000	0.32209	0.551000	0.68910	GCA		0.582	PLA2G16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396632.1		NM_001128203	
PRR16	51334	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	120021872	120021872	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:120021872G>T	ENST00000407149.2	+	2	592	c.383G>T	c.(382-384)aGg>aTg	p.R128M	PRR16_ENST00000446965.1_Missense_Mutation_p.R58M|PRR16_ENST00000379551.2_Missense_Mutation_p.R105M|PRR16_ENST00000505123.1_Missense_Mutation_p.R58M			Q569H4	LARGN_HUMAN	proline rich 16	128	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)			p.R105M(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CCTCCTCCAAGGTTGACACCT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											122.0	105.0	111.0					5																	120021872		2203	4300	6503	SO:0001583	missense	51334			AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.383G>T	5.37:g.120021872G>T	ENSP00000385118:p.Arg128Met	Somatic		WXS	Illumina HiSeq	Phase_I	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	37		.	.	.	.	.	.	.	.	.	.	G	22.2	4.259174	0.80246	.	.	ENSG00000184838	ENST00000407149;ENST00000379551;ENST00000509923;ENST00000505123;ENST00000446965	T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.66107	0.2756	L	0.59436	1.845	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.964	T	0.62586	-0.6823	9	.	.	.	-5.1224	18.6986	0.91611	0.0:0.0:1.0:0.0	.	128;105	Q569H4;Q569H4-3	PRR16_HUMAN;.	M	128;105;58;58;58	ENSP00000385118:R128M;ENSP00000368869:R105M;ENSP00000421256:R58M;ENSP00000423446:R58M;ENSP00000405491:R58M	.	R	+	2	0	PRR16	120049771	1.000000	0.71417	0.966000	0.40874	0.978000	0.69477	9.111000	0.94308	2.709000	0.92574	0.644000	0.83932	AGG		0.517	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1		NM_016644	
RANBP2	5903	broad.mit.edu;hgsc.bcm.edu	37	2	109384150	109384150	+	Silent	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr2:109384150A>G	ENST00000283195.6	+	20	7281	c.7155A>G	c.(7153-7155)agA>agG	p.R2385R		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2385	RanBD1 3. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R2385R(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CCAATCACAGAATAACTCCAG	0.363																																																	2	Substitution - coding silent(2)	kidney(2)											125.0	142.0	136.0					2																	109384150		2153	4171	6324	SO:0001819	synonymous_variant	5903			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7155A>G	2.37:g.109384150A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																				0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1		NM_006267	
RNF145	153830	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	158603687	158603687	+	Silent	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:158603687A>G	ENST00000424310.2	-	5	933	c.574T>C	c.(574-576)Ttg>Ctg	p.L192L	RNF145_ENST00000518802.1_Silent_p.L222L|RNF145_ENST00000519865.1_Silent_p.L192L|RNF145_ENST00000521606.2_Silent_p.L209L|RNF145_ENST00000274542.2_Silent_p.L220L|RNF145_ENST00000520638.1_Silent_p.L206L	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	192						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.L220L(1)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TAAGGTACCAAAAGATTAGAC	0.343																																																	1	Substitution - coding silent(1)	kidney(1)											62.0	61.0	62.0					5																	158603687		2203	4300	6503	SO:0001819	synonymous_variant	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.574T>C	5.37:g.158603687A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																				0.343	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1		NM_144726	
