#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
ADCY5	111	broad.mit.edu	37	3	123049743	123049743	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:123049743C>T	ENST00000462833.1	-	5	2851	c.1639G>A	c.(1639-1641)Gcc>Acc	p.A547T	ADCY5_ENST00000491190.1_Missense_Mutation_p.A180T|ADCY5_ENST00000309879.5_Missense_Mutation_p.A197T	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	547	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.A547T(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		TACGAGATGGCCTCGATCATG	0.612																																																	1	Substitution - Missense(1)	kidney(1)											89.0	74.0	79.0					3																	123049743		2203	4300	6503	SO:0001583	missense	111			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1639G>A	3.37:g.123049743C>T	ENSP00000419361:p.Ala547Thr		B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	36	5.678801	0.96764	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	5.78	5.78	0.91487	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.64402	D	0.000001	D	0.85314	0.5668	L	0.49699	1.58	0.80722	D	1	D;P	0.59767	0.986;0.91	P;P	0.57371	0.716;0.819	T	0.82629	-0.0363	10	0.33141	T	0.24	.	20.0204	0.97499	0.0:1.0:0.0:0.0	.	547;180	O95622;B3KWA8	ADCY5_HUMAN;.	T	547;180;197;106	ENSP00000419361:A547T;ENSP00000418537:A180T;ENSP00000308685:A197T;ENSP00000420082:A106T	ENSP00000308685:A197T	A	-	1	0	ADCY5	124532433	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.729000	0.93468	0.650000	0.86243	GCC		0.612	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4		XM_171048	
ARHGAP9	64333	broad.mit.edu;hgsc.bcm.edu	37	12	57871324	57871324	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr12:57871324G>T	ENST00000356411.2	-	4	812	c.674C>A	c.(673-675)cCc>cAc	p.P225H	ARHGAP9_ENST00000430041.2_Missense_Mutation_p.P41H|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.P304H|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.P296H|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.P225H|ARHGAP9_ENST00000550454.1_5'UTR|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.P225H			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	225	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)	p.P225H(1)		endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TCCAGAGTTGGGGTCCAGGTG	0.642																																																	1	Substitution - Missense(1)	kidney(1)											47.0	54.0	52.0					12																	57871324		2203	4300	6503	SO:0001583	missense	64333			AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.674C>A	12.37:g.57871324G>T	ENSP00000348782:p.Pro225His		B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	G	12.94	2.088981	0.36855	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139;ENST00000552604;ENST00000551452;ENST00000552066;ENST00000549602	T;T;T;T;T;T;T;T;T;D	0.83837	-1.13;-1.13;-1.13;-1.13;-1.13;0.87;0.87;0.87;0.87;-1.77	3.58	-0.0701	0.13748	WW/Rsp5/WWP (2);	0.362787	0.25500	N	0.030245	T	0.70710	0.3255	L	0.45352	1.415	0.27428	N	0.954084	B;B;B;B;B;B	0.20368	0.044;0.014;0.002;0.013;0.002;0.0	B;B;B;B;B;B	0.20384	0.029;0.013;0.002;0.018;0.003;0.0	T	0.59825	-0.7381	10	0.54805	T	0.06	.	2.6672	0.05056	0.3236:0.0:0.465:0.2114	.	225;304;225;225;225;41	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	.;.;RHG09_HUMAN;.;.;.	H	225;225;225;296;274;41;41;41;78;41;41	ENSP00000377380:P225H;ENSP00000348782:P225H;ENSP00000394307:P225H;ENSP00000377386:P296H;ENSP00000397950:P41H;ENSP00000449829:P41H;ENSP00000450256:P41H;ENSP00000446932:P78H;ENSP00000448424:P41H;ENSP00000450223:P41H	ENSP00000344852:P274H	P	-	2	0	ARHGAP9	56157591	0.256000	0.24012	0.898000	0.35279	0.997000	0.91878	0.321000	0.19558	-0.021000	0.14009	0.655000	0.94253	CCC		0.642	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_032496	
PHF7	51533	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52442512	52442512	+	5'Flank	SNP	T	T	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:52442512T>C	ENST00000327906.3	+	0	0				BAP1_ENST00000460680.1_Missense_Mutation_p.N78S|BAP1_ENST00000296288.5_Missense_Mutation_p.N78S|PHF7_ENST00000347025.2_5'Flank	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.N78S(2)|p.I72fs*7(1)|p.I76fs*45(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		GAACATGTTATTCACAATATC	0.488																																																	4	Substitution - Missense(2)|Deletion - Frameshift(2)	kidney(2)|eye(1)|pleura(1)											63.0	53.0	56.0					3																	52442512		2202	4299	6501	SO:0001631	upstream_gene_variant	8314			AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"""Zinc fingers, PHD-type"""	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52442512T>C	Exception_encountered		K4DI82	Missense_Mutation	SNP	ENST00000327906.3	37	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.931031	0.73327	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.40756	1.02;1.02	5.52	5.52	0.82312	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.090448	0.85682	D	0.000000	T	0.41926	0.1180	N	0.25031	0.7	0.80722	D	1	P	0.41978	0.767	P	0.49361	0.608	T	0.30909	-0.9962	10	0.42905	T	0.14	-2.8537	15.6492	0.77078	0.0:0.0:0.0:1.0	.	78	Q92560	BAP1_HUMAN	S	78	ENSP00000417132:N78S;ENSP00000296288:N78S	ENSP00000296288:N78S	N	-	2	0	BAP1	52417552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.005000	0.88553	2.106000	0.64143	0.533000	0.62120	AAT		0.488	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1		NM_016483	
KNOP1	400506	broad.mit.edu;ucsc.edu	37	16	19718398	19718398	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr16:19718398A>G	ENST00000219837.7	-	5	1289	c.1211T>C	c.(1210-1212)cTc>cCc	p.L404P	KNOP1_ENST00000568230.1_Missense_Mutation_p.L83P|AC002550.5_ENST00000565916.1_RNA	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	404	Interaction with ZNF106. {ECO:0000250}.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L404P(1)									CTTCTTGCCGAGGGCCATGTT	0.602																																																	1	Substitution - Missense(1)	kidney(1)											45.0	50.0	48.0					16																	19718398		1881	4097	5978	SO:0001583	missense	400506			BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.1211T>C	16.37:g.19718398A>G	ENSP00000219837:p.Leu404Pro		O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	37	CCDS42127.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.337104	0.60963	.	.	ENSG00000103550	ENST00000219837	T	0.37752	1.18	5.4	5.4	0.78164	.	0.418901	0.21077	N	0.080544	T	0.58708	0.2141	M	0.66939	2.045	0.47949	D	0.999558	D	0.89917	1.0	D	0.91635	0.999	T	0.58103	-0.7695	9	.	.	.	-9.2826	15.4145	0.74956	1.0:0.0:0.0:0.0	.	404	Q1ED39	CP088_HUMAN	P	404	ENSP00000219837:L404P	.	L	-	2	0	C16orf88	19625899	0.983000	0.35010	0.031000	0.17742	0.435000	0.31806	7.401000	0.79962	2.026000	0.59711	0.460000	0.39030	CTC		0.602	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2		NM_001012991	
