#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
A2M	2	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	9248168	9248168	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr12:9248168A>T	ENST00000318602.7	-	16	2287	c.1980T>A	c.(1978-1980)agT>agA	p.S660R		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	660					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.S660R(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TTTCATTTGTACTTGATACTG	0.378																																																	1	Substitution - Missense(1)	kidney(1)											129.0	128.0	128.0					12																	9248168		1872	4105	5977	SO:0001583	missense	2			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1980T>A	12.37:g.9248168A>T	ENSP00000323929:p.Ser660Arg		Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	A	9.148	1.015572	0.19355	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.29655	1.56	5.65	-1.21	0.09524	.	0.498207	0.21393	N	0.075274	T	0.14787	0.0357	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.17228	-1.0376	10	0.15066	T	0.55	.	2.2815	0.04115	0.4108:0.1245:0.3424:0.1223	.	660	P01023	A2MG_HUMAN	R	660;675	ENSP00000323929:S660R	ENSP00000323929:S660R	S	-	3	2	A2M	9139435	0.000000	0.05858	0.009000	0.14445	0.008000	0.06430	0.011000	0.13264	-0.056000	0.13221	0.528000	0.53228	AGT		0.378	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2		NM_000014	
ACO1	48	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	32408576	32408576	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr9:32408576C>A	ENST00000309951.6	+	4	469	c.331C>A	c.(331-333)Cca>Aca	p.P111T	ACO1_ENST00000379923.1_Missense_Mutation_p.P111T|ACO1_ENST00000541043.1_Missense_Mutation_p.P12T	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	111					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.P111T(2)		breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		AGGAGGAGATCCAGAGAAAAT	0.428																																																	2	Substitution - Missense(2)	kidney(2)											167.0	159.0	162.0					9																	32408576		2203	4300	6503	SO:0001583	missense	48			M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.331C>A	9.37:g.32408576C>A	ENSP00000309477:p.Pro111Thr		D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	37	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072872	0.93950	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000379921;ENST00000541043	T;T;T	0.20200	2.09;2.09;2.09	5.75	5.75	0.90469	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.096427	0.64402	D	0.000001	T	0.52901	0.1763	M	0.86953	2.85	0.80722	D	1	D	0.63880	0.993	D	0.70487	0.969	T	0.52801	-0.8527	10	0.38643	T	0.18	-14.7119	18.7222	0.91700	0.0:1.0:0.0:0.0	.	111	P21399	ACOC_HUMAN	T	147;111;111;111;12	ENSP00000309477:P111T;ENSP00000369255:P111T;ENSP00000438733:P12T	ENSP00000309477:P111T	P	+	1	0	ACO1	32398576	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.772000	0.85439	2.705000	0.92388	0.655000	0.94253	CCA		0.428	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3		NM_002197	
AHNAK2	113146	broad.mit.edu;hgsc.bcm.edu	37	14	105414746	105414746	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr14:105414746C>T	ENST00000333244.5	-	7	7161	c.7042G>A	c.(7042-7044)Gtg>Atg	p.V2348M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2348						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.V2348M(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCGGCCTCCACCTTCAACGCA	0.602																																																	1	Substitution - Missense(1)	kidney(1)											150.0	167.0	161.0					14																	105414746		2057	4195	6252	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7042G>A	14.37:g.105414746C>T	ENSP00000353114:p.Val2348Met		Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	11.32	1.604947	0.28623	.	.	ENSG00000185567	ENST00000333244	T	0.00995	5.46	3.12	1.13	0.20643	.	.	.	.	.	T	0.02119	0.0066	L	0.55743	1.74	0.09310	N	1	P	0.44946	0.846	P	0.55455	0.776	T	0.47623	-0.9103	9	0.33141	T	0.24	.	4.2239	0.10572	0.0:0.5808:0.1922:0.227	.	2348	Q8IVF2	AHNK2_HUMAN	M	2348	ENSP00000353114:V2348M	ENSP00000353114:V2348M	V	-	1	0	AHNAK2	104485791	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.557000	0.02166	0.038000	0.15604	0.485000	0.47835	GTG		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
AMPD3	272	hgsc.bcm.edu	37	11	10500152	10500153	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:10500152_10500153insC	ENST00000396554.3	+	3	669_670	c.328_329insC	c.(328-330)gcafs	p.A110fs	AMPD3_ENST00000444303.2_Intron	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	101					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GGGCCCCCCGGCAGCCAGTCCG	0.589																																																	0																																										SO:0001589	frameshift_variant	272			M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.329dupC	11.37:g.10500153_10500153dupC	ENSP00000379802:p.Ala110fs		A0AUX0|B7Z2S2|B7Z763|B7Z877	Frame_Shift_Ins	INS	ENST00000396554.3	37	CCDS7802.1																																																																																				0.589	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2		NM_000480	
AP2B1	163	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	33932800	33932800	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:33932800A>T	ENST00000262325.7	+	4	773	c.220A>T	c.(220-222)Atg>Ttg	p.M74L	AP2B1_ENST00000592545.1_Missense_Mutation_p.M74L|AP2B1_ENST00000538556.1_Missense_Mutation_p.M17L|AP2B1_ENST00000589344.1_Missense_Mutation_p.M74L|AP2B1_ENST00000537622.2_Missense_Mutation_p.M74L|AP2B1_ENST00000312678.8_Missense_Mutation_p.M74L	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	74					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)	p.M74L(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TCTCTACTTGATGAACTACGC	0.428																																																	1	Substitution - Missense(1)	kidney(1)											121.0	112.0	115.0					17																	33932800		2203	4300	6503	SO:0001583	missense	163			M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.220A>T	17.37:g.33932800A>T	ENSP00000262325:p.Met74Leu		A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	37	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956732	0.73902	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.23410	0.0566	L	0.32530	0.975	0.80722	D	1	B;B;B	0.27656	0.115;0.184;0.096	B;B;B	0.28991	0.086;0.097;0.037	T	0.03453	-1.1035	10	0.54805	T	0.06	-6.9412	14.8732	0.70474	1.0:0.0:0.0:0.0	.	74;74;74	B4DWG4;P63010;P63010-2	.;AP2B1_HUMAN;.	L	74;74;17;74	ENSP00000262325:M74L;ENSP00000314414:M74L;ENSP00000440563:M17L;ENSP00000437413:M74L	ENSP00000262325:M74L	M	+	1	0	AP2B1	30956913	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.339000	0.96797	2.104000	0.64026	0.383000	0.25322	ATG		0.428	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			
ARRDC5	645432	broad.mit.edu;hgsc.bcm.edu	37	19	4891119	4891119	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr19:4891119G>A	ENST00000381781.2	-	3	967	c.968C>T	c.(967-969)tCt>tTt	p.S323F	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	323								p.S323F(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		GCAGATGGCAGAGTCCACTGA	0.527																																																	1	Substitution - Missense(1)	kidney(1)											95.0	99.0	98.0					19																	4891119		2129	4238	6367	SO:0001583	missense	645432				CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.968C>T	19.37:g.4891119G>A	ENSP00000371200:p.Ser323Phe			Missense_Mutation	SNP	ENST00000381781.2	37	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.472876	0.26423	.	.	ENSG00000205784	ENST00000381781	T	0.22134	1.97	3.67	1.34	0.21922	Immunoglobulin E-set (1);	.	.	.	.	T	0.11836	0.0288	N	0.19112	0.55	0.09310	N	1	P	0.41041	0.736	B	0.35550	0.205	T	0.14896	-1.0456	9	0.59425	D	0.04	0.0578	8.0763	0.30718	0.0:0.0:0.5409:0.4591	.	323	A6NEK1	ARRD5_HUMAN	F	323	ENSP00000371200:S323F	ENSP00000371200:S323F	S	-	2	0	ARRDC5	4842119	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.734000	0.26101	0.458000	0.26988	0.650000	0.86243	TCT		0.527	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1		XM_292803	
BTNL3	10917	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	180420008	180420008	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:180420008G>A	ENST00000342868.6	+	2	429	c.245G>A	c.(244-246)cGa>cAa	p.R82Q		NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	82						integral component of membrane (GO:0016021)		p.R82Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			CCACAGTATCGAGGGAGAACT	0.527																																																	1	Substitution - Missense(1)	kidney(1)											71.0	68.0	69.0					5																	180420008		2074	3880	5954	SO:0001583	missense	10917			AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.245G>A	5.37:g.180420008G>A	ENSP00000341787:p.Arg82Gln		Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	37	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	G	0.041	-1.285247	0.01398	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.64618	-0.11	2.96	-5.92	0.02261	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36552	0.0971	N	0.11892	0.195	0.09310	N	1	B	0.20671	0.047	B	0.09377	0.004	T	0.23368	-1.0190	9	0.19590	T	0.45	.	11.3884	0.49800	0.3797:0.0:0.6203:0.0	.	82	Q6UXE8	BTNL3_HUMAN	Q	82	ENSP00000341787:R82Q	ENSP00000341787:R82Q	R	+	2	0	BTNL3	180352614	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.672000	0.01952	-1.499000	0.01821	-0.357000	0.07601	CGA		0.527	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2		NM_197975	
CADM3	57863	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	159161760	159161760	+	Silent	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:159161760G>A	ENST00000368125.4	+	2	280	c.123G>A	c.(121-123)gtG>gtA	p.V41V	CADM3_ENST00000368124.4_Silent_p.V75V	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	41	Ig-like V-type.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.V75V(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					AAACAGTGGTGGCTGGTGGCA	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											78.0	67.0	71.0					1																	159161760		2203	4300	6503	SO:0001819	synonymous_variant	57863			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17601	protein-coding gene	gene with protein product	"""nectin-like 1"""	609743	"""immunoglobulin superfamily, member 4B"""	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.123G>A	1.37:g.159161760G>A			Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																				0.542	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1		NM_021189	
CCDC112	153733	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	114620509	114620509	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs187304678		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:114620509G>A	ENST00000512261.1	-	0	252				CCDC112_ENST00000379611.5_Missense_Mutation_p.R72C|CCDC112_ENST00000506442.1_De_novo_Start_OutOfFrame|CCDC112_ENST00000395557.4_De_novo_Start_OutOfFrame|CCDC112_ENST00000503027.1_Intron			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112									p.R72C(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		TCTGCTGTGCGTACAAATTCT	0.313													G|||	1	0.000199681	0.0	0.0	5008	,	,		16473	0.0		0.001	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											60.0	58.0	59.0					5																	114620509		2202	4300	6502			153733			BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.-165C>T	5.37:g.114620509G>A			Q6A334	Missense_Mutation	SNP	ENST00000512261.1	37	CCDS4117.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.1	3.938636	0.73557	.	.	ENSG00000164221	ENST00000379611	T	0.27890	1.64	5.57	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.53769	0.1817	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.56823	-0.7915	9	0.87932	D	0	-0.6437	14.1589	0.65434	0.0:0.0:0.783:0.217	.	72	Q8NEF3-2	.	C	72	ENSP00000368931:R72C	ENSP00000368931:R72C	R	-	1	0	CCDC112	114648408	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	2.760000	0.47581	2.785000	0.95823	0.655000	0.94253	CGC		0.313	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370999.1		NM_152549	
CCDC88A	55704	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	55570817	55570817	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr2:55570817C>G	ENST00000436346.1	-	12	2141	c.1300G>C	c.(1300-1302)Gaa>Caa	p.E434Q	AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000336838.6_Missense_Mutation_p.E434Q|CCDC88A_ENST00000413716.2_Missense_Mutation_p.E434Q|CCDC88A_ENST00000263630.8_Missense_Mutation_p.E434Q	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	434					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.E434Q(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						GATATCTGTTCCAGTTCCCAG	0.318																																																	2	Substitution - Missense(2)	kidney(2)											128.0	123.0	125.0					2																	55570817		2203	4300	6503	SO:0001583	missense	55704			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1300G>C	2.37:g.55570817C>G	ENSP00000410608:p.Glu434Gln		A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	C	33	5.206299	0.95033	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.91	5.91	0.95273	.	0.000000	0.48767	U	0.000169	T	0.43986	0.1272	M	0.66297	2.02	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.994;0.992	T	0.11155	-1.0599	10	0.56958	D	0.05	-20.6428	20.3011	0.98612	0.0:1.0:0.0:0.0	.	434;434;434	B7ZM78;Q3V6T2-2;Q3V6T2-3	.;.;.	Q	434	ENSP00000338728:E434Q;ENSP00000263630:E434Q;ENSP00000410608:E434Q;ENSP00000404431:E434Q	ENSP00000263630:E434Q	E	-	1	0	CCDC88A	55424321	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.412000	0.80091	2.804000	0.96469	0.650000	0.86243	GAA		0.318	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding			NM_017571	