RPS2	6187	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	2012906	2012906	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr16:2012906A>T	ENST00000343262.4	-	5	436	c.380T>A	c.(379-381)tTt>tAt	p.F127Y	SNORA10_ENST00000384084.1_RNA|SNHG9_ENST00000459373.1_lincRNA|RPS2_ENST00000529806.1_Missense_Mutation_p.F97Y|RPS2_ENST00000526522.1_Intron|SNORA64_ENST00000384674.1_RNA|RPS2_ENST00000530225.1_Missense_Mutation_p.F127Y	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	127	S5 DRBM. {ECO:0000255|PROSITE- ProRule:PRU00268}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.F127Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						GATAGCAACAAATGCCTGCGA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											63.0	61.0	62.0					16																	2012906		2144	4157	6301	SO:0001583	missense	6187			AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"""S ribosomal proteins"""	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.380T>A	16.37:g.2012906A>T	ENSP00000341885:p.Phe127Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B2R5G0|D3DU82|Q3MIB1	Missense_Mutation	SNP	ENST00000343262.4	37	CCDS10452.1	.	.	.	.	.	.	.	.	.	.	a	21.9	4.212997	0.79352	.	.	ENSG00000140988	ENST00000533186;ENST00000530225;ENST00000343262;ENST00000529806;ENST00000527302	.	.	.	4.38	4.38	0.52667	Ribosomal protein S5, N-terminal, conserved site (1);Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	U	0.000000	T	0.68906	0.3052	M	0.80746	2.51	0.80722	D	1	B	0.21071	0.051	B	0.24848	0.056	T	0.70691	-0.4802	9	0.62326	D	0.03	.	12.9348	0.58307	1.0:0.0:0.0:0.0	.	127	P15880	RS2_HUMAN	Y	29;127;127;97;127	.	ENSP00000341885:F127Y	F	-	2	0	RPS2	1952907	1.000000	0.71417	0.834000	0.33040	0.600000	0.36913	9.100000	0.94213	1.645000	0.50612	0.524000	0.50904	TTT		0.607	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2		NM_002952	
RREB1	6239	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	7231393	7231393	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr6:7231393T>A	ENST00000349384.6	+	10	3375	c.3061T>A	c.(3061-3063)Tca>Aca	p.S1021T	RREB1_ENST00000334984.6_Missense_Mutation_p.S1021T|RREB1_ENST00000379938.2_Missense_Mutation_p.S1021T|RREB1_ENST00000379933.3_Missense_Mutation_p.S1021T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1021	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S1021T(2)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AATCTACTCCTCAGCCCTGGT	0.687																																																	2	Substitution - Missense(2)	kidney(2)											23.0	27.0	26.0					6																	7231393		2201	4288	6489	SO:0001583	missense	6239			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3061T>A	6.37:g.7231393T>A	ENSP00000305560:p.Ser1021Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.885299	0.51908	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.10477	2.99;2.95;2.99;2.87	5.59	3.16	0.36331	.	0.240037	0.27782	N	0.017873	T	0.02610	0.0079	L	0.57536	1.79	0.24058	N	0.996029	P;P;P	0.41848	0.729;0.682;0.763	B;B;B	0.35770	0.21;0.142;0.153	T	0.37337	-0.9710	10	0.13853	T	0.58	-12.8381	4.7674	0.13139	0.0:0.4532:0.0:0.5468	.	1021;1021;1021	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	T	1021	ENSP00000369265:S1021T;ENSP00000369270:S1021T;ENSP00000305560:S1021T;ENSP00000335574:S1021T	ENSP00000335574:S1021T	S	+	1	0	RREB1	7176392	0.998000	0.40836	0.148000	0.22405	0.932000	0.56968	3.551000	0.53698	0.903000	0.36546	0.533000	0.62120	TCA		0.687	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			
S100A5	6276	hgsc.bcm.edu;ucsc.edu	37	1	153509895	153509895	+	Silent	SNP	G	G	A	rs3795395	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:153509895G>A	ENST00000368718.1	-	4	437	c.156C>T	c.(154-156)atC>atT	p.I52I	S100A6_ENST00000368720.2_5'Flank|S100A6_ENST00000496817.1_5'Flank|S100A5_ENST00000368717.2_Silent_p.I52I|BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000368719.4_5'Flank|S100A5_ENST00000359215.1_Silent_p.I70I	NM_002962.1	NP_002953.2	P33763	S10A5_HUMAN	S100 calcium binding protein A5	52	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					neuronal cell body (GO:0043025)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	4	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCAAGTCATCGATGCTGCTCT	0.572													G|||	47	0.00938498	0.0	0.0	5008	,	,		20524	0.0456		0.0	False		,,,				2504	0.001																0													