BEAN1	146227	broad.mit.edu	37	16	66511499	66511499	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr16:66511499G>T	ENST00000536005.2	+	4	543	c.326G>T	c.(325-327)aGg>aTg	p.R109M	RP11-403P17.5_ENST00000561728.1_Intron|CTD-2258A20.5_ENST00000567528.1_RNA|BEAN1_ENST00000564819.1_5'UTR|BEAN1_ENST00000561796.1_5'UTR|BEAN1_ENST00000563075.1_Intron|CTD-2258A20.5_ENST00000569125.1_RNA|CTD-2258A20.5_ENST00000564618.1_RNA|BEAN1_ENST00000299694.8_5'UTR	NM_001178020.2	NP_001171491.1	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with NEDD4, 1	109	Arg-rich.				cell death (GO:0008219)	integral component of membrane (GO:0016021)		p.R109M(1)		kidney(1)	1						TCAAGCCGCAGGATGCGCTAT	0.632																																																	1	Substitution - Missense(1)	kidney(1)											41.0	49.0	46.0					16																	66511499		692	1591	2283	SO:0001583	missense	0			BC000818	CCDS54015.1, CCDS58469.1, CCDS58470.1	16q21	2014-07-30			ENSG00000166546	ENSG00000166546			24160	protein-coding gene	gene with protein product		612051	"""spinocerebellar ataxia 31"""	SCA31		11042109, 8619474, 23607545	Standard	NM_001178020		Approved		uc021tjl.1	Q3B7T3	OTTHUMG00000173370	ENST00000536005.2:c.326G>T	16.37:g.66511499G>T	ENSP00000442793:p.Arg109Met		B3KPC0|H3BP97	Translation_Start_Site	SNP	ENST00000536005.2	37	CCDS54015.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.381159	0.82792	.	.	ENSG00000166546	ENST00000536005;ENST00000299694	.	.	.	4.56	2.6	0.31112	.	0.313556	0.30547	N	0.009384	T	0.45975	0.1369	M	0.68317	2.08	0.22280	N	0.999235	.	.	.	.	.	.	T	0.38457	-0.9660	7	0.72032	D	0.01	-13.7645	6.1161	0.20127	0.222:0.0:0.778:0.0	.	.	.	.	M	109;100	.	ENSP00000299694:R100M	R	+	2	0	BEAN1	65069000	0.939000	0.31865	0.026000	0.17262	0.926000	0.56050	2.016000	0.40971	1.269000	0.44280	0.561000	0.74099	AGG		0.632	BEAN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422908.1		NM_001136106	
EFCAB13	124989	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	45452174	45452174	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr17:45452174C>G	ENST00000331493.2	+	12	1625	c.1214C>G	c.(1213-1215)tCt>tGt	p.S405C	EFCAB13_ENST00000517484.1_Missense_Mutation_p.S309C	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	405						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S405C(1)									GACTCAAAGTCTAAACCACAA	0.383																																																	1	Substitution - Missense(1)	kidney(1)											64.0	67.0	66.0					17																	45452174		2203	4300	6503	SO:0001583	missense	0			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1214C>G	17.37:g.45452174C>G	ENSP00000332111:p.Ser405Cys		G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742169	0.69418	.	.	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.70869	-0.12;-0.52	4.01	0.81	0.18732	.	0.526148	0.17011	N	0.190516	T	0.74238	0.3690	M	0.64997	1.995	0.09310	N	1	D;D;D	0.76494	0.999;0.995;0.995	D;P;P	0.64237	0.923;0.785;0.785	T	0.61787	-0.6991	9	.	.	.	-0.9435	3.141	0.06456	0.228:0.5397:0.0:0.2323	.	357;405;309	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	C	405;309;357	ENSP00000332111:S405C;ENSP00000430048:S309C	.	S	+	2	0	C17orf57	42807173	0.012000	0.17670	0.634000	0.29324	0.981000	0.71138	-0.383000	0.07398	0.095000	0.17434	0.585000	0.79938	TCT		0.383	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4		NM_152347	
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554|rs72122505|rs201781577|rs35753661	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:29287926_29287927insGCT	ENST00000331664.5	-	2	3674_3675	c.3675_3676insAGC	c.(3673-3678)agcgag>agcAGCgag	p.1225_1226insS	C2orf71_ENST00000602958.1_5'Flank	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1225			S -> SS. {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.S1225_E1226insS(2)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGGCTCTCCTCGCTGCTGCTGC	0.624														1871	0.373602	0.5257	0.2637	5008	,	,		17644	0.4931		0.2545	False		,,,				2504	0.2454																2	Insertion - In frame(2)	ovary(1)|breast(1)								1580,1994		462,656,669						5.2	1.0		dbSNP_130	16	1923,5511		406,1111,2200	no	coding	C2orf71	NM_001029883.1		868,1767,2869	A1A1,A1R,RR		25.8676,44.2082,31.8223				3503,7505				SO:0001652	inframe_insertion	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3673_3675dupAGC	2.37:g.29287933_29287935dupGCT	ENSP00000332809:p.Ser1225_Ser1225dup			In_Frame_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																				0.624	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3		NM_001029883	
C2orf83	56918	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	228497787	228497787	+	Silent	SNP	G	G	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:228497787G>A	ENST00000264387.4	-	1	101	c.15C>T	c.(13-15)gcC>gcT	p.A5A	C2orf83_ENST00000409066.1_Silent_p.A5A	NM_020161.3	NP_064546.3	Q53S99	CB083_HUMAN	chromosome 2 open reading frame 83	5					transport (GO:0006810)	membrane (GO:0016020)		p.A5A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(2)	11						CAAACGTCAGGGCATAGTCTT	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											129.0	103.0	112.0					2																	228497787		2203	4300	6503	SO:0001819	synonymous_variant	56918				CCDS33388.1, CCDS54434.1	2q36.3	2008-09-16			ENSG00000042304	ENSG00000042304			25344	protein-coding gene	gene with protein product							Standard	NM_020161		Approved	DKFZp547H025	uc002vph.3	Q53S99	OTTHUMG00000153550	ENST00000264387.4:c.15C>T	2.37:g.228497787G>A			A2RRG6|B8ZZI8|Q9NPW4	Silent	SNP	ENST00000264387.4	37	CCDS33388.1																																																																																				0.418	C2orf83-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331607.1		NM_020161	
ERMARD	55780	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	170179296	170179296	+	Silent	SNP	T	T	A	rs79095717		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr6:170179296T>A	ENST00000366773.3	+	17	1791	c.1758T>A	c.(1756-1758)ccT>ccA	p.P586P	ERMARD_ENST00000392095.4_Silent_p.P460P|ERMARD_ENST00000418781.3_Silent_p.P513P|ERMARD_ENST00000366772.2_Silent_p.P539P|ERMARD_ENST00000588451.1_Silent_p.P450P	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	586					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.P586P(1)									TACTGTCCCCTGTGCTCAGCC	0.393																																																	1	Substitution - coding silent(1)	kidney(1)											204.0	172.0	182.0					6																	170179296		2203	4300	6503	SO:0001819	synonymous_variant	55780			AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1758T>A	6.37:g.170179296T>A			B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																				0.393	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2		NM_018341	