CDH4	1002	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	60499473	60499473	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr20:60499473C>A	ENST00000360469.5	+	11	1798	c.1710C>A	c.(1708-1710)gaC>gaA	p.D570E	CDH4_ENST00000543233.1_Missense_Mutation_p.D496E	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	570	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D570E(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CAGTGCTGGACCGTGAGTCCC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											125.0	96.0	106.0					20																	60499473		2203	4300	6503	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1710C>A	20.37:g.60499473C>A	ENSP00000353656:p.Asp570Glu		B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.505462	0.44558	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.63255	-0.03;-0.03	4.44	2.18	0.27775	Cadherin (4);Cadherin-like (1);	0.046782	0.85682	N	0.000000	D	0.83119	0.5185	H	0.98507	4.25	0.58432	D	0.999997	D	0.63880	0.993	D	0.76575	0.988	T	0.80897	-0.1177	9	.	.	.	.	4.2181	0.10544	0.0:0.4087:0.0:0.5913	.	570	P55283	CADH4_HUMAN	E	570;478;496	ENSP00000353656:D570E;ENSP00000443301:D496E	.	D	+	3	2	CDH4	59932868	1.000000	0.71417	0.970000	0.41538	0.103000	0.19146	1.103000	0.31062	0.866000	0.35629	-0.258000	0.10820	GAC		0.617	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2		NM_001794	
CENPF	1063	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	214825173	214825173	+	Missense_Mutation	SNP	C	C	T	rs376987914		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:214825173C>T	ENST00000366955.3	+	15	8272	c.8104C>T	c.(8104-8106)Cgg>Tgg	p.R2702W	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2798	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.R2702W(2)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		ATATCAGCTACGGCTTCATGA	0.433																																					Colon(80;575 1284 11000 14801 43496)												2	Substitution - Missense(2)	lung(1)|kidney(1)						C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	102.0	105.0	104.0		8104	2.8	0.0	1		104	0,8600		0,0,4300	no	missense	CENPF	NM_016343.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2702/3115	214825173	1,13005	2203	4300	6503	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8104C>T	1.37:g.214825173C>T	ENSP00000355922:p.Arg2702Trp		Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036601	0.35893	2.27E-4	0.0	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.03496	3.91	3.91	2.8	0.32819	.	.	.	.	.	T	0.07593	0.0191	L	0.56769	1.78	0.09310	N	1	D	0.76494	0.999	P	0.50082	0.63	T	0.22661	-1.0210	9	0.59425	D	0.04	.	8.0726	0.30697	0.4234:0.5766:0.0:0.0	.	2798	P49454	CENPF_HUMAN	W	2702;101	ENSP00000355922:R2702W	ENSP00000355922:R2702W	R	+	1	2	CENPF	212891796	0.008000	0.16893	0.006000	0.13384	0.806000	0.45545	0.574000	0.23714	1.892000	0.54788	0.609000	0.83330	CGG		0.433	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1		NM_016343	
CLCN4	1183	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	10176319	10176319	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chrX:10176319C>T	ENST00000380833.4	+	9	1469	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	CLCN4_ENST00000421085.2_Missense_Mutation_p.R266C|CLCN4_ENST00000380829.1_Missense_Mutation_p.R329C	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	360					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R360C(2)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GTGCAGGAGGCGCAAGACCAC	0.597																																					Melanoma(74;1050 1296 1576 30544 38374)												2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											107.0	102.0	104.0					X																	10176319		2203	4300	6503	SO:0001583	missense	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1078C>T	X.37:g.10176319C>T	ENSP00000370213:p.Arg360Cys		A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	c	21.6	4.168308	0.78339	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.94828	-3.48;-3.53;-3.48	5.71	5.71	0.89125	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.98704	0.9565	H	0.99238	4.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99628	1.0985	10	0.87932	D	0	-28.1314	18.999	0.92826	0.0:1.0:0.0:0.0	.	360	P51793	CLCN4_HUMAN	C	360;329;266	ENSP00000370213:R360C;ENSP00000370209:R329C;ENSP00000405754:R266C	ENSP00000370209:R329C	R	+	1	0	CLCN4	10136319	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.188000	0.50958	2.436000	0.82500	0.592000	0.82586	CGC		0.597	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			
CFP	5199	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	47485783	47485783	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chrX:47485783C>T	ENST00000396992.3	-	7	1196	c.1076G>A	c.(1075-1077)cGa>cAa	p.R359Q	CFP_ENST00000247153.3_Missense_Mutation_p.R359Q|CFP_ENST00000480317.1_5'Flank|CFP_ENST00000377005.2_Missense_Mutation_p.R359Q	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	359	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R359Q(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						CCCGGCACATCGATGTCCGTC	0.612																																																	1	Substitution - Missense(1)	kidney(1)											64.0	55.0	58.0					X																	47485783		2203	4300	6503	SO:0001583	missense	5199			M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"""Complement system"""	8864	protein-coding gene	gene with protein product		300383	"""properdin P factor, complement"""	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.1076G>A	X.37:g.47485783C>T	ENSP00000380189:p.Arg359Gln		O15134|O15135|O15136|O75826	Missense_Mutation	SNP	ENST00000396992.3	37	CCDS14282.1	.	.	.	.	.	.	.	.	.	.	C	9.859	1.195811	0.22037	.	.	ENSG00000126759	ENST00000396992;ENST00000247153;ENST00000377005	T;T;T	0.50277	0.75;0.75;0.75	5.28	3.41	0.39046	.	0.504643	0.20634	N	0.088532	T	0.50188	0.1601	L	0.50847	1.595	0.09310	N	1	D;P	0.53885	0.963;0.552	P;B	0.54544	0.755;0.41	T	0.40021	-0.9585	10	0.12766	T	0.61	.	11.1291	0.48336	0.0:0.6366:0.3634:0.0	.	295;359	B3KVK6;P27918	.;PROP_HUMAN	Q	359	ENSP00000380189:R359Q;ENSP00000247153:R359Q;ENSP00000366204:R359Q	ENSP00000247153:R359Q	R	-	2	0	CFP	47370727	0.027000	0.19231	0.005000	0.12908	0.057000	0.15508	0.540000	0.23191	0.477000	0.27464	0.468000	0.43344	CGA		0.612	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2		NM_002621	
CNOT1	23019	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	58572759	58572763	+	Frame_Shift_Del	DEL	GTAGC	GTAGC	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	GTAGC	GTAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr16:58572759_58572763delGTAGC	ENST00000317147.5	-	36	5380_5384	c.5048_5052delGCTAC	c.(5047-5052)cgctacfs	p.RY1683fs	CNOT1_ENST00000569240.1_Frame_Shift_Del_p.RY1678fs|CNOT1_ENST00000245138.4_Frame_Shift_Del_p.RY534fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1683					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGCATTCCCTGTAGCGCAGCAGAAG	0.502																																																	0																																										SO:0001589	frameshift_variant	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.5048_5052delGCTAC	16.37:g.58572759_58572763delGTAGC	ENSP00000320949:p.Arg1683fs		Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	37	CCDS10799.1																																																																																				0.502	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3		NM_016284	
CRYZ	1429	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	75172631	75172631	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:75172631C>T	ENST00000340866.5	-	8	867	c.780G>A	c.(778-780)atG>atA	p.M260I	CRYZ_ENST00000370872.3_Missense_Mutation_p.M123I|CRYZ_ENST00000417775.1_Missense_Mutation_p.M260I|CRYZ_ENST00000492102.1_5'UTR|CRYZ_ENST00000370871.3_Missense_Mutation_p.M226I	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	260					protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)	p.M260I(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	ACTCCTTTGCCATGGTGTCTC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											168.0	169.0	169.0					1																	75172631		2203	4300	6503	SO:0001583	missense	1429				CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.780G>A	1.37:g.75172631C>T	ENSP00000339399:p.Met260Ile		A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.014841	0.35511	.	.	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871	T;T;T;T	0.26810	3.83;3.83;3.83;1.71	4.76	1.74	0.24563	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.124511	0.64402	N	0.000001	T	0.16085	0.0387	L	0.58428	1.81	0.58432	D	0.999994	B;B;B	0.29253	0.239;0.064;0.042	B;B;B	0.42995	0.404;0.119;0.078	T	0.05599	-1.0875	10	0.37606	T	0.19	-9.9975	6.5972	0.22681	0.1347:0.6623:0.1299:0.0731	.	123;226;260	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	I	260;123;260;226	ENSP00000339399:M260I;ENSP00000359909:M123I;ENSP00000399805:M260I;ENSP00000359908:M226I	ENSP00000339399:M260I	M	-	3	0	CRYZ	74945219	0.995000	0.38212	0.316000	0.25252	0.366000	0.29705	3.299000	0.51826	0.254000	0.21573	0.591000	0.81541	ATG		0.363	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1			
DHRS13	147015	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	27228249	27228249	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:27228249delA	ENST00000378895.4	-	4	567	c.441delT	c.(439-441)tttfs	p.F147fs	RP11-20B24.4_ENST00000580603.1_RNA|DHRS13_ENST00000581974.1_5'Flank|RP11-20B24.4_ENST00000579187.1_RNA|DHRS13_ENST00000394901.3_Frame_Shift_Del_p.F97fs|DHRS13_ENST00000426464.2_Frame_Shift_Del_p.F66fs	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	147						extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	9	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			GTGTCAGCAGAAAGGGACCGA	0.602																																																	0													90.0	88.0	89.0					17																	27228249		2203	4300	6503	SO:0001589	frameshift_variant	147015			BC015582	CCDS11246.2	17q11.2	2011-09-14			ENSG00000167536	ENSG00000167536	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	28326	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 5"""					12975309, 19027726	Standard	NM_144683		Approved	MGC23280, SDR7C5	uc002hde.4	Q6UX07	OTTHUMG00000132678	ENST00000378895.4:c.441delT	17.37:g.27228249delA	ENSP00000368173:p.Phe147fs		Q96BH7	Frame_Shift_Del	DEL	ENST00000378895.4	37	CCDS11246.2																																																																																				0.602	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1		NM_144683	
DHX37	57647	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	125462030	125462030	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr12:125462030G>A	ENST00000308736.2	-	5	843	c.745C>T	c.(745-747)Cgg>Tgg	p.R249W	DHX37_ENST00000544745.1_Missense_Mutation_p.R36W	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	249							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.R249W(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		AGCTTCAGCCGTTCCTCCTGG	0.562																																																	1	Substitution - Missense(1)	kidney(1)											53.0	46.0	49.0					12																	125462030		2203	4300	6503	SO:0001583	missense	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.745C>T	12.37:g.125462030G>A	ENSP00000311135:p.Arg249Trp		Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.286896	0.40494	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.15487	2.42;2.42	5.06	4.16	0.48862	.	0.055152	0.64402	D	0.000001	T	0.29620	0.0739	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.02829	-1.1105	10	0.87932	D	0	-19.5566	11.9651	0.53029	0.0:0.0:0.5269:0.4731	.	249	Q8IY37	DHX37_HUMAN	W	249;36	ENSP00000311135:R249W;ENSP00000439009:R36W	ENSP00000311135:R249W	R	-	1	2	DHX37	124027983	1.000000	0.71417	0.962000	0.40283	0.030000	0.12068	4.505000	0.60421	1.123000	0.41961	0.591000	0.81541	CGG		0.562	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_032656	
ECM2	1842	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	95272275	95272275	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr9:95272275A>C	ENST00000344604.5	-	6	1361	c.1212T>G	c.(1210-1212)aaT>aaG	p.N404K	ECM2_ENST00000444490.2_Missense_Mutation_p.N382K|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	404					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.N404K(1)|p.N382K(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						TCTGTATCAAATTATTTCCAT	0.323																																																	2	Substitution - Missense(2)	kidney(2)											84.0	83.0	83.0					9																	95272275		2201	4298	6499	SO:0001583	missense	1842			AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.1212T>G	9.37:g.95272275A>C	ENSP00000344758:p.Asn404Lys		B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	A	4.127	0.021765	0.08006	.	.	ENSG00000106823	ENST00000444490;ENST00000344604	T;T	0.56776	0.44;0.44	4.48	-2.69	0.06022	.	0.765588	0.12578	N	0.456641	T	0.24547	0.0595	N	0.19112	0.55	0.25411	N	0.988357	B;B;B	0.13594	0.001;0.008;0.001	B;B;B	0.14023	0.002;0.01;0.007	T	0.19353	-1.0308	10	0.12430	T	0.62	.	0.0243	0.00004	0.2773:0.2197:0.2153:0.2877	.	404;382;382	O94769;B4DK93;O94769-2	ECM2_HUMAN;.;.	K	382;404	ENSP00000393971:N382K;ENSP00000344758:N404K	ENSP00000344758:N404K	N	-	3	2	ECM2	94312096	0.994000	0.37717	0.097000	0.21041	0.918000	0.54935	0.505000	0.22642	-0.585000	0.05905	0.460000	0.39030	AAT		0.323	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1		NM_001393	
ERCC6	2074	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	50690813	50690813	+	Silent	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr10:50690813A>G	ENST00000355832.5	-	10	2167	c.2089T>C	c.(2089-2091)Tta>Cta	p.L697L	ERCC6_ENST00000542458.1_Silent_p.L67L	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	697					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.L697L(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AACGTGCCTAACTTTCCCGGG	0.483								Direct reversal of damage;Nucleotide excision repair (NER)																																									1	Substitution - coding silent(1)	kidney(1)											106.0	97.0	100.0					10																	50690813		2203	4300	6503	SO:0001819	synonymous_variant	2074			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2089T>C	10.37:g.50690813A>G			D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																				0.483	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1		NM_000124	
FAM171B	165215	hgsc.bcm.edu	37	2	187559050	187559050	+	Silent	SNP	A	A	G	rs2370705	byFrequency	TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr2:187559050A>G	ENST00000304698.5	+	1	353	c.150A>G	c.(148-150)caA>caG	p.Q50Q	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	50	Gln-rich.					integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						agcagcagcaacaacaacaac	0.637																																																	0													25.0	27.0	27.0					2																	187559050		2202	4300	6502	SO:0001819	synonymous_variant	165215			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.150A>G	2.37:g.187559050A>G			Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																				0.637	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1		NM_177454	