235.0	195.0	209.0					1																	153509895		2203	4300	6503	SO:0001819	synonymous_variant	6276			Z18954	CCDS1041.1, CCDS1041.2	1q21	2013-01-10	2001-11-28		ENSG00000196420	ENSG00000196420		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10495	protein-coding gene	gene with protein product		176991	"""S100 calcium-binding protein A5"""	S100D		8341667	Standard	NM_002962		Approved		uc001fbx.3	P33763	OTTHUMG00000013547	ENST00000368718.1:c.156C>T	1.37:g.153509895G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q52LE7|Q5RHS3	Silent	SNP	ENST00000368718.1	37	CCDS1041.2																																																																																				0.572	S100A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037719.1		NM_002962	
SCG2	7857	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	224463043	224463043	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr2:224463043C>A	ENST00000305409.2	-	2	1190	c.958G>T	c.(958-960)Gct>Tct	p.A320S		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0	Interaction with FANCD2.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.A320S(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTTCCTGCAGCATTTACTAAC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											132.0	135.0	134.0					2																	224463043		2203	4300	6503	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.958G>T	2.37:g.224463043C>A	ENSP00000304133:p.Ala320Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	C	5.032	0.191501	0.09547	.	.	ENSG00000171951	ENST00000305409;ENST00000450330	T	0.01745	4.66	5.6	4.7	0.59300	.	0.332965	0.31760	N	0.007111	T	0.01189	0.0039	N	0.16478	0.41	0.20563	N	0.999884	B	0.18610	0.029	B	0.14023	0.01	T	0.48559	-0.9025	10	0.09338	T	0.73	.	7.0092	0.24853	0.0:0.698:0.1531:0.1489	.	320	P13521	SCG2_HUMAN	S	320;180	ENSP00000304133:A320S	ENSP00000304133:A320S	A	-	1	0	SCG2	224171287	0.046000	0.20272	0.704000	0.30370	0.937000	0.57800	1.862000	0.39448	1.323000	0.45263	0.650000	0.86243	GCT		0.433	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2		NM_003469	
SLC6A12	6539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	318976	318976	+	Silent	SNP	G	G	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr12:318976G>C	ENST00000428720.1	-	3	920	c.177C>G	c.(175-177)gtC>gtG	p.V59V	SLC6A12_ENST00000424061.2_Silent_p.V59V|SLC6A12_ENST00000359674.4_Silent_p.V59V|SLC6A12_ENST00000397296.2_Silent_p.V59V|SLC6A12_ENST00000536824.1_Silent_p.V59V	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	59					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.V59V(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			GAAACCTCCAGACATTGCCCA	0.562																																																	1	Substitution - coding silent(1)	kidney(1)											201.0	167.0	178.0					12																	318976		2203	4300	6503	SO:0001819	synonymous_variant	6539			L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.177C>G	12.37:g.318976G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																				0.562	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2		NM_003044	
SNW1	22938	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	78217740	78217740	+	Silent	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr14:78217740A>G	ENST00000261531.7	-	3	314	c.252T>C	c.(250-252)aaT>aaC	p.N84N	SNW1_ENST00000554775.1_Intron|SNW1_ENST00000555761.1_Silent_p.N84N|SLIRP_ENST00000557431.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	84					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)	p.N84N(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		TGGCCAGCGCATTCGACATTT	0.423																																																	1	Substitution - coding silent(1)	kidney(1)											114.0	129.0	124.0					14																	78217740		2203	4300	6503	SO:0001819	synonymous_variant	22938			AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"""SKI interacting protein"""	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.252T>C	14.37:g.78217740A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	37	CCDS9867.1																																																																																				0.423	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1		NM_012245	