CELF3	11189	broad.mit.edu;hgsc.bcm.edu	37	1	151681728	151681728	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr1:151681728G>A	ENST00000290583.4	-	4	1167	c.374C>T	c.(373-375)aCt>aTt	p.T125I	CELF3_ENST00000290585.4_Missense_Mutation_p.T125I|CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000392706.3_5'Flank|AL589765.1_ENST00000442233.2_5'Flank|RP11-98D18.1_ENST00000457548.1_RNA|RIIAD1_ENST00000326413.3_5'Flank	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	125	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.T125I(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						CCGGAGCACAGTGCACTCGTC	0.612																																																	1	Substitution - Missense(1)	kidney(1)											180.0	171.0	174.0					1																	151681728		2203	4300	6503	SO:0001583	missense	11189			U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.374C>T	1.37:g.151681728G>A	ENSP00000290583:p.Thr125Ile		B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	21.7	4.188051	0.78789	.	.	ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000368833	D;D	0.84516	-1.86;-1.86	4.39	4.39	0.52855	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.86514	0.5951	L	0.39147	1.195	0.80722	D	1	D;D;D;D;D	0.89917	0.994;0.982;1.0;0.984;0.98	D;P;D;P;P	0.85130	0.95;0.864;0.997;0.844;0.758	D	0.88357	0.2985	10	0.72032	D	0.01	-10.1771	14.4846	0.67609	0.0:0.0:1.0:0.0	.	125;125;124;125;124	Q5SZQ7;Q5SZQ8-2;F8W6B7;Q5SZQ8;Q5SZQ8-3	.;.;.;CELF3_HUMAN;.	I	125;125;124	ENSP00000290585:T125I;ENSP00000290583:T125I	ENSP00000290583:T125I	T	-	2	0	CELF3	149948352	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.199000	0.95003	2.265000	0.75225	0.462000	0.41574	ACT		0.612	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2		NM_007185	
CHEK2	11200	broad.mit.edu;hgsc.bcm.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																															yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	9	Substitution - Missense(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)																																								SO:0001583	missense	11200			AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1		NM_001005735	
CLK4	57396	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	178050273	178050273	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr5:178050273A>G	ENST00000316308.4	-	2	313	c.145T>C	c.(145-147)Ttt>Ctt	p.F49L	CLK4_ENST00000520957.1_Missense_Mutation_p.F49L	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	49					protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.F49L(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		GATTCTTTAAACTGGTGATGT	0.368																																																	2	Substitution - Missense(2)	kidney(2)											229.0	212.0	218.0					5																	178050273		2203	4300	6503	SO:0001583	missense	57396			AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"""CDC-like kinases"""	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.145T>C	5.37:g.178050273A>G	ENSP00000316948:p.Phe49Leu			Missense_Mutation	SNP	ENST00000316308.4	37	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254303	0.59212	.	.	ENSG00000113240	ENST00000316308;ENST00000536763;ENST00000520957	T	0.06528	3.29	5.83	3.45	0.39498	.	0.515646	0.20802	N	0.085417	T	0.01870	0.0059	N	0.01048	-1.04	0.26457	N	0.975504	B;B;B;B;B	0.12013	0.005;0.0;0.001;0.0;0.002	B;B;B;B;B	0.08055	0.002;0.0;0.003;0.001;0.001	T	0.46456	-0.9190	10	0.11485	T	0.65	.	7.4904	0.27458	0.8304:0.0:0.1696:0.0	.	49;49;49;49;49	B7Z990;B7ZL31;E7EWJ6;Q4G0Z5;Q9HAZ1	.;.;.;.;CLK4_HUMAN	L	49	ENSP00000316948:F49L	ENSP00000316948:F49L	F	-	1	0	CLK4	177982879	0.999000	0.42202	1.000000	0.80357	0.919000	0.55068	1.392000	0.34486	0.479000	0.27511	0.402000	0.26972	TTT		0.368	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			
CXCR2	3579	broad.mit.edu;ucsc.edu	37	2	218999551	218999551	+	Silent	SNP	C	C	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:218999551C>T	ENST00000318507.2	+	3	454	c.27C>T	c.(25-27)gaC>gaT	p.D9D		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	9					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)	p.D9D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TGGAGAGTGACAGCTTTGAAG	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											78.0	75.0	76.0					2																	218999551		2203	4300	6503	SO:0001819	synonymous_variant	3579			U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.27C>T	2.37:g.218999551C>T			Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																				0.388	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2		NM_001557	
ELK1	2002	broad.mit.edu	37	X	47498682	47498682	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chrX:47498682G>A	ENST00000247161.3	-	3	365	c.266C>T	c.(265-267)cCt>cTt	p.P89L	ELK1_ENST00000376983.3_Missense_Mutation_p.P89L|ELK1_ENST00000343894.4_Missense_Mutation_p.P89L|ELK1_ENST00000592066.1_Missense_Mutation_p.P35L	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	89					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P89L(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	10						TGCGACCTCAGGGTAGGACAC	0.587																																																	2	Substitution - Missense(2)	kidney(2)											29.0	23.0	25.0					X																	47498682		2203	4300	6503	SO:0001583	missense	2002			M25269	CCDS14283.1, CCDS59165.1	Xp11.23	2010-07-20			ENSG00000126767	ENSG00000126767			3321	protein-coding gene	gene with protein product		311040				2539641	Standard	NM_001114123		Approved		uc010nhv.4	P19419	OTTHUMG00000021452	ENST00000247161.3:c.266C>T	X.37:g.47498682G>A	ENSP00000247161:p.Pro89Leu		B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	37	CCDS14283.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804456	0.90623	.	.	ENSG00000126767	ENST00000247161;ENST00000376983;ENST00000343894	T;T;T	0.55760	0.5;0.5;0.5	5.52	5.52	0.82312	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (1);	0.000000	0.85682	D	0.000000	T	0.62624	0.2443	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.65841	-0.6070	10	0.72032	D	0.01	.	15.9232	0.79590	0.0:0.0:1.0:0.0	.	89	P19419	ELK1_HUMAN	L	89	ENSP00000247161:P89L;ENSP00000366182:P89L;ENSP00000345585:P89L	ENSP00000247161:P89L	P	-	2	0	ELK1	47383626	1.000000	0.71417	0.914000	0.36105	0.862000	0.49288	9.465000	0.97660	2.448000	0.82819	0.600000	0.82982	CCT		0.587	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1		NM_005229	
ENC1	8507	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	73931537	73931537	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr5:73931537C>G	ENST00000302351.4	-	2	1904	c.774G>C	c.(772-774)aaG>aaC	p.K258N	ENC1_ENST00000510316.1_Missense_Mutation_p.K185N|ENC1_ENST00000537006.1_Missense_Mutation_p.K258N	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	258					multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.K258N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		TCTTTCTCTGCTTGGTGATGA	0.512																																																	1	Substitution - Missense(1)	kidney(1)											80.0	91.0	87.0					5																	73931537		2203	4300	6503	SO:0001583	missense	8507			AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.774G>C	5.37:g.73931537C>G	ENSP00000306356:p.Lys258Asn		B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	37	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	C	9.682	1.149491	0.21288	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.71341	-0.55;-0.56;-0.55	6.04	3.96	0.45880	.	0.146864	0.64402	D	0.000010	T	0.46014	0.1371	N	0.08118	0	0.47441	D	0.999422	B	0.02656	0.0	B	0.04013	0.001	T	0.36212	-0.9757	10	0.09590	T	0.72	.	11.4841	0.50344	0.0:0.7902:0.0:0.2098	.	258	O14682	ENC1_HUMAN	N	258;185;258	ENSP00000306356:K258N;ENSP00000423804:K185N;ENSP00000446289:K258N	ENSP00000306356:K258N	K	-	3	2	ENC1	73967293	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.779000	0.26746	1.568000	0.49683	0.561000	0.74099	AAG		0.512	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2		NM_003633	