FANCE	2178	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	35426171	35426171	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr6:35426171G>A	ENST00000229769.2	+	5	1252	c.1067G>A	c.(1066-1068)aGc>aAc	p.S356N		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	356	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S356N(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						CCTGATCTCAGCCTCAGCAAT	0.577			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																														yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	1	Substitution - Missense(1)	kidney(1)											177.0	167.0	171.0					6																	35426171		2203	4300	6503	SO:0001583	missense	2178	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1067G>A	6.37:g.35426171G>A	ENSP00000229769:p.Ser356Asn		A8K907|Q4ZGH2	Missense_Mutation	SNP	ENST00000229769.2	37	CCDS4805.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263112	0.80358	.	.	ENSG00000112039	ENST00000229769	T	0.57436	0.4	5.41	5.41	0.78517	Fanconi Anaemia group E protein, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66499	0.2795	M	0.76328	2.33	0.44485	D	0.997426	D	0.76494	0.999	D	0.79108	0.992	T	0.70687	-0.4803	10	0.87932	D	0	-14.2081	14.7023	0.69164	0.0:0.0:1.0:0.0	.	356	Q9HB96	FANCE_HUMAN	N	356	ENSP00000229769:S356N	ENSP00000229769:S356N	S	+	2	0	FANCE	35534149	1.000000	0.71417	0.392000	0.26245	0.977000	0.68977	5.664000	0.68045	2.537000	0.85549	0.561000	0.74099	AGC		0.577	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1			
FLJ33360	401172	broad.mit.edu	37	5	6312623	6312623	+	lincRNA	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:6312623A>G	ENST00000507444.1	-	0	349					NR_028351.1																						GAGAGCAGGCAGAGGAACCCC	0.577																																																	0													80.0	82.0	82.0					5																	6312623		1981	4166	6147			401172																															5.37:g.6312623A>G				Missense_Mutation	SNP	ENST00000507444.1	37																																																																																					0.577	CTD-2324F15.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000365707.1			
GCNT1	2650	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	79117316	79117316	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr9:79117316C>T	ENST00000376730.4	+	4	502	c.19C>T	c.(19-21)Cga>Tga	p.R7*	GCNT1_ENST00000488136.1_3'UTR|GCNT1_ENST00000442371.1_Nonsense_Mutation_p.R7*|GCNT1_ENST00000536223.1_Nonsense_Mutation_p.R7*|GCNT1_ENST00000444201.2_Nonsense_Mutation_p.R7*	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	7	Mediates interaction with GOLPH3 and is necessary and sufficent for localization to the Golgi.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)	p.R7*(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						GACGTTGCTGCGAAGGAGACT	0.418																																																	1	Substitution - Nonsense(1)	kidney(1)											92.0	93.0	92.0					9																	79117316		2203	4300	6503	SO:0001587	stop_gained	2650			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.19C>T	9.37:g.79117316C>T	ENSP00000365920:p.Arg7*		Q6DJZ4	Nonsense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	c	11.19	1.565901	0.27915	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	.	.	.	5.21	-0.443	0.12249	.	0.581648	0.16726	N	0.202059	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	4.5779	0.12243	0.5049:0.3155:0.0:0.1796	.	.	.	.	X	7	.	ENSP00000365920:R7X	R	+	1	2	GCNT1	78307136	0.162000	0.22906	0.037000	0.18230	0.066000	0.16364	-0.002000	0.12924	0.051000	0.15978	-0.145000	0.13849	CGA		0.418	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1		NM_001097634	
GNAS	2778	broad.mit.edu	37	20	57428891	57428891	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr20:57428891G>C	ENST00000371100.4	+	1	1123	c.571G>C	c.(571-573)Gct>Cct	p.A191P	GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371099.2_Missense_Mutation_p.A191P|GNAS-AS1_ENST00000424094.2_RNA|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371102.4_Missense_Mutation_p.A191P|GNAS_ENST00000371075.3_Intron|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000306120.3_Silent_p.V127V	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.A191P(1)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			AGGCCCAGGTGCTGCAGGGGT	0.622			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)			Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	1	Substitution - Missense(1)	kidney(1)											13.0	15.0	15.0					20																	57428891		1893	4111	6004	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.571G>C	20.37:g.57428891G>C	ENSP00000360141:p.Ala191Pro		A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	37	CCDS46622.1	.	.	.	.	.	.	.	.	.	.	G	6.537	0.467275	0.12402	.	.	ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102	D;D	0.92099	-2.97;-2.96	0.235	0.235	0.15431	.	9.526550	0.00397	N	0.000040	D	0.89441	0.6716	N	0.22421	0.69	0.09310	N	1	P	0.48350	0.909	P	0.51297	0.665	T	0.80324	-0.1430	9	0.26408	T	0.33	.	.	.	.	.	191	Q5JWF2	GNAS1_HUMAN	P	191	ENSP00000360141:A191P;ENSP00000360143:A191P	ENSP00000360140:A191P	A	+	1	0	GNAS	56862286	0.000000	0.05858	0.005000	0.12908	0.856000	0.48823	0.039000	0.13884	0.308000	0.22923	0.313000	0.20887	GCT		0.622	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3		NM_000516	
GOSR1	9527	broad.mit.edu;hgsc.bcm.edu	37	17	28846964	28846964	+	Missense_Mutation	SNP	A	A	G	rs540823264		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:28846964A>G	ENST00000225724.5	+	8	625	c.553A>G	c.(553-555)Atg>Gtg	p.M185V	GOSR1_ENST00000451249.2_Missense_Mutation_p.M183V|GOSR1_ENST00000581721.1_Missense_Mutation_p.M171V|GOSR1_ENST00000467337.2_Missense_Mutation_p.M120V	NM_001007024.1|NM_001007025.1|NM_004871.2	NP_001007025.1|NP_001007026.1|NP_004862.1	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1	185					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.M185V(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	12						CAGCATTGCTATGGCAACAAA	0.383													A|||	1	0.000199681	0.0	0.0	5008	,	,		19519	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											154.0	156.0	156.0					17																	28846964		2203	4300	6503	SO:0001583	missense	9527			AF047438	CCDS11258.1, CCDS45643.1, CCDS45644.1	17q11	2011-04-15			ENSG00000108587	ENSG00000108587			4430	protein-coding gene	gene with protein product	"""golgi integral membrane protein 2"""	604026				8638159, 9653160, 15004235	Standard	XM_005258072		Approved	GOS28, P28, GS28, GOS-28, GOLIM2	uc002hfe.3	O95249	OTTHUMG00000132796	ENST00000225724.5:c.553A>G	17.37:g.28846964A>G	ENSP00000225724:p.Met185Val		J3KST5|O75392	Missense_Mutation	SNP	ENST00000225724.5	37	CCDS11258.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.170579	0.78452	.	.	ENSG00000108587	ENST00000225724;ENST00000451249;ENST00000414833	T;T	0.75260	-0.92;-0.92	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.79021	0.4376	M	0.78637	2.42	0.80722	D	1	P;P	0.37636	0.603;0.603	P;P	0.44673	0.457;0.457	T	0.75542	-0.3281	10	0.15952	T	0.53	-16.1039	15.8218	0.78654	1.0:0.0:0.0:0.0	.	185;183	O95249;E9PCW1	GOSR1_HUMAN;.	V	185;183;120	ENSP00000225724:M185V;ENSP00000414441:M183V	ENSP00000225724:M185V	M	+	1	0	GOSR1	25871090	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.535000	0.90623	2.326000	0.78906	0.533000	0.62120	ATG		0.383	GOSR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256208.2			
GPR180	160897	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	95271760	95271762	+	In_Frame_Del	DEL	GTT	GTT	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr13:95271760_95271762delGTT	ENST00000376958.4	+	5	750_752	c.725_727delGTT	c.(724-729)agtttg>atg	p.242_243SL>M		NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180	242					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					TTTATGGGAAGTTTGGCAGAATG	0.305																																																	0																																										SO:0001651	inframe_deletion	160897			AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"""intimal thickness related receptor"""	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.725_727delGTT	13.37:g.95271760_95271762delGTT	ENSP00000366157:p.Ser242_Leu243delinsMet		A8K1D5	In_Frame_Del	DEL	ENST00000376958.4	37	CCDS9472.1																																																																																				0.305	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3		NM_180989	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				SO:0001652	inframe_insertion	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered		Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				0.629	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1		NM_014696	
GRM1	2911	hgsc.bcm.edu;ucsc.edu	37	6	146351323	146351324	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr6:146351323_146351324insA	ENST00000282753.1	+	1	905_906	c.670_671insA	c.(670-672)tggfs	p.W224fs	GRM1_ENST00000355289.4_Frame_Shift_Ins_p.W224fs|GRM1_ENST00000507907.1_Frame_Shift_Ins_p.W224fs|GRM1_ENST00000392299.2_Frame_Shift_Ins_p.W224fs|GRM1_ENST00000361719.2_Frame_Shift_Ins_p.W224fs|GRM1_ENST00000492807.2_Frame_Shift_Ins_p.W224fs			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	224					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		ACGTTACAATTGGACCTATGTC	0.465																																																	0																																										SO:0001589	frameshift_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	Exception_encountered	6.37:g.146351323_146351324insA	ENSP00000282753:p.Trp224fs		B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Frame_Shift_Del	INS	ENST00000282753.1	37	CCDS5209.1																																																																																				0.465	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1		NM_000838	
HPN	3249	broad.mit.edu;ucsc.edu	37	19	35540222	35540222	+	Silent	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr19:35540222A>G	ENST00000262626.2	+	3	870	c.45A>G	c.(43-45)agA>agG	p.R15R	HPN_ENST00000392226.1_Silent_p.R15R|HPN_ENST00000597419.1_Intron	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	15					basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.R15R(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	GCTGCTCCAGACCCAAGGTGG	0.662																																																	1	Substitution - coding silent(1)	kidney(1)											101.0	96.0	98.0					19																	35540222		2203	4300	6503	SO:0001819	synonymous_variant	3249				CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"""Serine peptidases / Transmembrane"""	5155	protein-coding gene	gene with protein product	"""transmembrane protease, serine 1"""	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.45A>G	19.37:g.35540222A>G			B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																				0.662	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1		NM_002151	
HSP90AB1	3326	hgsc.bcm.edu;ucsc.edu	37	6	44219603	44219604	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr6:44219603_44219604insC	ENST00000371554.1	+	9	1658_1659	c.1444_1445insC	c.(1444-1446)tccfs	p.S482fs	SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000353801.3_Frame_Shift_Ins_p.S482fs|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000371646.5_Frame_Shift_Ins_p.S482fs			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	482					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GACACAGAAGTCCATCTATTAC	0.505																																																	0																																										SO:0001589	frameshift_variant	3326			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.1446dupC	6.37:g.44219605_44219605dupC	ENSP00000360609:p.Ser482fs		B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Frame_Shift_Ins	INS	ENST00000371554.1	37	CCDS4909.1																																																																																				0.505	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1		NM_007355	
HSPA8	3312	broad.mit.edu;hgsc.bcm.edu	37	11	122930262	122930262	+	Nonsense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:122930262G>A	ENST00000532636.1	-	5	1158	c.1039C>T	c.(1039-1041)Cag>Tag	p.Q347*	SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000453788.2_Nonsense_Mutation_p.Q347*|HSPA8_ENST00000533540.1_Nonsense_Mutation_p.Q201*|HSPA8_ENST00000227378.3_Nonsense_Mutation_p.Q347*|HSPA8_ENST00000534319.1_Nonsense_Mutation_p.Q111*|HSPA8_ENST00000526862.1_5'UTR|HSPA8_ENST00000526110.1_Nonsense_Mutation_p.Q328*|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534624.1_Nonsense_Mutation_p.Q347*|SNORD14E_ENST00000364009.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	347	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.Q347*(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AGAAGCTTCTGAATCTTGGGG	0.438																																					Colon(21;486 594 5900 6733 14272)												1	Substitution - Nonsense(1)	kidney(1)											83.0	84.0	84.0					11																	122930262		2202	4299	6501	SO:0001587	stop_gained	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1039C>T	11.37:g.122930262G>A	ENSP00000437125:p.Gln347*		Q9H3R6	Nonsense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	G	40	8.123914	0.98665	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000528292	.	.	.	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.3736	17.9506	0.89052	0.0:0.0:1.0:0.0	.	.	.	.	X	347;201;347;347;347;111;328;287	.	ENSP00000227378:Q347X	Q	-	1	0	HSPA8	122435472	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.693000	0.98684	2.308000	0.77769	0.556000	0.70494	CAG		0.438	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			