TBC1D19	55296	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	26741524	26741524	+	Silent	SNP	T	T	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr4:26741524T>C	ENST00000264866.4	+	17	1434	c.1156T>C	c.(1156-1158)Ttg>Ctg	p.L386L	TBC1D19_ENST00000511789.1_Silent_p.L321L	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	386	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.L386L(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				ACCTTCCAAATTGTATCAGAT	0.303																																																	1	Substitution - coding silent(1)	kidney(1)											192.0	181.0	185.0					4																	26741524		2202	4299	6501	SO:0001819	synonymous_variant	55296			AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1156T>C	4.37:g.26741524T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																				0.303	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2		NM_018317	
TSPAN1	10103	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	46646810	46646810	+	Missense_Mutation	SNP	A	A	G	rs184135661		TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr1:46646810A>G	ENST00000372003.1	+	3	495	c.31A>G	c.(31-33)Atg>Gtg	p.M11V	TSPAN1_ENST00000498443.1_3'UTR	NM_005727.3	NP_005718.2	O60635	TSN1_HUMAN	tetraspanin 1	11					cell migration (GO:0016477)|cell proliferation (GO:0008283)|positive regulation of endocytosis (GO:0045807)|protein stabilization (GO:0050821)|thiamine transmembrane transport (GO:0071934)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.M11V(1)		kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)	Medulloblastoma(700;0.00498)|all_neural(321;0.0212)				TAAGACCATGATGATCCTCTT	0.522													A|||	1	0.000199681	0.0	0.0	5008	,	,		21832	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											190.0	150.0	163.0					1																	46646810		2203	4300	6503	SO:0001583	missense	10103			BC013404	CCDS530.1	1p33	2013-02-14			ENSG00000117472	ENSG00000117472		"""Tetraspanins"""	20657	protein-coding gene	gene with protein product		613170				9714763, 10719184	Standard	NM_005727		Approved	TSPAN-1, NET-1	uc001cpd.3	O60635	OTTHUMG00000007602	ENST00000372003.1:c.31A>G	1.37:g.46646810A>G	ENSP00000361072:p.Met11Val	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQ14|O60745|Q5VST0	Missense_Mutation	SNP	ENST00000372003.1	37	CCDS530.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	A	20.4	3.987690	0.74589	.	.	ENSG00000117472	ENST00000372003	T	0.75938	-0.98	4.86	4.86	0.63082	.	.	.	.	.	T	0.81912	0.4923	M	0.73430	2.235	0.54753	D	0.999985	D	0.54047	0.964	P	0.55577	0.779	D	0.83669	0.0165	9	0.52906	T	0.07	.	13.7825	0.63091	1.0:0.0:0.0:0.0	.	11	O60635	TSN1_HUMAN	V	11	ENSP00000361072:M11V	ENSP00000361072:M11V	M	+	1	0	TSPAN1	46419397	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	8.136000	0.89610	2.046000	0.60703	0.379000	0.24179	ATG		0.522	TSPAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020135.1		NM_005727	
UIMC1	51720	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	176332369	176332369	+	Silent	SNP	A	A	G			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:176332369A>G	ENST00000377227.4	-	15	2206	c.2074T>C	c.(2074-2076)Tta>Cta	p.L692L	UIMC1_ENST00000506128.1_Silent_p.L526L|UIMC1_ENST00000511320.1_Silent_p.L692L|UIMC1_ENST00000377219.2_Silent_p.L693L			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	692					double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)	p.L692L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGTCCACTAAGCAATCTGTG	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											96.0	100.0	99.0					5																	176332369		2203	4300	6503	SO:0001819	synonymous_variant	51720			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.2074T>C	5.37:g.176332369A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Silent	SNP	ENST00000377227.4	37	CCDS4408.1																																																																																				0.463	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1		NM_016290	