EPPK1	83481	hgsc.bcm.edu	37	8	144940506	144940506	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr8:144940506C>T	ENST00000525985.1	-	2	6987	c.6916G>A	c.(6916-6918)Gcc>Acc	p.A2306T				P58107	EPIPL_HUMAN	epiplakin 1	2306						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCGGTGACGGCGCGCTCGGCC	0.697																																																	0													140.0	138.0	139.0					8																	144940506		2183	4261	6444	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6916G>A	8.37:g.144940506C>T	ENSP00000436337:p.Ala2306Thr		Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	33	5.255137	0.95336	.	.	ENSG00000227184	ENST00000525985	T	0.72505	-0.66	4.63	4.63	0.57726	.	.	.	.	.	D	0.83885	0.5351	M	0.81802	2.56	0.46901	D	0.999247	D	0.89917	1.0	D	0.97110	1.0	D	0.84928	0.0858	9	0.48119	T	0.1	.	15.1031	0.72299	0.0:1.0:0.0:0.0	.	2306	E9PPU0	.	T	2306	ENSP00000436337:A2306T	ENSP00000436337:A2306T	A	-	1	0	EPPK1	145012494	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.755000	0.62198	2.416000	0.81992	0.586000	0.80456	GCC		0.697	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1		NM_031308	
GRID1	2894	broad.mit.edu;ucsc.edu	37	10	87628903	87628903	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr10:87628903T>G	ENST00000327946.7	-	6	900	c.815A>C	c.(814-816)cAt>cCt	p.H272P		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	272					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.H272P(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						AAGGGCACTATGGACCAGATC	0.507										Multiple Myeloma(13;0.14)																																							1	Substitution - Missense(1)	kidney(1)											152.0	132.0	139.0					10																	87628903		2203	4300	6503	SO:0001583	missense	2894			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.815A>C	10.37:g.87628903T>G	ENSP00000330148:p.His272Pro		B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814772	0.70912	.	.	ENSG00000182771	ENST00000327946	D	0.82255	-1.59	5.82	5.82	0.92795	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89019	0.6596	L	0.57536	1.79	0.80722	D	1	D	0.71674	0.998	D	0.68483	0.958	D	0.89901	0.4044	10	0.72032	D	0.01	.	15.3729	0.74581	0.0:0.0:0.0:1.0	.	272	Q9ULK0	GRID1_HUMAN	P	272	ENSP00000330148:H272P	ENSP00000330148:H272P	H	-	2	0	GRID1	87618883	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.274000	0.72587	2.216000	0.71823	0.533000	0.62120	CAT		0.507	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3		XM_043613	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377220	168377220	+	lincRNA	SNP	T	T	A	rs79173693	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr6:168377220T>A	ENST00000538528.1	-	0	399																											TGCAGTGTGTTGGGAGGAGAA	0.622													N|||	297	0.0593051	0.0371	0.0634	5008	,	,		16845	0.0675		0.0417	False		,,,				2504	0.0961																0													3.0	5.0	4.0					6																	168377220		585	1382	1967			100128124																															6.37:g.168377220T>A				Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
IGDCC4	57722	hgsc.bcm.edu	37	15	65681661	65681662	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr15:65681661_65681662insC	ENST00000352385.2	-	14	2705_2706	c.2496_2497insG	c.(2494-2499)gggcctfs	p.P833fs		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	833	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GAGCCGAAAGGCCCATCCATGT	0.579																																																	0																																										SO:0001589	frameshift_variant	57722				CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2497dupG	15.37:g.65681664_65681664dupC	ENSP00000319623:p.Pro833fs		Q9HCE4	Frame_Shift_Ins	INS	ENST00000352385.2	37	CCDS10206.1																																																																																				0.579	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2		NM_020962	
ITGA1	3672	broad.mit.edu;ucsc.edu	37	5	52145320	52145320	+	Splice_Site	SNP	G	G	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr5:52145320G>T	ENST00000282588.6	+	2	640		c.e2+1			NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1						activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)	p.?(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				AAGGAAAATGGTAAGCCAGTG	0.318																																																	1	Unknown(1)	kidney(1)											96.0	97.0	96.0					5																	52145320		2203	4300	6503	SO:0001630	splice_region_variant	3672			X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.182+1G>T	5.37:g.52145320G>T			B2RNU0	Splice_Site	SNP	ENST00000282588.6	37	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158652	0.78226	.	.	ENSG00000213949	ENST00000282588	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.314	0.94204	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGA1	52181077	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	8.318000	0.89990	2.932000	0.99384	0.644000	0.83932	.		0.318	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3		NM_181501	Intron
KLF9	687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	73027946	73027946	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr9:73027946C>A	ENST00000377126.2	-	1	1594	c.334G>T	c.(334-336)Gag>Tag	p.E112*		NM_001206.2	NP_001197.1	Q13886	KLF9_HUMAN	Kruppel-like factor 9	112	Asp/Glu-rich (acidic).				cellular response to thyroid hormone stimulus (GO:0097067)|embryo implantation (GO:0007566)|progesterone receptor signaling pathway (GO:0050847)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E112*(1)		endometrium(2)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	9						TGTCTCTCCTCCGGGCTGTGG	0.627																																																	1	Substitution - Nonsense(1)	kidney(1)											107.0	102.0	104.0					9																	73027946		2203	4300	6503	SO:0001587	stop_gained	687			BC069431	CCDS6633.1	9q21.11	2013-01-08	2004-11-29	2004-12-01	ENSG00000119138	ENSG00000119138		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	1123	protein-coding gene	gene with protein product		602902	"""basic transcription element binding protein 1"""	BTEB1		1356762	Standard	NM_001206		Approved		uc004aht.3	Q13886	OTTHUMG00000019991	ENST00000377126.2:c.334G>T	9.37:g.73027946C>A	ENSP00000366330:p.Glu112*		B2R943|Q16196	Nonsense_Mutation	SNP	ENST00000377126.2	37	CCDS6633.1	.	.	.	.	.	.	.	.	.	.	C	48	14.745859	0.99808	.	.	ENSG00000119138	ENST00000377126	.	.	.	4.85	4.85	0.62838	.	0.097710	0.42682	D	0.000674	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	16.7593	0.85507	0.0:1.0:0.0:0.0	.	.	.	.	X	112	.	ENSP00000366330:E112X	E	-	1	0	KLF9	72217766	0.866000	0.29940	0.993000	0.49108	0.984000	0.73092	2.647000	0.46639	2.250000	0.74265	0.557000	0.71058	GAG		0.627	KLF9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052602.1		NM_001206	