HSPA8	3312	broad.mit.edu;hgsc.bcm.edu	37	11	122930264	122930264	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:122930264A>T	ENST00000532636.1	-	5	1156	c.1037T>A	c.(1036-1038)aTt>aAt	p.I346N	SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.I346N|HSPA8_ENST00000533540.1_Missense_Mutation_p.I200N|HSPA8_ENST00000227378.3_Missense_Mutation_p.I346N|HSPA8_ENST00000534319.1_Missense_Mutation_p.I110N|HSPA8_ENST00000526862.1_5'UTR|HSPA8_ENST00000526110.1_Missense_Mutation_p.I327N|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000534624.1_Missense_Mutation_p.I346N|SNORD14E_ENST00000364009.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	346	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.I346N(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AAGCTTCTGAATCTTGGGGAT	0.443																																					Colon(21;486 594 5900 6733 14272)												1	Substitution - Missense(1)	kidney(1)											83.0	83.0	83.0					11																	122930264		2202	4299	6501	SO:0001583	missense	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1037T>A	11.37:g.122930264A>T	ENSP00000437125:p.Ile346Asn		Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.691568	0.88735	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000528292	T;T;T;T;T;T;T;T	0.01240	5.12;5.12;5.12;5.12;5.12;5.12;5.12;5.12	4.65	4.65	0.58169	Heat shock protein 70, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.15782	0.0380	H	0.98701	4.305	0.80722	D	1	D;D;P;D	0.62365	0.991;0.964;0.955;0.991	D;P;P;D	0.63192	0.912;0.71;0.462;0.912	T	0.30563	-0.9974	10	0.87932	D	0	-18.1205	14.4185	0.67168	1.0:0.0:0.0:0.0	.	346;346;346;346	Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;HSP7C_HUMAN	N	346;200;346;346;346;110;327;286	ENSP00000437125:I346N;ENSP00000437189:I200N;ENSP00000432083:I346N;ENSP00000404372:I346N;ENSP00000227378:I346N;ENSP00000433316:I110N;ENSP00000433584:I327N;ENSP00000432884:I286N	ENSP00000227378:I346N	I	-	2	0	HSPA8	122435474	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.174000	0.94824	1.871000	0.54225	0.454000	0.30748	ATT		0.443	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			
IGF2R	3482	broad.mit.edu;ucsc.edu	37	6	160526024	160526024	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr6:160526024delG	ENST00000356956.1	+	48	7532	c.7384delG	c.(7384-7386)gggfs	p.G2462fs	IGF2R_ENST00000475584.1_Intron	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2462					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GGCGAGGAAAGGGAAGTCCAG	0.592																																																	0													97.0	81.0	87.0					6																	160526024		2203	4300	6503	SO:0001589	frameshift_variant	3482			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.7384delG	6.37:g.160526024delG	ENSP00000349437:p.Gly2462fs		Q7Z7G9|Q96PT5	Frame_Shift_Del	DEL	ENST00000356956.1	37	CCDS5273.1																																																																																				0.592	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1		NM_000876	
IL21	59067	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	123542048	123542048	+	Missense_Mutation	SNP	C	C	T	rs141748932		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr4:123542048C>T	ENST00000264497.3	-	1	176	c.119G>A	c.(118-120)cGt>cAt	p.R40H	IL21-AS1_ENST00000417927.1_RNA	NM_001207006.2|NM_021803.3	NP_001193935.1|NP_068575.1	Q9HBE4	IL21_HUMAN	interleukin 21	33					cell maturation (GO:0048469)|immune response (GO:0006955)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	cytokine receptor binding (GO:0005126)|interleukin-2 receptor binding (GO:0005134)	p.R40H(2)		NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(3)	8						TATAAGTTGACGCATTCTAAT	0.363													C|||	1	0.000199681	0.0	0.0	5008	,	,		19969	0.0		0.001	False		,,,				2504	0.0																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)						C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	125.0	121.0	122.0		119,119	-0.0	1.0	4	dbSNP_134	122	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	IL21	NM_021803.2,NM_001207006.1	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	40/163,40/154	123542048	2,13004	2203	4300	6503	SO:0001583	missense	59067			AF254069	CCDS3727.1, CCDS75189.1	4q26-q27	2011-07-15			ENSG00000138684	ENSG00000138684		"""Interleukins and interleukin receptors"""	6005	protein-coding gene	gene with protein product		605384				11081504, 17947662	Standard	NM_001207006		Approved	Za11, IL-21	uc003ies.3	Q9HBE4	OTTHUMG00000133073	ENST00000264497.3:c.119G>A	4.37:g.123542048C>T	ENSP00000264497:p.Arg40His		A5J0L4	Missense_Mutation	SNP	ENST00000264497.3	37	CCDS3727.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.30	1.895179	0.33442	0.0	2.33E-4	ENSG00000138684	ENST00000264497	.	.	.	5.63	-0.0121	0.13989	.	0.724719	0.12759	N	0.441510	T	0.41328	0.1154	M	0.66939	2.045	0.09310	N	1	B;B	0.20261	0.035;0.043	B;B	0.19148	0.014;0.024	T	0.39210	-0.9625	9	0.52906	T	0.07	-2.9323	5.8143	0.18484	0.3248:0.4574:0.0:0.2178	.	33;33	Q9HBE4-2;Q9HBE4	.;IL21_HUMAN	H	40	.	ENSP00000264497:R40H	R	-	2	0	IL21	123761498	0.926000	0.31397	0.986000	0.45419	0.995000	0.86356	0.902000	0.28459	0.027000	0.15297	0.655000	0.94253	CGT		0.363	IL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256713.1		NM_021803	
INTS10	55174	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	19687916	19687916	+	Splice_Site	SNP	G	G	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr8:19687916G>C	ENST00000397977.3	+	10	1538		c.e10-1			NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10						snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.?(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TCTTTAAGCAGAGTTCAGACG	0.363																																																	1	Unknown(1)	kidney(1)											62.0	57.0	58.0					8																	19687916		1832	4098	5930	SO:0001630	splice_region_variant	55174			AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.1141-1G>C	8.37:g.19687916G>C			Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Splice_Site	SNP	ENST00000397977.3	37	CCDS6011.2	.	.	.	.	.	.	.	.	.	.	G	17.68	3.448893	0.63178	.	.	ENSG00000104613	ENST00000397977;ENST00000523846	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9858	0.92769	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	INTS10	19732196	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	9.242000	0.95408	2.832000	0.97577	0.655000	0.94253	.		0.363	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2		NM_018142	Intron
IRF9	10379	broad.mit.edu;hgsc.bcm.edu	37	14	24635394	24635394	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr14:24635394T>C	ENST00000396864.3	+	9	1458	c.1171T>C	c.(1171-1173)Tcc>Ccc	p.S391P	RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.V331A	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN	interferon regulatory factor 9	391					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S391P(1)		NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(265;0.00853)		AGCCATTCTGTCCCTGGTGTA	0.532																																																	1	Substitution - Missense(1)	kidney(1)											63.0	64.0	64.0					14																	24635394		2203	4300	6503	SO:0001583	missense	10379			M87503	CCDS9615.1	14q11.2	2007-07-06	2007-07-06	2007-07-06	ENSG00000213928	ENSG00000213928			6131	protein-coding gene	gene with protein product		147574	"""interferon-stimulated transcription factor 3, gamma (48kD)"", ""interferon-stimulated transcription factor 3, gamma 48kDa"""	ISGF3G		1630447, 10199920	Standard	NM_006084		Approved		uc001wmq.3	Q00978	OTTHUMG00000028799	ENST00000396864.3:c.1171T>C	14.37:g.24635394T>C	ENSP00000380073:p.Ser391Pro		D3DS61	Missense_Mutation	SNP	ENST00000396864.3	37	CCDS9615.1	.	.	.	.	.	.	.	.	.	.	T	9.653	1.142141	0.21205	.	.	ENSG00000213928	ENST00000396864;ENST00000324076	D;D	0.99023	-4.31;-5.34	4.65	-0.787	0.10943	.	0.660445	0.12025	U	0.506489	D	0.96589	0.8887	L	0.56769	1.78	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	D	0.91802	0.5452	10	0.87932	D	0	-3.5031	0.8634	0.01198	0.1546:0.2638:0.1604:0.4212	.	391	Q00978	IRF9_HUMAN	P	391;207	ENSP00000380073:S391P;ENSP00000313529:S207P	ENSP00000313529:S207P	S	+	1	0	IRF9	23705234	0.011000	0.17503	0.006000	0.13384	0.108000	0.19459	-0.541000	0.06099	-0.194000	0.10399	0.459000	0.35465	TCC		0.532	IRF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071927.2			
LGALS8	3964	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	236711354	236711354	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:236711354A>C	ENST00000366584.4	+	10	1413	c.847A>C	c.(847-849)Aat>Cat	p.N283H	LGALS8_ENST00000352231.2_Missense_Mutation_p.N325H|LGALS8_ENST00000341872.6_Missense_Mutation_p.N283H|LGALS8_ENST00000527974.1_Missense_Mutation_p.N325H|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000526634.1_Missense_Mutation_p.N283H|LGALS8_ENST00000526589.1_Missense_Mutation_p.N325H|LGALS8_ENST00000450372.2_Missense_Mutation_p.N325H|LGALS8_ENST00000323938.6_Missense_Mutation_p.N256H|LGALS8_ENST00000416919.2_Missense_Mutation_p.N266H|LGALS8_ENST00000525042.1_Missense_Mutation_p.N266H	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	283	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.N325H(1)		kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GGTTGCAGTAAATGGCGTACA	0.383																																																	1	Substitution - Missense(1)	kidney(1)											125.0	119.0	121.0					1																	236711354		2203	4300	6503	SO:0001583	missense	3964			X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"""Lectins, galactoside-binding"""	6569	protein-coding gene	gene with protein product	"""galectin 8"""	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.847A>C	1.37:g.236711354A>C	ENSP00000355543:p.Asn283His		O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.786269	0.70337	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11;2.11;2.11;2.11;2.11;2.11	4.97	4.97	0.65823	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.048075	0.85682	D	0.000000	T	0.59197	0.2176	H	0.95114	3.625	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.73088	-0.4093	10	0.87932	D	0	-17.1406	15.1035	0.72303	1.0:0.0:0.0:0.0	.	266;283;325	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	H	325;325;325;283;325;283;324;266;256;283;266	ENSP00000431398:N325H;ENSP00000309576:N325H;ENSP00000435460:N325H;ENSP00000342139:N283H;ENSP00000408657:N325H;ENSP00000355543:N283H;ENSP00000410843:N266H;ENSP00000434860:N256H;ENSP00000437040:N283H;ENSP00000431884:N266H	ENSP00000434860:N256H	N	+	1	0	LGALS8	234777977	1.000000	0.71417	0.737000	0.30932	0.980000	0.70556	5.487000	0.66863	2.212000	0.71576	0.528000	0.53228	AAT		0.383	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2		NM_006499	
LOC146880	146880	broad.mit.edu	37	17	62750126	62750126	+	RNA	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:62750126A>G	ENST00000400873.3	-	0	2231					NR_026899.1																						GACTTACCTGAAAGATATTTG	0.383																																																	0																																												146880																															17.37:g.62750126A>G				RNA	SNP	ENST00000400873.3	37																																																																																					0.383	hsa-mir-6080.1-201	KNOWN	basic	processed_transcript	processed_transcript				
LOC441666	441666	broad.mit.edu	37	10	42832122	42832122	+	RNA	SNP	C	C	T	rs200758966		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr10:42832122C>T	ENST00000609841.1	-	0	1781					NR_024380.1																						CAGTAAAAGGCTTTGCCACAT	0.348																																																	0																																												441666																															10.37:g.42832122C>T				RNA	SNP	ENST00000609841.1	37																																																																																					0.348	RP11-313J2.1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472483.1			
MALAT1	378938	broad.mit.edu;hgsc.bcm.edu	37	11	65270626	65270626	+	lincRNA	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:65270626C>T	ENST00000534336.1	+	0	5394					NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		TGCTTCATTTCATCTGGGAGC	0.428																																																	0													21.0	19.0	20.0					11																	65270626		874	1986	2860			378938			AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65270626C>T				RNA	SNP	ENST00000534336.1	37																																																																																					0.428	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1		NR_002819	
MEI1	150365	hgsc.bcm.edu	37	22	42180689	42180690	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr22:42180689_42180690insC	ENST00000401548.3	+	26	3287_3288	c.3247_3248insC	c.(3247-3249)gccfs	p.A1083fs	MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000300398.4_Frame_Shift_Ins_p.A91fs|MEI1_ENST00000400107.1_Frame_Shift_Ins_p.A416fs	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GCCCTCAGGGGCCCAGCCACTG	0.599																																																	0										342,3398		0,342,1528						-8.4	0.0		dbSNP_78	31	561,7385		0,561,3412	no	frameshift	MEI1	NM_152513.3		0,903,4940	A1A1,A1R,RR		7.0602,9.1444,7.7272				903,10783				SO:0001589	frameshift_variant	150365			AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3250dupC	22.37:g.42180692_42180692dupC	ENSP00000384115:p.Ala1083fs			Frame_Shift_Ins	INS	ENST00000401548.3	37	CCDS46718.1																																																																																				0.599	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3		NM_152513	
TPR	7175	broad.mit.edu;hgsc.bcm.edu	37	1	186281526	186281526	+	3'UTR	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:186281526A>C	ENST00000367478.4	-	0	8965				PRG4_ENST00000367486.3_Intron|PRG4_ENST00000445192.2_Intron|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Intron|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Intron	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein						carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ATTGTGTTAAAAAAATCCTTA	0.333			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	0													58.0	62.0	61.0					1																	186281526		2203	4300	6503	SO:0001624	3_prime_UTR_variant	100302192			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.*1577T>G	1.37:g.186281526A>C			Q15655|Q5SWY0|Q99968	RNA	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																				0.333	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2		NM_003292	