ZFP3	124961	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	4995604	4995604	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr17:4995604A>C	ENST00000318833.3	+	2	1141	c.805A>C	c.(805-807)Att>Ctt	p.I269L		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I269L(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						TTCACAGCTTATTCAGCATCA	0.393																																																	1	Substitution - Missense(1)	kidney(1)											63.0	61.0	62.0					17																	4995604		2203	4300	6503	SO:0001583	missense	124961			BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"""Zinc fingers, C2H2-type"""	12861	protein-coding gene	gene with protein product		194480	"""zinc finger protein homologous to Zfp-3 in mouse"", ""zinc finger protein 3 homolog (mouse)"""				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.805A>C	17.37:g.4995604A>C	ENSP00000320347:p.Ile269Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A5PLL4	Missense_Mutation	SNP	ENST00000318833.3	37	CCDS11067.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.923969	0.34002	.	.	ENSG00000180787	ENST00000318833	T	0.14766	2.48	3.93	3.93	0.45458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37012	N	0.002288	T	0.22898	0.0553	L	0.56199	1.76	0.24652	N	0.993515	D	0.53462	0.96	P	0.61592	0.891	T	0.05022	-1.0911	10	0.29301	T	0.29	-12.6766	6.1079	0.20084	0.8882:0.0:0.1118:0.0	.	269	Q96NJ6	ZFP3_HUMAN	L	269	ENSP00000320347:I269L	ENSP00000320347:I269L	I	+	1	0	ZFP3	4936328	0.001000	0.12720	1.000000	0.80357	0.998000	0.95712	1.617000	0.36943	2.011000	0.59026	0.460000	0.39030	ATT		0.393	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1		NM_153018	
ZNF611	81856	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	53209367	53209367	+	Missense_Mutation	SNP	C	C	A	rs144132013	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr19:53209367C>A	ENST00000319783.1	-	7	1257	c.941G>T	c.(940-942)cGt>cTt	p.R314L	ZNF611_ENST00000602162.1_Missense_Mutation_p.R245L|ZNF611_ENST00000540744.1_Missense_Mutation_p.R314L|ZNF611_ENST00000543227.1_Missense_Mutation_p.R314L|ZNF611_ENST00000453741.2_Missense_Mutation_p.R245L|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000595798.1_Missense_Mutation_p.R245L	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R314L(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		ACAATTGTAACGTTTTACTCC	0.398																																																	1	Substitution - Missense(1)	kidney(1)											144.0	134.0	137.0					19																	53209367		2203	4300	6503	SO:0001583	missense	81856			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.941G>T	19.37:g.53209367C>A	ENSP00000322427:p.Arg314Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	11.62	1.693321	0.30052	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	1.72	0.591	0.17465	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08403	0.0209	N	0.04686	-0.185	0.23271	N	0.998002	B	0.02656	0.0	B	0.08055	0.003	T	0.32295	-0.9912	9	0.56958	D	0.05	.	8.8864	0.35406	0.0:0.2353:0.7647:0.0	.	314	Q8N823	ZN611_HUMAN	L	314;314;245;314	ENSP00000437616:R314L;ENSP00000439211:R314L;ENSP00000443505:R245L;ENSP00000322427:R314L	ENSP00000322427:R314L	R	-	2	0	ZNF611	57901179	0.004000	0.15560	0.002000	0.10522	0.006000	0.05464	1.133000	0.31430	0.076000	0.16826	-0.686000	0.03744	CGT		0.398	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1		NM_030972	