RP11-467H10.2	0	broad.mit.edu	37	7	76681226	76681226	+	RNA	SNP	G	G	C	rs200475663	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr7:76681226G>C	ENST00000459742.1	+	0	58																											TGTCACACTTGAAGGAGGCAG	0.453																																																	0																																												100132832																															7.37:g.76681226G>C				RNA	SNP	ENST00000459742.1	37																																																																																					0.453	RP11-467H10.2-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473089.1			
LTBR	4055	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	6495606	6495606	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr12:6495606G>T	ENST00000228918.4	+	6	989	c.663G>T	c.(661-663)atG>atT	p.M221I	LTBR_ENST00000541102.1_Missense_Mutation_p.M114I|LTBR_ENST00000543190.1_3'UTR|LTBR_ENST00000539925.1_Missense_Mutation_p.M202I	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	221					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.M221I(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						CCCCAGAGATGTCAGGTGAGG	0.547																																																	1	Substitution - Missense(1)	kidney(1)											45.0	44.0	44.0					12																	6495606		2203	4300	6503	SO:0001583	missense	4055			L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"""Tumor necrosis factor receptor superfamily"""	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.663G>T	12.37:g.6495606G>T	ENSP00000228918:p.Met221Ile		B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	37	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	G	9.184	1.024228	0.19433	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000536876;ENST00000541102	D;D;D;T	0.89196	-2.1;-2.1;-2.48;-0.16	4.4	4.4	0.53042	.	2.378430	0.01614	N	0.022682	D	0.86029	0.5835	L	0.51422	1.61	0.25676	N	0.985844	P;B;B	0.36535	0.557;0.421;0.421	B;B;B	0.28139	0.086;0.039;0.039	T	0.72070	-0.4401	10	0.22109	T	0.4	-0.0138	12.3627	0.55213	0.0:0.0:1.0:0.0	.	202;202;221	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	I	202;221;114;216;114	ENSP00000440875:M202I;ENSP00000228918:M221I;ENSP00000437647:M216I;ENSP00000438605:M114I	ENSP00000228918:M221I	M	+	3	0	LTBR	6365867	0.977000	0.34250	0.988000	0.46212	0.055000	0.15305	1.204000	0.32296	2.290000	0.77057	0.561000	0.74099	ATG		0.547	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			
MFSD9	84804	hgsc.bcm.edu	37	2	103353153	103353153	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:103353153delG	ENST00000258436.5	-	1	160	c.117delC	c.(115-117)gccfs	p.A39fs	TMEM182_ENST00000409528.1_5'Flank|TMEM182_ENST00000409173.1_5'Flank	NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	39					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						GGGCTCCGACGGCACCGGAGT	0.657																																																	0										0,4262		0,0,2131	33.0	39.0	37.0			-2.3	0.0	2		37	1,8243		0,1,4121	no	frameshift	MFSD9	NM_032718.3		0,1,6252	A1A1,A1R,RR		0.0121,0.0,0.0080			103353153	1,12505	2203	4300	6503	SO:0001589	frameshift_variant	84804				CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.117delC	2.37:g.103353153delG	ENSP00000258436:p.Ala39fs		Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Frame_Shift_Del	DEL	ENST00000258436.5	37	CCDS2063.1																																																																																				0.657	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2		NM_032718	
MUC4	4585	hgsc.bcm.edu	37	3	195510073	195510073	+	Missense_Mutation	SNP	G	G	A	rs200663432	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:195510073G>A	ENST00000463781.3	-	2	8837	c.8378C>T	c.(8377-8379)gCa>gTa	p.A2793V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2793V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGG	0.587													.|||	15	0.00299521	0.0113	0.0	5008	,	,		6295	0.0		0.0	False		,,,				2504	0.0																0													57.0	33.0	41.0					3																	195510073		689	1521	2210	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8378C>T	3.37:g.195510073G>A	ENSP00000417498:p.Ala2793Val		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	2.540	-0.306588	0.05458	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.54	0.918	-0.419	0.12340	.	.	.	.	.	T	0.12689	0.0308	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30090	-0.9990	8	.	.	.	.	5.3055	0.15801	0.579:0.0:0.421:0.0	.	2665	E7ESK3	.	V	2793	ENSP00000417498:A2793V;ENSP00000420243:A2793V	.	A	-	2	0	MUC4	196994852	0.000000	0.05858	0.034000	0.17996	0.015000	0.08874	0.293000	0.19029	-1.755000	0.01320	-1.973000	0.00462	GCA		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195510156	195510156	+	Silent	SNP	G	G	A	rs201141296	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:195510156G>A	ENST00000463781.3	-	2	8754	c.8295C>T	c.(8293-8295)caC>caT	p.H2765H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2765H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H2765H(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.572													.|||	185	0.0369409	0.0129	0.0447	5008	,	,		4806	0.0298		0.0437	False		,,,				2504	0.0644																1	Substitution - coding silent(1)	prostate(1)											28.0	17.0	21.0					3																	195510156		686	1527	2213	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8295C>T	3.37:g.195510156G>A			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
ORC4	5000	hgsc.bcm.edu;ucsc.edu	37	2	148695897	148695897	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:148695897C>G	ENST00000392857.5	-	12	1131	c.1024G>C	c.(1024-1026)Gag>Cag	p.E342Q	ORC4_ENST00000488761.1_5'Flank|ORC4_ENST00000536575.1_Missense_Mutation_p.E258Q|AC009480.1_ENST00000584553.1_RNA|ORC4_ENST00000392858.1_Missense_Mutation_p.E342Q|ORC4_ENST00000540442.1_Missense_Mutation_p.E268Q|ORC4_ENST00000542387.1_Missense_Mutation_p.E125Q|ORC4_ENST00000535373.1_Missense_Mutation_p.E342Q|ORC4_ENST00000264169.2_Missense_Mutation_p.E342Q	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	342					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						TTAAATGGCTCTTCCTCATAG	0.318																																																	0													68.0	77.0	74.0					2																	148695897		2200	4298	6498	SO:0001583	missense	5000			AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.1024G>C	2.37:g.148695897C>G	ENSP00000376597:p.Glu342Gln		B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352267	0.61183	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000536575;ENST00000392857;ENST00000542387	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.68274	0.2983	L	0.48362	1.52	0.80722	D	1	P;B	0.36392	0.551;0.307	B;B	0.28011	0.085;0.055	T	0.66384	-0.5937	10	0.33141	T	0.24	-14.2119	20.3812	0.98933	0.0:1.0:0.0:0.0	.	342;342	B7Z2M4;O43929	.;ORC4_HUMAN	Q	342;342;342;268;258;342;125	ENSP00000264169:E342Q;ENSP00000441953:E342Q;ENSP00000376598:E342Q;ENSP00000438326:E268Q;ENSP00000441502:E258Q;ENSP00000376597:E342Q;ENSP00000437440:E125Q	ENSP00000264169:E342Q	E	-	1	0	ORC4	148412367	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.281000	0.78621	2.821000	0.97095	0.650000	0.86243	GAG		0.318	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3		NM_181742	