TPR	7175	broad.mit.edu;hgsc.bcm.edu	37	1	186281553	186281553	+	3'UTR	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:186281553A>C	ENST00000367478.4	-	0	8938				PRG4_ENST00000367486.3_Intron|PRG4_ENST00000445192.2_Intron|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Intron|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Intron	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein						carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AGTAGATGTAATACAGTTTCT	0.323			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	0													35.0	37.0	36.0					1																	186281553		2201	4297	6498	SO:0001624	3_prime_UTR_variant	100302192			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.*1550T>G	1.37:g.186281553A>C			Q15655|Q5SWY0|Q99968	RNA	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																				0.323	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2		NM_003292	
KMT2C	58508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	151877175	151877175	+	Nonsense_Mutation	SNP	G	G	A	rs535169721		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr7:151877175G>A	ENST00000262189.6	-	37	7404	c.7186C>T	c.(7186-7188)Cag>Tag	p.Q2396*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.Q2396*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2396					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Q2396*(2)									TTCTTCTGCTGTTGCTGCTGG	0.463													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18519	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Nonsense(2)	kidney(2)											222.0	199.0	207.0					7																	151877175		2203	4300	6503	SO:0001587	stop_gained	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.7186C>T	7.37:g.151877175G>A	ENSP00000262189:p.Gln2396*		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	50	16.140017	0.99855	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.5	4.62	0.57501	.	0.000000	0.44285	D	0.000472	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	14.2468	0.65993	0.0717:0.0:0.9283:0.0	.	.	.	.	X	2396	.	ENSP00000262189:Q2396X	Q	-	1	0	MLL3	151508108	1.000000	0.71417	0.959000	0.39883	0.990000	0.78478	8.891000	0.92485	1.325000	0.45301	0.650000	0.86243	CAG		0.463	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			
MRPS18A	55168	broad.mit.edu	37	6	43655468	43655468	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr6:43655468C>A	ENST00000372133.3	-	1	60	c.49G>T	c.(49-51)Ggg>Tgg	p.G17W	MRPS18A_ENST00000372116.1_Missense_Mutation_p.G17W	NM_018135.3	NP_060605.1	Q9NVS2	RT18A_HUMAN	mitochondrial ribosomal protein S18A	17					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)	p.G17W(2)		kidney(3)|large_intestine(1)	4	all_cancers(18;6.56e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000479)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0102)|OV - Ovarian serous cystadenocarcinoma(102;0.137)			GCTAGTAGCCCACGGAGAAGC	0.617																																																	2	Substitution - Missense(2)	kidney(2)											16.0	15.0	15.0					6																	43655468		2193	4278	6471	SO:0001583	missense	55168			AB049952	CCDS4906.1, CCDS55006.1	6p21.3	2012-09-13			ENSG00000096080	ENSG00000096080		"""Mitochondrial ribosomal proteins / small subunits"""	14515	protein-coding gene	gene with protein product		611981				11279123, 11543634	Standard	NM_018135		Approved	FLJ10548, MRPS18-3	uc003ovy.2	Q9NVS2	OTTHUMG00000014750	ENST00000372133.3:c.49G>T	6.37:g.43655468C>A	ENSP00000361206:p.Gly17Trp		A6XND3|Q5QPA4	Missense_Mutation	SNP	ENST00000372133.3	37	CCDS4906.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786598	0.31593	.	.	ENSG00000096080	ENST00000372133;ENST00000372118;ENST00000372116;ENST00000427312	.	.	.	5.01	1.14	0.20703	.	1.003210	0.08037	N	0.994437	T	0.35624	0.0938	L	0.50919	1.6	0.09310	N	1	D;D;P;P	0.67145	0.996;0.995;0.947;0.947	P;D;B;B	0.64321	0.908;0.924;0.417;0.417	T	0.12785	-1.0534	9	0.66056	D	0.02	-3.1478	5.6411	0.17565	0.0:0.4946:0.3281:0.1773	.	17;17;17;17	Q5QPA5;Q9NVS2-2;Q5QPA4;Q9NVS2	.;.;.;RT18A_HUMAN	W	17	.	ENSP00000361188:G17W	G	-	1	0	MRPS18A	43763446	0.009000	0.17119	0.009000	0.14445	0.150000	0.21749	0.467000	0.22035	0.017000	0.15025	0.655000	0.94253	GGG		0.617	MRPS18A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040697.1		NM_018135	
KAT6A	7994	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	41836218	41836218	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr8:41836218G>A	ENST00000396930.3	-	7	1528	c.985C>T	c.(985-987)Cgg>Tgg	p.R329W	KAT6A_ENST00000265713.2_Missense_Mutation_p.R329W|KAT6A_ENST00000406337.1_Missense_Mutation_p.R329W|KAT6A_ENST00000485568.1_Missense_Mutation_p.R329W	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	329	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R329W(1)									GTATAGCGCCGTTTTATCTGT	0.383																																																	1	Substitution - Missense(1)	kidney(1)											301.0	293.0	296.0					8																	41836218		2203	4300	6503	SO:0001583	missense	0			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.985C>T	8.37:g.41836218G>A	ENSP00000380136:p.Arg329Trp		Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.417848	0.42918	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.85556	0.02;0.02;0.02;-2.0	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000003	D	0.91047	0.7183	M	0.64997	1.995	0.53688	D	0.999973	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91611	0.5303	10	0.72032	D	0.01	-20.936	15.7483	0.77965	0.0:0.0:0.8632:0.1368	.	329;329	A5PLL3;Q92794	.;KAT6A_HUMAN	W	329	ENSP00000265713:R329W;ENSP00000385888:R329W;ENSP00000380136:R329W;ENSP00000430606:R329W	ENSP00000265713:R329W	R	-	1	2	KAT6A	41955375	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.195000	0.65131	2.572000	0.86782	0.644000	0.83932	CGG		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1		NM_006766	
NAV3	89795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	78400974	78400974	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr12:78400974G>T	ENST00000397909.2	+	8	1829	c.1656G>T	c.(1654-1656)gaG>gaT	p.E552D	NAV3_ENST00000228327.6_Missense_Mutation_p.E552D|NAV3_ENST00000536525.2_Missense_Mutation_p.E552D|NAV3_ENST00000266692.7_Missense_Mutation_p.E552D			Q8IVL0	NAV3_HUMAN	neuron navigator 3	552						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.E552D(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AAGAGTCTGAGAAATTCAGGA	0.468										HNSCC(70;0.22)																																							1	Substitution - Missense(1)	kidney(1)											69.0	69.0	69.0					12																	78400974		1895	4116	6011	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1656G>T	12.37:g.78400974G>T	ENSP00000381007:p.Glu552Asp		Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	11.54	1.670053	0.29693	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51	5.29	-1.44	0.08856	.	0.000000	0.40222	U	0.001152	T	0.12092	0.0294	L	0.56769	1.78	0.80722	D	1	B;B	0.32101	0.0;0.356	B;B	0.33454	0.001;0.164	T	0.05419	-1.0886	10	0.48119	T	0.1	-12.9977	7.0584	0.25111	0.5289:0.1255:0.3456:0.0	.	552;552	Q8IVL0;Q8IVL0-2	NAV3_HUMAN;.	D	552	ENSP00000446628:E552D;ENSP00000446132:E552D;ENSP00000381007:E552D;ENSP00000228327:E552D;ENSP00000266692:E552D	ENSP00000228327:E552D	E	+	3	2	NAV3	76925105	0.996000	0.38824	0.952000	0.39060	0.961000	0.63080	0.643000	0.24750	-0.487000	0.06735	-1.000000	0.02509	GAG		0.468	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1		NM_001024383	
NEO1	4756	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	73575304	73575304	+	Splice_Site	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr15:73575304G>A	ENST00000339362.5	+	24	3709		c.e24-1		NEO1_ENST00000261908.6_Splice_Site|NEO1_ENST00000560262.1_Splice_Site|NEO1_ENST00000558964.1_Splice_Site			Q92859	NEO1_HUMAN	neogenin 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.?(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TCTCTCTGCAGGCAGTAACAG	0.438																																																	1	Unknown(1)	kidney(1)											324.0	332.0	330.0					15																	73575304		2198	4297	6495	SO:0001630	splice_region_variant	4756			U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.3263-1G>A	15.37:g.73575304G>A			B7ZKM9|B7ZKN0|O00340|Q17RX1	Splice_Site	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639450	0.67244	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.333	0.94299	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NEO1	71362357	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	7.761000	0.85260	2.644000	0.89710	0.655000	0.94253	.		0.438	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2		NM_002499	Intron
NFAM1	150372	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	42807545	42807546	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr22:42807545_42807546insC	ENST00000329021.5	-	2	355_356	c.318_319insG	c.(316-321)gagaacfs	p.N107fs		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	107	Ig-like V-type.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						TGGCTCTGGTTCTCTGTGCCCA	0.574																																																	0																																										SO:0001589	frameshift_variant	150372			BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.319dupG	22.37:g.42807546_42807546dupC	ENSP00000333680:p.Asn107fs		B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Frame_Shift_Ins	INS	ENST00000329021.5	37	CCDS14034.1																																																																																				0.574	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1		NM_145912	
NPNT	255743	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	106848531	106848531	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr4:106848531G>A	ENST00000379987.2	+	3	427	c.211G>A	c.(211-213)Ggg>Agg	p.G71R	NPNT_ENST00000305572.8_Missense_Mutation_p.G71R|RP11-710F7.2_ENST00000512514.1_RNA|NPNT_ENST00000514622.1_Missense_Mutation_p.G71R|NPNT_ENST00000506666.1_Missense_Mutation_p.G71R|NPNT_ENST00000427316.2_Missense_Mutation_p.G71R|RP11-710F7.2_ENST00000511059.1_RNA|NPNT_ENST00000453617.2_Missense_Mutation_p.G88R|NPNT_ENST00000513430.1_3'UTR	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	71	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.G71R(1)		kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		TGAATGTATCGGGCCAAACAA	0.413																																																	1	Substitution - Missense(1)	kidney(1)											141.0	113.0	122.0					4																	106848531		2203	4300	6503	SO:0001583	missense	255743				CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.211G>A	4.37:g.106848531G>A	ENSP00000369323:p.Gly71Arg		A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.5|23.5	4.428949|4.428949	0.83667|0.83667	.|.	.|.	ENSG00000168743|ENSG00000168743	ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451|ENST00000514837	D;D;D;D;D;D;D|.	0.83250|.	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73450|0.73450	0.3588|0.3588	L|L	0.58428|0.58428	1.81|1.81	0.80722|0.80722	D|D	1|1	D;D;D;D;P;D|.	0.61080|.	0.989;0.977;0.987;0.958;0.937;0.98|.	P;P;P;P;P;P|.	0.57679|.	0.781;0.65;0.777;0.65;0.664;0.825|.	T|T	0.68750|0.68750	-0.5326|-0.5326	10|5	0.87932|.	D|.	0|.	.|.	19.9435|19.9435	0.97174|0.97174	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	71;71;71;88;71;71|.	E9PF04;E9PE64;E9PCQ1;E9PCK8;Q6UXI9-2;Q6UXI9|.	.;.;.;.;.;NPNT_HUMAN|.	R|Q	71;88;71;71;71;71;88|47	ENSP00000369323:G71R;ENSP00000402884:G88R;ENSP00000389252:G71R;ENSP00000422044:G71R;ENSP00000302557:G71R;ENSP00000422474:G71R;ENSP00000426146:G88R|.	ENSP00000302557:G71R|.	G|R	+|+	1|2	0|0	NPNT|NPNT	107067980|107067980	1.000000|1.000000	0.71417|0.71417	0.952000|0.952000	0.39060|0.39060	0.261000|0.261000	0.26267|0.26267	9.650000|9.650000	0.98490|0.98490	2.885000|2.885000	0.99019|0.99019	0.650000|0.650000	0.86243|0.86243	GGG|CGG		0.413	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1		NM_198278	
P4HA2	8974	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	131543565	131543565	+	Nonsense_Mutation	SNP	G	G	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:131543565G>A	ENST00000401867.1	-	9	1484	c.916C>T	c.(916-918)Cag>Tag	p.Q306*	P4HA2_ENST00000379104.2_Nonsense_Mutation_p.Q306*|P4HA2_ENST00000360568.3_Nonsense_Mutation_p.Q306*|P4HA2_ENST00000379086.1_Nonsense_Mutation_p.Q306*|P4HA2_ENST00000379100.2_Nonsense_Mutation_p.Q306*|P4HA2_ENST00000166534.4_Nonsense_Mutation_p.Q306*			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	306					peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.Q306*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	AGCCTCTTCTGTCTACGGGGT	0.577																																					Esophageal Squamous(68;117 1135 17362 19256 34242)												1	Substitution - Nonsense(1)	kidney(1)											139.0	141.0	140.0					5																	131543565		2203	4300	6503	SO:0001587	stop_gained	8974			U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"""4-PH alpha 2"", ""collagen prolyl 4-hydroxylase alpha(II)"""	600608	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"""			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.916C>T	5.37:g.131543565G>A	ENSP00000384999:p.Gln306*		D3DQ85|D3DQ86|Q8WWN0	Nonsense_Mutation	SNP	ENST00000401867.1	37	CCDS4151.1	.	.	.	.	.	.	.	.	.	.	G	40	8.409539	0.98799	.	.	ENSG00000072682	ENST00000401867;ENST00000379086;ENST00000166534;ENST00000360568;ENST00000379104;ENST00000379100	.	.	.	5.87	4.96	0.65561	.	0.164529	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-23.3121	17.0006	0.86380	0.0:0.0:0.8724:0.1276	.	.	.	.	X	306	.	ENSP00000166534:Q306X	Q	-	1	0	P4HA2	131571464	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	5.294000	0.65687	2.941000	0.99782	0.655000	0.94253	CAG		0.577	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4		NM_004199	