ZNF622	90441	hgsc.bcm.edu;ucsc.edu	37	5	16465400	16465400	+	Missense_Mutation	SNP	C	C	G	rs113566156	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr5:16465400C>G	ENST00000308683.2	-	1	501	c.375G>C	c.(373-375)aaG>aaC	p.K125N		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	125					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K125N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						TCATGGCATCCTTGTCCACAC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											162.0	148.0	153.0					5																	16465400		2203	4300	6503	SO:0001583	missense	90441			AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.375G>C	5.37:g.16465400C>G	ENSP00000310042:p.Lys125Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000308683.2	37	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676684	0.47886	.	.	ENSG00000173545	ENST00000308683	.	.	.	4.88	4.02	0.46733	.	0.202317	0.51477	D	0.000088	T	0.46600	0.1401	M	0.74881	2.28	0.54753	D	0.999982	P	0.43094	0.799	B	0.38562	0.276	T	0.43442	-0.9391	9	0.30854	T	0.27	-10.0841	5.555	0.17111	0.0:0.6678:0.0:0.3322	.	125	Q969S3	ZN622_HUMAN	N	125	.	ENSP00000310042:K125N	K	-	3	2	ZNF622	16518400	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.743000	0.26231	1.278000	0.44430	0.650000	0.86243	AAG		0.577	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1		NM_033414	
VHL	7428	ucsc.edu	37	3	10188190	10188196	+	Splice_Site	DEL	CCCGATA	CCCGATA	-	rs372340900|rs191201783	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	CCCGATA	CCCGATA	CCCGATA	-	CCCGATA	CCCGATA	Unknown	Valid	Somatic	Phase_I	WXS	PGM	.		Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr3:10188190_10188196delCCCGATA	ENST00000256474.2	+	2	1180		c.e2-1		VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_Splice_Site	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase						cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(9)		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)		CTTTGCTTGTCCCGATAGGTCACCTTT	0.541		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"""	9	Unknown(9)	kidney(9)	GRCh37	CS071275	VHL	S																																				SO:0001630	splice_region_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.341-1CCCGATA>-	3.37:g.10188190_10188196delCCCGATA		Somatic		WXS	Illumina HiSeq	.	B2RE45|Q13599|Q6PDA9	Splice_Site	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.541	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	Intron
SMG1P7	100506060	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	A	C			TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr16:70268158A>C	ENST00000459379.1	-	0	0																											TTCTTCATTAAAACAGCTACT	0.333																																																	0																																												0																															16.37:g.70268158A>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.333	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
NPIPB15	440348	broad.mit.edu	37	16	74411881	74411881	+	Missense_Mutation	SNP	C	C	T	rs199550230	byFrequency	TCGA-BP-5170-01A-01D-1429-08	TCGA-BP-5170-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68761b2c-66b9-4adf-9b60-955f79ed0f11	bd5e01bf-68f5-4812-be2b-ccf301ca6b1b	g.chr16:74411881C>T	ENST00000429990.1	+	1	106	c.10C>T	c.(10-12)Cgc>Tgc	p.R4C				A6NHN6	NPB15_HUMAN	nuclear pore complex interacting protein family, member B15	4						extracellular region (GO:0005576)		p.R4C(2)									CATGCGGCTGCGCTTTTGGCT	0.642																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	0			BC160029		16q22.3	2013-06-11	2013-06-11	2013-06-11	ENSG00000196436	ENSG00000196436			34409	protein-coding gene	gene with protein product			"""nuclear pore complex interacting protein-like 2"""	NPIPL2			Standard	XM_005256273		Approved	LOC440348	uc010vmt.1	A6NHN6	OTTHUMG00000156916	ENST00000429990.1:c.10C>T	16.37:g.74411881C>T	ENSP00000411140:p.Arg4Cys	Somatic		WXS	Illumina GAIIx	Phase_I	C9J9U8	Missense_Mutation	SNP	ENST00000429990.1	37		.	.	.	.	.	.	.	.	.	.	c	5.238	0.229376	0.09916	.	.	ENSG00000196436	ENST00000429990	T	0.53640	0.61	.	.	.	.	.	.	.	.	T	0.26340	0.0643	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.24977	-1.0145	5	0.87932	D	0	.	.	.	.	.	4	A6NHN6	NPPL2_HUMAN	C	4	ENSP00000411140:R4C	ENSP00000411140:R4C	R	+	1	0	NPIPL2	72969382	0.110000	0.22057	0.111000	0.21465	0.111000	0.19643	0.055000	0.14229	0.064000	0.16427	0.064000	0.15345	CGC		0.642	NPIPB15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346597.2		NM_001018059	