PCDH15	65217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	55700700	55700700	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr10:55700700G>A	ENST00000320301.6	-	24	3552	c.3158C>T	c.(3157-3159)aCc>aTc	p.T1053I	PCDH15_ENST00000395433.1_Missense_Mutation_p.T1031I|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.T1053I|PCDH15_ENST00000395445.1_Missense_Mutation_p.T1060I|PCDH15_ENST00000395430.1_Missense_Mutation_p.T1053I|PCDH15_ENST00000395432.2_Missense_Mutation_p.T1016I|PCDH15_ENST00000409834.1_Missense_Mutation_p.T664I|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.T1060I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.T1058I|PCDH15_ENST00000437009.1_Missense_Mutation_p.T982I|PCDH15_ENST00000395438.1_Missense_Mutation_p.T1053I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1053	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.T1053I(2)|p.T1058I(2)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ACCAACCATGGTCCCTTTGGT	0.358										HNSCC(58;0.16)																																							4	Substitution - Missense(4)	kidney(4)											100.0	97.0	98.0					10																	55700700		2203	4300	6503	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3158C>T	10.37:g.55700700G>A	ENSP00000322604:p.Thr1053Ile		A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915937	0.52546	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.37	5.37	0.77165	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.78572	0.4304	M	0.91663	3.23	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.999;0.999;1.0;1.0;0.999;0.999;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.992;0.997;0.999;0.997;0.997;0.997;0.992;0.985;0.997;0.998;0.99;0.985;0.999	T	0.83306	-0.0025	9	0.87932	D	0	.	16.3821	0.83472	0.0:0.0:1.0:0.0	.	1031;1053;1053;1058;982;1016;1053;1053;1060;1060;1053;1058;1053	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	I	1060;1058;1053;1053;664;1060;1016;1053;1031;1053;1053;1058;982	ENSP00000363076:T1060I;ENSP00000410304:T1058I;ENSP00000378826:T1053I;ENSP00000386693:T664I;ENSP00000378832:T1060I;ENSP00000378820:T1016I;ENSP00000354950:T1053I;ENSP00000378821:T1031I;ENSP00000322604:T1053I;ENSP00000378818:T1053I;ENSP00000412628:T982I	ENSP00000322604:T1053I	T	-	2	0	PCDH15	55370706	1.000000	0.71417	0.544000	0.28141	0.025000	0.11179	6.882000	0.75589	2.671000	0.90904	0.585000	0.79938	ACC		0.358	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2		NM_033056	
PCDHGA3	56112	broad.mit.edu	37	5	140725547	140725547	+	Silent	SNP	C	C	T	rs544633115	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr5:140725547C>T	ENST00000253812.6	+	1	1947	c.1947C>T	c.(1945-1947)caC>caT	p.H649H	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	649	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H649H(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGGACCACGGCCAGCCCC	0.711													.|||	8	0.00159744	0.0053	0.0	5008	,	,		14827	0.0		0.001	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											12.0	19.0	17.0					5																	140725547		2129	4231	6360	SO:0001819	synonymous_variant	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1947C>T	5.37:g.140725547C>T			Q9Y5D4	Silent	SNP	ENST00000253812.6	37	CCDS47290.1																																																																																				0.711	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1		NM_018916	
PRUNE2	158471	broad.mit.edu	37	9	79469063	79469063	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr9:79469063T>C	ENST00000376718.3	-	2	221	c.98A>G	c.(97-99)gAt>gGt	p.D33G	PRUNE2_ENST00000428286.1_5'UTR|PRUNE2_ENST00000376713.3_Missense_Mutation_p.D33G	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	33					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.D33G(2)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AATGAGAGAATCCAAGTCACA	0.353																																																	2	Substitution - Missense(2)	kidney(2)											121.0	106.0	111.0					9																	79469063		2203	4300	6503	SO:0001583	missense	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.98A>G	9.37:g.79469063T>C	ENSP00000365908:p.Asp33Gly		B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735035	0.69189	.	.	ENSG00000106772	ENST00000376718;ENST00000422033;ENST00000376713	T;T	0.16897	2.31;2.31	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	M	0.67517	2.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.31081	-0.9956	10	0.87932	D	0	.	15.7343	0.77831	0.0:0.0:0.0:1.0	.	33;33	Q8WUY3;D6RTK6	PRUN2_HUMAN;.	G	33;32;33	ENSP00000365908:D33G;ENSP00000365903:D33G	ENSP00000365903:D33G	D	-	2	0	PRUNE2	78658883	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	5.203000	0.65174	2.115000	0.64714	0.533000	0.62120	GAT		0.353	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2		NM_138818	
RASGRP2	10235	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64503123	64503123	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr11:64503123G>A	ENST00000354024.3	-	11	1439	c.1187C>T	c.(1186-1188)aCg>aTg	p.T396M	RASGRP2_ENST00000377497.3_Missense_Mutation_p.T396M|RASGRP2_ENST00000377494.1_Missense_Mutation_p.T396M|RASGRP2_ENST00000394432.3_Missense_Mutation_p.T396M	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	396					blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.T458M(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGTGCAACTCGTGGGGCTGGT	0.662																																																	1	Substitution - Missense(1)	kidney(1)											29.0	31.0	30.0					11																	64503123		2200	4296	6496	SO:0001583	missense	10235			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1187C>T	11.37:g.64503123G>A	ENSP00000338864:p.Thr396Met		A6NDC7|O00538|Q9UL65	Missense_Mutation	SNP	ENST00000354024.3	37	CCDS31598.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.695665	0.48202	.	.	ENSG00000068831	ENST00000377494;ENST00000394432;ENST00000377497;ENST00000354024	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	4.83	2.93	0.34026	Ras guanine nucleotide exchange factor, domain (1);	0.760869	0.12616	N	0.453424	T	0.27205	0.0667	L	0.27053	0.805	0.80722	D	1	P;P	0.43633	0.63;0.813	B;B	0.33568	0.081;0.166	T	0.02983	-1.1086	10	0.37606	T	0.19	-21.3443	5.0129	0.14321	0.1803:0.0:0.6546:0.165	.	396;396	Q7LDG7;A6NDC7	GRP2_HUMAN;.	M	396	ENSP00000366714:T396M;ENSP00000377953:T396M;ENSP00000366717:T396M;ENSP00000338864:T396M	ENSP00000338864:T396M	T	-	2	0	RASGRP2	64259699	0.128000	0.22383	0.485000	0.27403	0.742000	0.42306	0.559000	0.23485	0.559000	0.29153	0.561000	0.74099	ACG		0.662	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1		NM_153819	