PCBD2	84105	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	134294744	134294744	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:134294744G>T	ENST00000512783.1	+	3	251	c.231G>T	c.(229-231)atG>atT	p.M77I	PCBD2_ENST00000510013.1_3'UTR|PCBD2_ENST00000254908.6_Missense_Mutation_p.M77I			Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	77					positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|tetrahydrobiopterin biosynthetic process (GO:0006729)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|phenylalanine 4-monooxygenase activity (GO:0004505)	p.M77I(1)		kidney(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTGGCTTTATGTCCCGAGTTG	0.413																																																	1	Substitution - Missense(1)	kidney(1)											124.0	117.0	119.0					5																	134294744		1944	4151	6095	SO:0001583	missense	84105			AF499009	CCDS43364.1	5q31.1	2008-02-05	2006-01-10			ENSG00000132570			24474	protein-coding gene	gene with protein product		609836	"""6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2"""			15182178, 11980910	Standard	NM_032151		Approved	DCOHM, DCOH2	uc010jdz.3	Q9H0N5		ENST00000512783.1:c.231G>T	5.37:g.134294744G>T	ENSP00000421544:p.Met77Ile		Q8TD40	Missense_Mutation	SNP	ENST00000512783.1	37	CCDS43364.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492215	0.84962	.	.	ENSG00000132570	ENST00000254908;ENST00000512783	D;D	0.90261	-2.64;-2.64	5.52	4.65	0.58169	.	0.038284	0.85682	N	0.000000	D	0.95130	0.8422	M	0.83603	2.65	0.80722	D	1	P	0.45986	0.87	D	0.63877	0.919	D	0.95488	0.8566	10	0.72032	D	0.01	-11.1982	14.5004	0.67716	0.0713:0.0:0.9287:0.0	.	77	Q9H0N5	PHS2_HUMAN	I	77	ENSP00000254908:M77I;ENSP00000421544:M77I	ENSP00000254908:M77I	M	+	3	0	PCBD2	134322643	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.773000	0.98989	1.329000	0.45376	-0.157000	0.13467	ATG		0.413	PCBD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371578.1		NM_032151	
PLAC8L1	153770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	145477733	145477733	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:145477733C>T	ENST00000311450.4	-	2	299	c.242G>A	c.(241-243)aGa>aAa	p.R81K	RP11-118M9.3_ENST00000514002.1_RNA	NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	81								p.R81K(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCCTATCTCTGCAGACACT	0.498																																																	1	Substitution - Missense(1)	kidney(1)											54.0	59.0	57.0					5																	145477733		2203	4300	6503	SO:0001583	missense	153770				CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.242G>A	5.37:g.145477733C>T	ENSP00000309087:p.Arg81Lys			Missense_Mutation	SNP	ENST00000311450.4	37	CCDS34264.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749755	0.69533	.	.	ENSG00000173261	ENST00000311450	T	0.40756	1.02	4.7	3.83	0.44106	.	0.112824	0.64402	D	0.000009	T	0.30039	0.0752	N	0.14661	0.345	0.27099	N	0.962659	P	0.38280	0.625	P	0.46110	0.504	T	0.14448	-1.0472	10	0.18710	T	0.47	-3.8924	9.0273	0.36239	0.0:0.8989:0.0:0.1011	.	81	A1L4L8	PL8L1_HUMAN	K	81	ENSP00000309087:R81K	ENSP00000309087:R81K	R	-	2	0	PLAC8L1	145457926	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	1.772000	0.38552	1.339000	0.45563	0.455000	0.32223	AGA		0.498	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1		XM_087761	
PPA2	27068	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	106395063	106395063	+	Missense_Mutation	SNP	G	G	A	rs142379853		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr4:106395063G>A	ENST00000341695.5	-	1	175	c.145C>T	c.(145-147)Cgc>Tgc	p.R49C	PPA2_ENST00000357415.4_Missense_Mutation_p.R49C|PPA2_ENST00000509426.1_5'UTR|PPA2_ENST00000432483.2_Missense_Mutation_p.R49C|PPA2_ENST00000354147.3_Missense_Mutation_p.R49C|PPA2_ENST00000380004.2_Missense_Mutation_p.R49C|PPA2_ENST00000310267.7_5'UTR|PPA2_ENST00000348706.5_Missense_Mutation_p.R49C	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	49					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)	p.R49C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		AAGAAGAGGCGGTAATTCTGC	0.672											OREG0016281	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)						G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,4403		0,1,2201	22.0	25.0	24.0		145,145,145,145	3.2	0.8	4	dbSNP_134	24	0,8594		0,0,4297	no	missense,missense,missense,missense	PPA2	NM_006903.4,NM_176866.2,NM_176867.3,NM_176869.2	180,180,180,180	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	49/306,49/233,49/169,49/335	106395063	1,12997	2202	4297	6499	SO:0001583	missense	27068				CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.145C>T	4.37:g.106395063G>A	ENSP00000343885:p.Arg49Cys	1396	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.801780	0.31869	2.27E-4	0.0	ENSG00000138777	ENST00000341695;ENST00000348706;ENST00000354147;ENST00000432483;ENST00000357415;ENST00000380004;ENST00000510015;ENST00000504028	T;T;T;T;T;T;T;T	0.60171	0.73;0.73;0.21;0.73;0.73;0.73;0.73;0.73	3.19	3.19	0.36642	.	0.214648	0.36444	N	0.002582	T	0.68035	0.2957	M	0.78344	2.41	0.80722	D	1	P;D;P;B;B	0.76494	0.948;0.999;0.544;0.218;0.408	B;P;B;B;B	0.56343	0.096;0.796;0.236;0.049;0.097	T	0.72707	-0.4212	10	0.72032	D	0.01	-13.1555	10.0509	0.42214	0.0:0.0:1.0:0.0	.	49;49;49;49;49	Q9H2U2-4;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.;.;.;.;IPYR2_HUMAN	C	49	ENSP00000343885:R49C;ENSP00000313061:R49C;ENSP00000340352:R49C;ENSP00000389957:R49C;ENSP00000349996:R49C;ENSP00000369340:R49C;ENSP00000423363:R49C;ENSP00000421177:R49C	ENSP00000343885:R49C	R	-	1	0	PPA2	106614512	1.000000	0.71417	0.758000	0.31321	0.012000	0.07955	3.047000	0.49854	1.770000	0.52166	0.455000	0.32223	CGC		0.672	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4		NM_176869	
PPP6R1	22870	broad.mit.edu;hgsc.bcm.edu	37	19	55748092	55748092	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr19:55748092C>T	ENST00000412770.2	-	17	2473	c.1907G>A	c.(1906-1908)gGg>gAg	p.G636E	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Missense_Mutation_p.G636E	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	636	Glu-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)	p.G636E(1)		breast(1)	1						ATCAGACTCCCCTGAGCCCTG	0.622																																																	1	Substitution - Missense(1)	kidney(1)											53.0	55.0	54.0					19																	55748092		1982	4151	6133	SO:0001583	missense	22870			AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1907G>A	19.37:g.55748092C>T	ENSP00000414202:p.Gly636Glu		Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392411	0.42410	.	.	ENSG00000105063	ENST00000412770	T	0.41400	1.0	4.95	1.52	0.23074	.	0.162599	0.29355	N	0.012390	T	0.18002	0.0432	N	0.19112	0.55	0.25168	N	0.990306	B	0.20052	0.041	B	0.19666	0.026	T	0.23762	-1.0179	10	0.02654	T	1	-23.7426	2.9102	0.05734	0.1807:0.528:0.1898:0.1015	.	636	Q9UPN7	PP6R1_HUMAN	E	636	ENSP00000414202:G636E	ENSP00000414202:G636E	G	-	2	0	PPP6R1	60439904	0.994000	0.37717	0.950000	0.38849	0.971000	0.66376	1.515000	0.35845	0.551000	0.29008	0.563000	0.77884	GGG		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1		NM_014931	
PURG	29942	hgsc.bcm.edu;ucsc.edu	37	8	30889951	30889958	+	Frame_Shift_Del	DEL	CTTCAGCT	CTTCAGCT	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	CTTCAGCT	CTTCAGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr8:30889951_30889958delCTTCAGCT	ENST00000475541.1	-	1	1273_1280	c.341_348delAGCTGAAG	c.(340-348)gagctgaagfs	p.ELK114fs	WRN_ENST00000298139.5_5'Flank|PURG_ENST00000339382.2_Frame_Shift_Del_p.ELK114fs	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	114						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		CTAGACAGTCCTTCAGCTCCGCTGCCAC	0.587																																																	0																																										SO:0001589	frameshift_variant	29942			AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.341_348delAGCTGAAG	8.37:g.30889951_30889958delCTTCAGCT	ENSP00000418721:p.Glu114fs		Q8TE64	Frame_Shift_Del	DEL	ENST00000475541.1	37	CCDS6081.1																																																																																				0.587	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1		NM_013357	
RAD54L	8438	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	46726269	46726269	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:46726269delC	ENST00000371975.4	+	6	1137	c.463delC	c.(463-465)cctfs	p.P155fs	RAD54L_ENST00000442598.1_Frame_Shift_Del_p.P155fs	NM_003579.3	NP_003570.2	Q92698	RAD54_HUMAN	RAD54-like (S. cerevisiae)	155					chromosome organization (GO:0051276)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		GGTTTTGCGGCCTCATCAGAG	0.537								Direct reversal of damage;Homologous recombination																																									0													138.0	127.0	131.0					1																	46726269		2203	4300	6503	SO:0001589	frameshift_variant	8438			X97795	CCDS532.1	1p32	2008-02-05	2001-11-28		ENSG00000085999	ENSG00000085999			9826	protein-coding gene	gene with protein product		603615	"""RAD54 (S.cerevisiae)-like"""			8805304	Standard	NM_003579		Approved	hHR54, hRAD54, RAD54A	uc009vye.2	Q92698	OTTHUMG00000007772	ENST00000371975.4:c.463delC	1.37:g.46726269delC	ENSP00000361043:p.Pro155fs		Q5TE31|Q6IUY3	Frame_Shift_Del	DEL	ENST00000371975.4	37	CCDS532.1																																																																																				0.537	RAD54L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021272.1		NM_003579	
RAI14	26064	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	34757614	34757614	+	Silent	SNP	C	C	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:34757614C>G	ENST00000265109.3	+	3	365	c.78C>G	c.(76-78)gcC>gcG	p.A26A	RAI14_ENST00000397449.1_Silent_p.A19A|RAI14_ENST00000428746.2_Silent_p.A26A|RAI14_ENST00000512629.1_Silent_p.A26A|RAI14_ENST00000515799.1_Silent_p.A29A|RAI14_ENST00000503673.1_Silent_p.A26A|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000506376.1_Silent_p.A18A	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	26						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.A26A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					TACTGCAGGCCGTGGAGAATG	0.552																																																	1	Substitution - coding silent(1)	kidney(1)											93.0	90.0	91.0					5																	34757614		2203	4300	6503	SO:0001819	synonymous_variant	26064			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.78C>G	5.37:g.34757614C>G			E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																				0.552	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1		NM_015577	
RAPGEF6	51735	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	130764648	130764648	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:130764648T>G	ENST00000509018.1	-	27	4932	c.4727A>C	c.(4726-4728)cAg>cCg	p.Q1576P	RAPGEF6_ENST00000307984.5_Intron|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.Q1584P|RAPGEF6_ENST00000507093.1_Intron|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.Q1626P	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1576					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)	p.Q1576P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ATGGAATGGCTGCAAATTATG	0.458																																					Melanoma(168;435 1955 13113 13877 23213)												1	Substitution - Missense(1)	kidney(1)											132.0	123.0	126.0					5																	130764648		2203	4300	6503	SO:0001583	missense	51735			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.4727A>C	5.37:g.130764648T>G	ENSP00000421684:p.Gln1576Pro		A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.143942	0.37825	.	.	ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000296859;ENST00000514667	T;T;T	0.24151	1.87;1.87;1.96	4.72	4.72	0.59763	.	0.370611	0.25941	N	0.027304	T	0.25457	0.0619	L	0.44542	1.39	0.80722	D	1	P;P;P	0.46706	0.883;0.883;0.883	B;B;B	0.42188	0.379;0.379;0.379	T	0.02991	-1.1085	10	0.46703	T	0.11	.	14.3443	0.66649	0.0:0.0:0.0:1.0	.	1584;1626;1576	B7ZML2;E9PCH4;Q8TEU7	.;.;RPGF6_HUMAN	P	1576;1584;1626	ENSP00000421684:Q1576P;ENSP00000296859:Q1584P;ENSP00000426948:Q1626P	ENSP00000426948:Q1626P	Q	-	2	0	RAPGEF6;FNIP1	130792547	1.000000	0.71417	0.996000	0.52242	0.303000	0.27691	3.936000	0.56568	1.996000	0.58369	0.533000	0.62120	CAG		0.458	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1		NM_016340	
RNF20	56254	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	104316360	104316360	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr9:104316360G>T	ENST00000389120.3	+	14	2082	c.1992G>T	c.(1990-1992)atG>atT	p.M664I		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	664					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M664I(1)		breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TTCAGCTGATGGCAGCTGAGA	0.438																																																	1	Substitution - Missense(1)	kidney(1)											146.0	122.0	130.0					9																	104316360		2203	4300	6503	SO:0001583	missense	56254			AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.1992G>T	9.37:g.104316360G>T	ENSP00000373772:p.Met664Ile		A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	32	5.182650	0.94885	.	.	ENSG00000155827	ENST00000389120	T	0.33654	1.4	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.53578	0.1805	M	0.75085	2.285	0.80722	D	1	P	0.46395	0.877	P	0.50440	0.641	T	0.45366	-0.9266	10	0.37606	T	0.19	-26.6788	20.1963	0.98243	0.0:0.0:1.0:0.0	.	664	Q5VTR2	BRE1A_HUMAN	I	664	ENSP00000373772:M664I	ENSP00000373772:M664I	M	+	3	0	RNF20	103356181	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.444000	0.97578	2.878000	0.98634	0.650000	0.86243	ATG		0.438	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1		NM_019592	
ROCK1	6093	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	18586538	18586538	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr18:18586538T>A	ENST00000399799.2	-	16	2599	c.1659A>T	c.(1657-1659)ttA>ttT	p.L553F		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	553	Interaction with FHOD1.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L553F(1)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					CTGTCCTAAGTAAGTCATTGG	0.348																																																	1	Substitution - Missense(1)	kidney(1)											100.0	87.0	91.0					18																	18586538		2203	4299	6502	SO:0001583	missense	6093				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.1659A>T	18.37:g.18586538T>A	ENSP00000382697:p.Leu553Phe		B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	17.16	3.318193	0.60524	.	.	ENSG00000067900	ENST00000399799	T	0.65732	-0.17	5.44	4.29	0.51040	.	0.076828	0.52532	D	0.000072	T	0.63450	0.2512	M	0.72479	2.2	0.53005	D	0.999966	D	0.54047	0.964	P	0.47044	0.535	T	0.64584	-0.6373	10	0.49607	T	0.09	.	8.4413	0.32816	0.0:0.2146:0.0:0.7854	.	553	Q13464	ROCK1_HUMAN	F	553	ENSP00000382697:L553F	ENSP00000382697:L553F	L	-	3	2	ROCK1	16840536	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.743000	0.26231	1.090000	0.41315	0.533000	0.62120	TTA		0.348	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2		NM_005406	