RRAD	6236	broad.mit.edu	37	16	66956073	66956073	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr16:66956073G>T	ENST00000299759.6	-	5	1083	c.833C>A	c.(832-834)gCg>gAg	p.A278E	RRAD_ENST00000420652.1_Missense_Mutation_p.A278E			P55042	RAD_HUMAN	Ras-related associated with diabetes	278	Calmodulin-binding.				small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A278E(6)		endometrium(2)|kidney(4)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GAAGCGCTTCGCCTTTTTGCC	0.612																																																	6	Substitution - Missense(6)	kidney(4)|prostate(1)|endometrium(1)											94.0	75.0	81.0					16																	66956073		2200	4300	6500	SO:0001583	missense	6236			L24564	CCDS10824.1	16q22	2014-05-09			ENSG00000166592	ENSG00000166592			10446	protein-coding gene	gene with protein product		179503				7859947	Standard	NM_004165		Approved	REM3, RAD	uc002eqo.2	P55042	OTTHUMG00000137511	ENST00000299759.6:c.833C>A	16.37:g.66956073G>T	ENSP00000299759:p.Ala278Glu		Q96F39	Missense_Mutation	SNP	ENST00000299759.6	37	CCDS10824.1	.	.	.	.	.	.	.	.	.	.	G	36	5.625454	0.96671	.	.	ENSG00000166592	ENST00000420652;ENST00000299759	T;T	0.68181	-0.31;-0.31	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.83524	0.5273	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84232	0.0467	10	0.87932	D	0	.	20.328	0.98708	0.0:0.0:1.0:0.0	.	278	P55042	RAD_HUMAN	E	278	ENSP00000388744:A278E;ENSP00000299759:A278E	ENSP00000299759:A278E	A	-	2	0	RRAD	65513574	1.000000	0.71417	0.969000	0.41365	0.983000	0.72400	9.471000	0.97696	2.802000	0.96397	0.561000	0.74099	GCG		0.612	RRAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268830.1		NM_004165	
RRM2	6241	hgsc.bcm.edu	37	2	10262859	10262859	+	5'UTR	SNP	G	G	A	rs72542787	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:10262859G>A	ENST00000304567.5	+	0	3				RRM2_ENST00000360566.2_Silent_p.G38G|RP11-254F7.4_ENST00000607140.1_lincRNA	NM_001034.3	NP_001025.1	P31350	RIR2_HUMAN	ribonucleotide reductase M2						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|skin(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)|OV - Ovarian serous cystadenocarcinoma(76;0.221)	Cladribine(DB00242)|Gallium nitrate(DB05260)	GGAGTGAGGGGTCGCCCGTGC	0.682													G|||	204	0.0407348	0.0265	0.0418	5008	,	,		12237	0.001		0.0875	False		,,,				2504	0.0521																0								G		49,1335		1,47,644	27.0	48.0	42.0		114	-4.5	0.0	2	dbSNP_130	42	325,2855		15,295,1280	no	coding-synonymous	RRM2	NM_001165931.1		16,342,1924	AA,AG,GG		10.2201,3.5405,8.1946		38/450	10262859	374,4190	692	1590	2282	SO:0001623	5_prime_UTR_variant	6241				CCDS1669.1, CCDS54334.1	2p25-p24	2012-10-02	2009-07-10		ENSG00000171848	ENSG00000171848	1.17.4.1		10452	protein-coding gene	gene with protein product		180390	"""ribonucleotide reductase M2 polypeptide"""				Standard	NM_001034		Approved		uc021vdr.1	P31350	OTTHUMG00000090449	ENST00000304567.5:c.-67G>A	2.37:g.10262859G>A			B2R9B5|J3KP43|Q5WRU7	Silent	SNP	ENST00000304567.5	37	CCDS1669.1																																																																																				0.682	RRM2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364902.2			
SPOCD1	90853	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	32266115	32266115	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr1:32266115A>T	ENST00000360482.2	-	4	1658	c.1529T>A	c.(1528-1530)gTc>gAc	p.V510D	SPOCD1_ENST00000533231.1_Missense_Mutation_p.V510D|SPOCD1_ENST00000257100.3_Missense_Mutation_p.V3D|SPOCD1_ENST00000373648.2_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	510					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.V510D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		GGGTGAGCTGACCTCCATCAA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											41.0	35.0	37.0					1																	32266115		2203	4300	6503	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1529T>A	1.37:g.32266115A>T	ENSP00000353670:p.Val510Asp		Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607814	0.46527	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000533231;ENST00000528791;ENST00000525930	T;T;T	0.57273	0.41;1.42;1.42	4.96	-2.66	0.06077	.	.	.	.	.	T	0.49677	0.1571	N	0.19112	0.55	0.19300	N	0.999978	D;D	0.58268	0.982;0.969	P;P	0.59546	0.859;0.727	T	0.52313	-0.8592	9	0.87932	D	0	-6.0623	10.7012	0.45928	0.4145:0.0:0.5855:0.0	.	510;510	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	D	3;510;510;3;3	ENSP00000257100:V3D;ENSP00000353670:V510D;ENSP00000435851:V510D	ENSP00000257100:V3D	V	-	2	0	SPOCD1	32038702	0.000000	0.05858	0.434000	0.26772	0.448000	0.32197	-0.192000	0.09587	-0.377000	0.07930	-0.263000	0.10527	GTC		0.607	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1		NM_144569	
ST3GAL3	6487	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	44386570	44386570	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr1:44386570T>A	ENST00000361392.4	+	11	1185	c.1008T>A	c.(1006-1008)taT>taA	p.Y336*	ST3GAL3_ENST00000531816.1_Intron|ST3GAL3_ENST00000528371.1_Intron|ST3GAL3_ENST00000361812.4_Intron|ST3GAL3_ENST00000372375.2_Nonsense_Mutation_p.Y390*|ST3GAL3_ENST00000372367.1_Intron|ST3GAL3_ENST00000262915.3_Nonsense_Mutation_p.Y405*|ST3GAL3_ENST00000533933.1_Intron|ST3GAL3_ENST00000335430.6_3'UTR|ST3GAL3_ENST00000372362.2_Intron|ST3GAL3_ENST00000372366.1_Intron|ST3GAL3_ENST00000372372.2_Nonsense_Mutation_p.Y374*|ST3GAL3_ENST00000372365.1_Intron|ST3GAL3_ENST00000531993.1_Intron|ST3GAL3_ENST00000351035.3_Nonsense_Mutation_p.Y374*|ST3GAL3_ENST00000545417.1_Intron|ST3GAL3_ENST00000347631.2_Nonsense_Mutation_p.Y351*|ST3GAL3_ENST00000361746.4_Nonsense_Mutation_p.Y405*|ST3GAL3_ENST00000361400.4_Nonsense_Mutation_p.Y320*|ST3GAL3_ENST00000531451.1_Intron|ST3GAL3_ENST00000330208.2_Intron|ST3GAL3_ENST00000372374.2_Nonsense_Mutation_p.Y305*|ST3GAL3_ENST00000372369.1_Nonsense_Mutation_p.Y306*|ST3GAL3_ENST00000372368.2_Nonsense_Mutation_p.Y390*|ST3GAL3_ENST00000332628.6_Nonsense_Mutation_p.Y305*|ST3GAL3_ENST00000372377.4_3'UTR|ST3GAL3_ENST00000353126.3_Intron	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	336					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)	p.Y405*(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				TGCACTACTATGAGACCGTTC	0.577																																																	1	Substitution - Nonsense(1)	kidney(1)											83.0	61.0	68.0					1																	44386570		2203	4300	6503	SO:0001587	stop_gained	6487			L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"""Sialyltransferases"""	10866	protein-coding gene	gene with protein product	"""ST3Gal III"""	606494	"""sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)"", ""mental retardation, non-syndromic, autosomal recessive, 12"""	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.1008T>A	1.37:g.44386570T>A	ENSP00000355341:p.Tyr336*		A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Nonsense_Mutation	SNP	ENST00000361392.4	37	CCDS492.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	37|37	6.130264|6.130264	0.97310|0.97310	.|.	.|.	ENSG00000126091|ENSG00000126091	ENST00000490502|ENST00000361392;ENST00000361400;ENST00000262915;ENST00000372375;ENST00000351035;ENST00000372374;ENST00000347631;ENST00000372369;ENST00000361746;ENST00000372368;ENST00000372372;ENST00000332628	.|.	.|.	.|.	4.67|4.67	1.96|1.96	0.26148|0.26148	.|.	.|0.135487	.|0.51477	.|D	.|0.000089	T|.	0.27241|.	0.0668|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.15578|.	-1.0432|.	4|.	.|0.02654	.|T	.|1	.|.	8.1693|8.1693	0.31245|0.31245	0.0:0.2449:0.0:0.7551|0.0:0.2449:0.0:0.7551	.|.	.|.	.|.	.|.	K|X	135|336;320;405;390;374;305;351;306;405;390;374;305	.|.	.|ENSP00000262915:Y405X	M|Y	+|+	2|3	0|2	ST3GAL3|ST3GAL3	44159157|44159157	0.980000|0.980000	0.34600|0.34600	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.183000|0.183000	0.16919|0.16919	0.735000|0.735000	0.32537|0.32537	0.482000|0.482000	0.46254|0.46254	ATG|TAT		0.577	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1		NM_174963	