SASS6	163786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	100575995	100575995	+	Silent	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:100575995A>G	ENST00000287482.5	-	8	854	c.714T>C	c.(712-714)gaT>gaC	p.D238D	SASS6_ENST00000535161.1_Silent_p.D71D|SASS6_ENST00000462159.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	238					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)		p.D238D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		GGATTTCTAAATCTTTTTTCT	0.328																																																	1	Substitution - coding silent(1)	kidney(1)											164.0	156.0	159.0					1																	100575995		2203	4299	6502	SO:0001819	synonymous_variant	163786			AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.714T>C	1.37:g.100575995A>G			D3DT55|Q8N3K0	Silent	SNP	ENST00000287482.5	37	CCDS764.1																																																																																				0.328	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2		NM_194292	
SCN9A	6335	hgsc.bcm.edu;ucsc.edu	37	2	167060645	167060645	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr2:167060645delT	ENST00000409435.1	-	25	4593	c.4594delA	c.(4594-4596)atgfs	p.M1533fs	SCN9A_ENST00000375387.4_Frame_Shift_Del_p.M1534fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.M1522fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.M1534fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1533					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTACCATCATGGTTACCATG	0.338																																																	0													118.0	107.0	110.0					2																	167060645		1886	4144	6030	SO:0001589	frameshift_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4594delA	2.37:g.167060645delT	ENSP00000386330:p.Met1533fs		A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	CCDS46441.1																																																																																				0.338	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1		NM_002977	
SCUBE1	80274	broad.mit.edu;hgsc.bcm.edu	37	22	43625097	43625097	+	Silent	SNP	G	G	A	rs375170368		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr22:43625097G>A	ENST00000360835.4	-	9	1191	c.1065C>T	c.(1063-1065)taC>taT	p.Y355Y		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	355	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.Y355Y(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GGGTTGTCCCGTAGAGGATGT	0.677											OREG0026614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)						G		0,4406		0,0,2203	71.0	50.0	57.0		1065	-5.6	0.7	22		57	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	SCUBE1	NM_173050.3		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		355/989	43625097	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	80274				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1065C>T	22.37:g.43625097G>A		917	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																				0.677	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3		NM_173050	
SERF2	10169	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	44085976	44085976	+	3'UTR	SNP	G	G	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr15:44085976G>C	ENST00000381359.1	+	0	1114				SERF2_ENST00000409614.1_3'UTR|SERF2_ENST00000409960.2_Missense_Mutation_p.V107L|SERF2_ENST00000249786.4_3'UTR|SERF2_ENST00000339624.5_Missense_Mutation_p.V70L|SERF2_ENST00000402131.1_3'UTR|SERF2_ENST00000403425.1_3'UTR|SERF2_ENST00000594896.1_Intron|RP11-296A16.1_ENST00000417761.2_Intron|MIR1282_ENST00000408865.1_RNA|SERF2_ENST00000409646.1_Intron|HYPK_ENST00000406925.1_5'Flank|SERF2_ENST00000409291.1_Intron	NM_001199877.1	NP_001186806.1	P84101	SERF2_HUMAN	small EDRK-rich factor 2							cytosol (GO:0005829)|nucleus (GO:0005634)		p.V107L(1)		lung(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		AAGTAGCTTTGTGGCTTCGTG	0.582																																																	1	Substitution - Missense(1)	kidney(1)											186.0	147.0	160.0					15																	44085976		2198	4298	6496	SO:0001624	3_prime_UTR_variant	10169			AF073298	CCDS32218.1, CCDS55963.1, CCDS55964.1, CCDS55965.1	15q15.1	2008-01-18			ENSG00000140264	ENSG00000140264			10757	protein-coding gene	gene with protein product		605054				9731538	Standard	NM_001199876		Approved	H4F5rel, 4F5REL, FAM2C, HsT17089	uc010bdq.3	P84101	OTTHUMG00000059935	ENST00000381359.1:c.*5G>C	15.37:g.44085976G>C			A6NL45|B5MCG1|B9A026|O75918|O88891|Q9BZH7	Missense_Mutation	SNP	ENST00000381359.1	37	CCDS32218.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484425	0.44147	.	.	ENSG00000140264	ENST00000409960;ENST00000339624	T;T	0.55052	0.54;0.61	5.93	3.82	0.43975	.	.	.	.	.	T	0.29588	0.0738	N	0.08118	0	0.80722	D	1	B;B	0.20780	0.048;0.0	B;B	0.22386	0.039;0.001	T	0.25606	-1.0127	9	0.87932	D	0	.	5.4847	0.16743	0.101:0.0:0.6986:0.2004	.	70;107	A6NL45;B9A026	.;.	L	107;70	ENSP00000387187:V107L;ENSP00000339647:V70L	ENSP00000339647:V70L	V	+	1	0	SERF2	41873268	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.414000	0.44627	2.798000	0.96311	0.655000	0.94253	GTG		0.582	SERF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133233.2		NM_005770	
SECISBP2L	9728	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	49284863	49284864	+	Missense_Mutation	DNP	CA	CA	TC			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C|A	C|A	C|A	T|C	C|A	C|A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr15:49284863_49284864CA>TC	ENST00000559471.1	-	18	3146_3147	c.2883_2884TG>GA	c.(2881-2886)acTGgc>acGAgc	p.G962S	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.G917S	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	962							poly(A) RNA binding (GO:0044822)	p.G917S(2)|p.T916T(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TCCAAAGAGCCAGTCTCTGTAC	0.49																																																	3	Substitution - Missense(2)|Substitution - coding silent(1)	kidney(3)																																								SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2883_2884delinsTC	15.37:g.49284863_49284864delinsTC	ENSP00000453854:p.Gly962Ser		Q8N767	Missense_Mutation|Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																				0.490	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1		NM_014701	
SFMBT1	51460	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52960072	52960073	+	Missense_Mutation	DNP	GC	GC	CT			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr3:52960072_52960073GC>CT	ENST00000394752.3	-	10	1487_1488	c.1105_1106GC>AG	c.(1105-1107)GCt>AGt	p.A369S	SFMBT1_ENST00000296295.6_Missense_Mutation_p.A369S|SFMBT1_ENST00000394750.1_Missense_Mutation_p.A369S|SFMBT1_ENST00000358080.2_Missense_Mutation_p.A369S	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	369					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)	p.A369T(1)|p.A369G(1)|p.A369S(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		CTGGGGAGCAGCTTCAGCACCA	0.574																																																	3	Substitution - Missense(3)	kidney(3)																																								SO:0001583	missense	51460			AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"""Sterile alpha motif (SAM) domain containing"""	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.1105_1106delinsCT	3.37:g.52960072_52960073delinsCT	ENSP00000378235:p.Ala369Ser		Q402F7|Q96C73|Q9Y4Q9	Missense_Mutation	SNP	ENST00000394752.3	37	CCDS2867.1																																																																																				0.574	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3		NM_016329	
SLC15A3	51296	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60709539	60709539	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:60709539C>T	ENST00000227880.3	-	4	1308	c.1075G>A	c.(1075-1077)Gtg>Atg	p.V359M		NM_016582.2	NP_057666.1	Q8IY34	S15A3_HUMAN	solute carrier family 15 (oligopeptide transporter), member 3	359					ion transport (GO:0006811)|peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	symporter activity (GO:0015293)	p.V359M(1)		central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)	17						CTCAGGGCCACAGAGATGTTG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											178.0	175.0	176.0					11																	60709539		2203	4299	6502	SO:0001583	missense	51296			AB020598	CCDS7998.1	11q12.2	2013-07-18	2013-07-18		ENSG00000110446	ENSG00000110446		"""Solute carriers"""	18068	protein-coding gene	gene with protein product		610408	"""solute carrier family 15, member 3"""			11336635, 11741232	Standard	NM_016582		Approved	PHT2, hPTR3	uc001nqn.2	Q8IY34	OTTHUMG00000167804	ENST00000227880.3:c.1075G>A	11.37:g.60709539C>T	ENSP00000227880:p.Val359Met		Q9P2X9	Missense_Mutation	SNP	ENST00000227880.3	37	CCDS7998.1	.	.	.	.	.	.	.	.	.	.	c	4.354	0.065219	0.08388	.	.	ENSG00000110446	ENST00000227880;ENST00000536491	T;T	0.05139	3.49;3.49	4.39	-8.78	0.00824	Major facilitator superfamily domain, general substrate transporter (1);	4.059570	0.00424	N	0.000062	T	0.04363	0.0120	L	0.31664	0.95	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.23261	-1.0193	10	0.38643	T	0.18	0.3729	3.6597	0.08234	0.2707:0.4279:0.0792:0.2221	.	359;359	F5H1C8;Q8IY34	.;S15A3_HUMAN	M	359;172	ENSP00000227880:V359M;ENSP00000439535:V172M	ENSP00000227880:V359M	V	-	1	0	SLC15A3	60466115	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-3.154000	0.00580	-3.138000	0.00234	-1.439000	0.01073	GTG		0.572	SLC15A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396366.1		NM_016582	
ZBED3	84327	broad.mit.edu;hgsc.bcm.edu	37	5	76376388	76376388	+	Intron	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr5:76376388A>G	ENST00000255198.2	-	2	213				ZBED3_ENST00000505685.1_Intron|SNORA47_ENST00000458862.1_RNA	NM_032367.2	NP_115743.1	Q96IU2	ZBED3_HUMAN	zinc finger, BED-type containing 3						negative regulation of protein phosphorylation (GO:0001933)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_lung(232;0.00645)|Lung NSC(167;0.0135)|Ovarian(174;0.0798)|Prostate(461;0.121)		OV - Ovarian serous cystadenocarcinoma(54;2.24e-51)|Epithelial(54;9.06e-46)|all cancers(79;2.48e-41)		TCACCTTCTCAGTCCTCCACA	0.552																																																	0													58.0	53.0	55.0					5																	76376388		876	1991	2867	SO:0001627	intron_variant	677828			BC007239	CCDS4036.1	5q13.2	2013-05-03			ENSG00000132846	ENSG00000132846		"""Zinc fingers, BED-type"""	20711	protein-coding gene	gene with protein product		615250				23533661	Standard	NM_032367		Approved	MGC15435	uc003kev.1	Q96IU2	OTTHUMG00000102131	ENST00000255198.2:c.152-1835T>C	5.37:g.76376388A>G				RNA	SNP	ENST00000255198.2	37	CCDS4036.1																																																																																				0.552	ZBED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219970.1		NM_032367	
STAT6	6778	hgsc.bcm.edu	37	12	57499020	57499021	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr12:57499020_57499021insG	ENST00000300134.3	-	9	1239_1240	c.914_915insC	c.(913-915)ccafs	p.P305fs	STAT6_ENST00000537215.2_Frame_Shift_Ins_p.P195fs|STAT6_ENST00000556155.1_Frame_Shift_Ins_p.P305fs|STAT6_ENST00000538913.2_Frame_Shift_Ins_p.P195fs|STAT6_ENST00000454075.3_Frame_Shift_Ins_p.P305fs|STAT6_ENST00000543873.2_Frame_Shift_Ins_p.P305fs	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	305					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						GAGGCTTGGCTGGGGCCCCCAG	0.629																																																	0																																										SO:0001589	frameshift_variant	6778			BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.915dupC	12.37:g.57499024_57499024dupG	ENSP00000300134:p.Pro305fs		A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Frame_Shift_Ins	INS	ENST00000300134.3	37	CCDS8931.1																																																																																				0.629	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3		NM_003153	
TAF1L	138474	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	32630843	32630844	+	Missense_Mutation	DNP	GC	GC	TG			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr9:32630843_32630844GC>TG	ENST00000242310.4	-	1	4823_4824	c.4734_4735GC>CA	c.(4732-4737)aaGCac>aaCAac	p.1578_1579KH>NN	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1578	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.K1578N(1)|p.H1579N(1)|p.K1578_H1579>NN(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGATACTTGTGCTTGGAGATGT	0.386																																																	3	Substitution - Missense(2)|Complex - compound substitution(1)	kidney(3)																																								SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4734_4735delinsTG	9.37:g.32630843_32630844delinsTG	ENSP00000418379:p.K1578_H1579delinsNN		Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.386	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			
THBS1	7057	broad.mit.edu;hgsc.bcm.edu	37	15	39882824	39882824	+	Splice_Site	SNP	G	G	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr15:39882824G>T	ENST00000260356.5	+	14	2418	c.2253G>T	c.(2251-2253)agG>agT	p.R751S	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	751					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.?(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CAGATGACAGGGTAAAAACAG	0.403																																																	1	Unknown(1)	kidney(1)											115.0	111.0	112.0					15																	39882824		2200	4297	6497	SO:0001630	splice_region_variant	7057				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2253+1G>T	15.37:g.39882824G>T			A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029059	0.93518	.	.	ENSG00000137801	ENST00000260356	D	0.98207	-4.79	5.99	5.99	0.97316	.	0.000000	0.38217	N	0.001763	D	0.97926	0.9318	L	0.44542	1.39	0.80722	D	1	P;D	0.57571	0.629;0.98	B;P	0.57846	0.439;0.828	D	0.97201	0.9864	10	0.29301	T	0.29	-8.004	19.0269	0.92935	0.0:0.0:1.0:0.0	.	666;751	B4E3J7;P07996	.;TSP1_HUMAN	S	751	ENSP00000260356:R751S	ENSP00000260356:R751S	R	+	3	2	THBS1	37670116	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.770000	0.74990	2.843000	0.97960	0.655000	0.94253	AGG		0.403	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2		NM_003246	Missense_Mutation
TMEM45B	120224	broad.mit.edu;hgsc.bcm.edu	37	11	129728494	129728494	+	Missense_Mutation	SNP	G	G	A	rs563776197		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr11:129728494G>A	ENST00000524567.1	+	6	1023	c.742G>A	c.(742-744)Gga>Aga	p.G248R	TMEM45B_ENST00000281441.3_Missense_Mutation_p.G248R			Q96B21	TM45B_HUMAN	transmembrane protein 45B	248						integral component of membrane (GO:0016021)		p.G248R(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		GAAGAGACACGGAAGGGGAGA	0.458													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18620	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											51.0	52.0	51.0					11																	129728494		2201	4297	6498	SO:0001583	missense	120224			AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.742G>A	11.37:g.129728494G>A	ENSP00000436293:p.Gly248Arg		A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	37	CCDS8482.1	.	.	.	.	.	.	.	.	.	.	G	6.147	0.395299	0.11638	.	.	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.29397	1.57;1.57	5.53	1.89	0.25635	.	3.982800	0.00166	N	0.000007	T	0.16854	0.0405	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.21518	-1.0243	10	0.16896	T	0.51	-19.7194	1.5134	0.02500	0.2253:0.168:0.436:0.1707	.	248	Q96B21	TM45B_HUMAN	R	248	ENSP00000281441:G248R;ENSP00000436293:G248R	ENSP00000281441:G248R	G	+	1	0	TMEM45B	129233704	0.000000	0.05858	0.005000	0.12908	0.243000	0.25628	0.211000	0.17474	1.191000	0.43056	0.591000	0.81541	GGA		0.458	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1		NM_138788	
TNRC6C	57690	hgsc.bcm.edu	37	17	76083029	76083029	+	Frame_Shift_Del	DEL	G	G	-	rs373105504		TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:76083029delG	ENST00000588061.1	+	15	4384	c.3657delG	c.(3655-3657)ccgfs	p.P1222fs	TNRC6C_ENST00000301624.4_Frame_Shift_Del_p.P1222fs|TNRC6C_ENST00000335749.4_Frame_Shift_Del_p.P1219fs|TNRC6C_ENST00000544502.1_Frame_Shift_Del_p.P1219fs|TNRC6C_ENST00000541771.1_Frame_Shift_Del_p.P1222fs|TNRC6C_ENST00000588847.1_Frame_Shift_Del_p.P1219fs			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1222	Pro-rich.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.P1216P(1)|p.P1219P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CACCGCCACCGCCCCCGCCGC	0.667																																																	2	Substitution - coding silent(2)	lung(2)											40.0	52.0	48.0					17																	76083029		2092	4209	6301	SO:0001589	frameshift_variant	57690			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.3657delG	17.37:g.76083029delG	ENSP00000468647:p.Pro1222fs		G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Frame_Shift_Del	DEL	ENST00000588061.1	37	CCDS45798.1																																																																																				0.667	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1		NM_018996	
TOM1L2	146691	broad.mit.edu;ucsc.edu	37	17	17769632	17769632	+	Silent	SNP	G	G	T			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr17:17769632G>T	ENST00000379504.3	-	10	1145	c.1062C>A	c.(1060-1062)ctC>ctA	p.L354L	TOM1L2_ENST00000478943.1_Silent_p.L87L|TOM1L2_ENST00000318094.10_Silent_p.L309L|TOM1L2_ENST00000395739.4_Silent_p.L309L|TOM1L2_ENST00000542206.1_Silent_p.L206L|TOM1L2_ENST00000535933.1_Silent_p.L301L|TOM1L2_ENST00000581396.1_Silent_p.L304L|TOM1L2_ENST00000577517.1_5'UTR|TOM1L2_ENST00000540946.1_Silent_p.L256L	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	354					intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)	p.L354L(1)|p.L304L(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GCTGGGAGGAGAGGGAAGATG	0.562																																					Melanoma(192;2505 2909 14455 25269)												2	Substitution - coding silent(2)	kidney(2)											69.0	59.0	62.0					17																	17769632		2203	4300	6503	SO:0001819	synonymous_variant	146691			AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"""target of myb1 (chicken) homolog-like 1"""			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.1062C>A	17.37:g.17769632G>T			B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Silent	SNP	ENST00000379504.3	37	CCDS42270.1																																																																																				0.562	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1			
CEP41	95681	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	130042593	130042593	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr7:130042593T>C	ENST00000223208.5	-	7	740	c.470A>G	c.(469-471)aAg>aGg	p.K157R	CEP41_ENST00000343969.5_Missense_Mutation_p.K157R|CEP41_ENST00000541543.1_Missense_Mutation_p.K141R	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	157					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)		p.K157R(1)									CTCTGCTTTCTTCACTGGCCC	0.478																																																	1	Substitution - Missense(1)	kidney(1)											307.0	273.0	284.0					7																	130042593		2203	4300	6503	SO:0001583	missense	0			AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.470A>G	7.37:g.130042593T>C	ENSP00000223208:p.Lys157Arg		A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.865553	0.71949	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000492389;ENST00000472739;ENST00000477003;ENST00000475282	D;D;D;D;D;D;D	0.89485	-2.52;-2.17;-2.48;-2.15;-2.15;-2.17;-1.72	5.96	5.96	0.96718	Rhodanese-like (2);	0.182774	0.64402	D	0.000017	D	0.91703	0.7377	M	0.72479	2.2	0.49389	D	0.99978	D;B;B	0.60575	0.988;0.2;0.126	P;B;B	0.53861	0.736;0.047;0.032	D	0.91066	0.4889	10	0.38643	T	0.18	-25.1502	15.2725	0.73717	0.0:0.0:0.0:1.0	.	141;157;157	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	R	157;141;157;122;122;154;122	ENSP00000223208:K157R;ENSP00000445888:K141R;ENSP00000342738:K157R;ENSP00000419192:K122R;ENSP00000417593:K122R;ENSP00000420670:K154R;ENSP00000418363:K122R	ENSP00000223208:K157R	K	-	2	0	TSGA14	129829829	0.999000	0.42202	1.000000	0.80357	0.576000	0.36127	1.551000	0.36233	2.285000	0.76669	0.533000	0.62120	AAG		0.478	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2		NM_018718	
UBXN6	80700	broad.mit.edu;hgsc.bcm.edu	37	19	4446542	4446542	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr19:4446542A>C	ENST00000301281.6	-	8	999	c.875T>G	c.(874-876)tTc>tGc	p.F292C	UBXN6_ENST00000394765.3_Missense_Mutation_p.F239C|MIR4746_ENST00000579802.1_RNA|CTB-50L17.7_ENST00000588798.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	292						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.F292C(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						GAGGTTGAAGAAGTCCCCAGG	0.697																																																	1	Substitution - Missense(1)	kidney(1)											25.0	27.0	26.0					19																	4446542		2200	4300	6500	SO:0001583	missense	80700			AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.875T>G	19.37:g.4446542A>C	ENSP00000301281:p.Phe292Cys		D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.011851	0.75046	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.65364	0.21;-0.15	5.25	5.25	0.73442	.	0.045831	0.85682	D	0.000000	D	0.82351	0.5018	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86331	0.1698	10	0.87932	D	0	-31.3314	14.3057	0.66384	1.0:0.0:0.0:0.0	.	239;292	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	C	292;239	ENSP00000301281:F292C;ENSP00000378246:F239C	ENSP00000301281:F292C	F	-	2	0	UBXN6	4397542	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	8.578000	0.90777	1.987000	0.57996	0.402000	0.26972	TTC		0.697	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3		NM_025241	
OVOS2	144203	broad.mit.edu	37	12	31279359	31279359	+	IGR	SNP	A	A	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr12:31279359A>C								RP11-551L14.1 (8954 upstream) : FAM60A (154158 downstream)														p.Y1132D(1)									GCAAAAGCATAAGCTAGAATT	0.423																																																	1	Substitution - Missense(1)	kidney(1)											106.0	103.0	104.0					12																	31279359		1910	4144	6054	SO:0001628	intergenic_variant	0																															12.37:g.31279359A>C				Missense_Mutation	SNP		37																																																																																				0	0.423									
USP26	83844	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	132160271	132160271	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chrX:132160271A>G	ENST00000511190.1	-	6	2447	c.1978T>C	c.(1978-1980)Tat>Cat	p.Y660H	USP26_ENST00000370832.1_Missense_Mutation_p.Y660H|USP26_ENST00000406273.1_Missense_Mutation_p.Y660H	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	660	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.Y660H(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					TCTTCCAGATACGTCATTAAG	0.423																																					NSCLC(104;342 1621 36940 47097 52632)												1	Substitution - Missense(1)	kidney(1)											104.0	93.0	97.0					X																	132160271		2203	4300	6503	SO:0001583	missense	83844			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1978T>C	X.37:g.132160271A>G	ENSP00000423390:p.Tyr660His		B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	A	3.623	-0.077174	0.07184	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.52526	0.66;0.66;0.66	4.04	-7.82	0.01205	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.883650	0.01638	N	0.023873	T	0.19046	0.0457	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.18263	0.021	T	0.20306	-1.0279	10	0.12103	T	0.63	1.4315	0.1891	0.00132	0.2413:0.1927:0.2042:0.3618	.	660	Q9BXU7	UBP26_HUMAN	H	660	ENSP00000359869:Y660H;ENSP00000423390:Y660H;ENSP00000384360:Y660H	ENSP00000359869:Y660H	Y	-	1	0	USP26	131987937	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.395000	0.01053	-1.798000	0.01250	0.486000	0.48141	TAT		0.423	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1		NM_031907	
VANGL2	57216	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	160385972	160385972	+	Splice_Site	SNP	G	G	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr1:160385972G>C	ENST00000368061.2	+	3	666	c.192G>C	c.(190-192)cgG>cgC	p.R64R		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	64					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)		p.R64R(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGGATGAGCGGGTGAGCACTG	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											37.0	42.0	40.0					1																	160385972		2203	4300	6503	SO:0001630	splice_region_variant	57216			AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.192+1G>C	1.37:g.160385972G>C			D3DVE9|Q5T212	Silent	SNP	ENST00000368061.2	37	CCDS30915.1																																																																																				0.642	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1		NM_020335	Silent
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191482	10191482	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr3:10191482delA	ENST00000256474.2	+	3	1315	c.475delA	c.(475-477)aaafs	p.K159fs	VHL_ENST00000345392.2_Frame_Shift_Del_p.K118fs|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	159	Interaction with Elongin BC complex.		K -> E (in VHLD; type II).		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.K159*(2)|p.L158_K159del(1)|p.T157fs*14(1)|p.K159fs*10(1)|p.K159fs*13(1)|p.V155_K159delVYTLK(1)|p.T157_K159del(1)|p.K159E(1)|p.T157_K159>I(1)|p.L158fs*6(1)|p.Y156*(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTATACTCTGAAAGAGCGATG	0.507		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"""	12	Deletion - Frameshift(4)|Deletion - In frame(3)|Substitution - Nonsense(2)|Complex - frameshift(1)|Complex - deletion inframe(1)|Substitution - Missense(1)	kidney(11)|adrenal_gland(1)	GRCh37	CM961430	VHL	M							90.0	82.0	84.0					3																	10191482		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.475delA	3.37:g.10191482delA	ENSP00000256474:p.Lys159fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.507	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
YTHDC1	91746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	69204039	69204039	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr4:69204039T>C	ENST00000344157.4	-	2	427	c.92A>G	c.(91-93)tAt>tGt	p.Y31C	YTHDC1_ENST00000355665.3_Missense_Mutation_p.Y31C|YTHDC1_ENST00000579690.1_Missense_Mutation_p.Y31C	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	31					mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y31C(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						CTCTGGATTATACAGTTCATC	0.279																																																	1	Substitution - Missense(1)	kidney(1)											97.0	91.0	93.0					4																	69204039		2199	4295	6494	SO:0001583	missense	91746			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.92A>G	4.37:g.69204039T>C	ENSP00000339245:p.Tyr31Cys		Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.800648	0.50315	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.27104	1.69;1.73	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.32071	0.0817	N	0.11560	0.145	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.99	T	0.29274	-1.0017	10	0.37606	T	0.19	.	15.6407	0.76997	0.0:0.0:0.0:1.0	.	31;31	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	C	31	ENSP00000339245:Y31C;ENSP00000347888:Y31C	ENSP00000339245:Y31C	Y	-	2	0	YTHDC1	68886634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.406000	0.80017	2.143000	0.66587	0.528000	0.53228	TAT		0.279	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1		NM_133370	
ZNF534	147658	broad.mit.edu	37	19	52942411	52942411	+	Silent	SNP	G	G	A	rs113700997	byFrequency	TCGA-B0-5099-01A-01D-1421-08	TCGA-B0-5099-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3150136-ae55-49d0-9212-86728464167d	1b289013-495e-4a64-a3d1-4e5618c62f4c	g.chr19:52942411G>A	ENST00000332323.6	+	4	1798	c.1737G>A	c.(1735-1737)gcG>gcA	p.A579A	ZNF534_ENST00000433050.1_Silent_p.A566A|ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000432303.2_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	579					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.A579A(4)		central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						CACACCTTGCGCGACATAGGA	0.443																																																	4	Substitution - coding silent(4)	kidney(4)											63.0	62.0	62.0					19																	52942411		692	1591	2283	SO:0001819	synonymous_variant	147658			AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"""Zinc fingers, C2H2-type"", ""-"""	26337	protein-coding gene	gene with protein product			"""KRAB domain only 3"""	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.1737G>A	19.37:g.52942411G>A			Q76KX9	Silent	SNP	ENST00000332323.6	37	CCDS46165.1																																																																																				0.443	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1		NM_182512	