STK31	56164	broad.mit.edu	37	7	23750185	23750185	+	Intron	SNP	C	C	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr7:23750185C>A	ENST00000355870.3	+	1	169				STK31_ENST00000433467.2_Intron|STK31_ENST00000428484.1_5'UTR|STK31_ENST00000354639.3_5'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31							acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TCCATGAAGACGCGGTCACGC	0.512																																																	0																																										SO:0001627	intron_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.50+231C>A	7.37:g.23750185C>A			B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Intron	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				0.512	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2		NM_031414	
TARM1	441864	hgsc.bcm.edu	37	19	54573304	54573304	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr19:54573304T>C	ENST00000432826.1	-	5	793	c.769A>G	c.(769-771)Agc>Ggc	p.S257G	TARM1_ENST00000446034.2_Missense_Mutation_p.S265G	NM_001135686.1	NP_001129158.2	B6A8C7	TARM1_HUMAN	T cell-interacting, activating receptor on myeloid cells 1	257						integral component of membrane (GO:0016021)				endometrium(1)|stomach(2)	3						ACATTCCGGCTGTACCAGGCC	0.547																																																	0													77.0	75.0	76.0					19																	54573304		692	1591	2283	SO:0001583	missense	441864				CCDS46173.1	19q13.42	2013-01-29			ENSG00000248385	ENSG00000248385		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	37250	protein-coding gene	gene with protein product							Standard	XM_005258952		Approved		uc010yei.1	B6A8C7		ENST00000432826.1:c.769A>G	19.37:g.54573304T>C	ENSP00000439454:p.Ser257Gly		B4DWY4	Missense_Mutation	SNP	ENST00000432826.1	37	CCDS46173.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402378	0.42613	.	.	ENSG00000248385	ENST00000432826;ENST00000446034	T;T	0.00534	6.89;6.74	2.98	2.98	0.34508	.	.	.	.	.	T	0.01254	0.0041	M	0.81112	2.525	0.09310	N	1	D	0.55172	0.97	P	0.51833	0.681	T	0.47275	-0.9130	9	0.51188	T	0.08	.	7.8033	0.29187	0.0:0.0:0.0:1.0	.	257	B6A8C7	TARM1_HUMAN	G	257;265	ENSP00000439454:S257G;ENSP00000441055:S265G	ENSP00000439454:S257G	S	-	1	0	TARM1	59265116	0.008000	0.16893	0.017000	0.16124	0.008000	0.06430	0.164000	0.16542	1.626000	0.50381	0.413000	0.27773	AGC		0.547	TARM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465679.1		NM_001135686	
TEX14	56155	broad.mit.edu	37	17	56651592	56651592	+	Silent	SNP	T	T	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr17:56651592T>C	ENST00000240361.8	-	23	3562	c.3477A>G	c.(3475-3477)gaA>gaG	p.E1159E	TEX14_ENST00000349033.5_Silent_p.E1113E|TEX14_ENST00000389934.3_Silent_p.E1153E			Q8IWB6	TEX14_HUMAN	testis expressed 14	1159					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.E1159E(1)|p.E1113E(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGATGTCTCTTCTTGTTCAT	0.383																																																	2	Substitution - coding silent(2)	kidney(2)											281.0	233.0	249.0					17																	56651592		2203	4300	6503	SO:0001819	synonymous_variant	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.3477A>G	17.37:g.56651592T>C			A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																				0.383	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			
UHRF1	29128	hgsc.bcm.edu	37	19	4954679	4954680	+	RNA	INS	-	-	C	rs397767650|rs55946225	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr19:4954679_4954680insC	ENST00000592666.1	+	0	2551_2552							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		CCCGAGCAGGGCGGGTCCCCGC	0.683																																																	0									,	3444,10		1720,4,3					,	-6.1	0.0		dbSNP_131	9	7668,10		3830,8,1	no	frameshift,frameshift	UHRF1	NM_013282.3,NM_001048201.1	,	5550,12,4	A1A1,A1R,RR		0.1302,0.2895,0.1797	,	,		11112,20						29128			AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"""RING-type (C3HC4) zinc fingers"""	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4954680_4954680dupC			A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Frame_Shift_Ins	INS	ENST00000592666.1	37																																																																																					0.683	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1		NM_001048201	
LOC100288069	100288069	broad.mit.edu	37	1	713786	713787	+	lincRNA	INS	-	-	GCT	rs142583823|rs372604488		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr1:713786_713787insGCT	ENST00000428504.1	-	0	219_220					NR_033908.1																						catgttgctaggctgctcttgg	0.535																																																	0																																												0																															1.37:g.713790_713792dupGCT				RNA	INS	ENST00000428504.1	37																																																																																					0.535	RP11-206L10.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000006889.1			
ZNF813	126017	broad.mit.edu	37	19	54007225	54007225	+	IGR	SNP	C	C	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr19:54007225C>T	ENST00000396421.4	+	0	300				CTD-2224J9.8_ENST00000601966.1_RNA			Q6ZN06	ZN813_HUMAN	zinc finger protein 813						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		GGGGCTCATGCTCTGGGGCAG	0.597																																																	0																																										SO:0001628	intergenic_variant	0			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309		19.37:g.54007225C>T				RNA	SNP	ENST00000396421.4	37																																																																																					0.597	ZNF813-201	KNOWN	basic	protein_coding	protein_coding			NM_001004301	
NDUFS1	4719	broad.mit.edu	37	2	206981155	206981155	+	3'UTR	DEL	C	C	-	rs71410864	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr2:206981155delC	ENST00000233190.6	-	0	10204				AC007383.4_ENST00000453039.1_RNA	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)						apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGGCAGGGCGCGGCAGGTGCC	0.627													C|C|-|deletion	1897	0.378794	0.4841	0.5432	5008	,	,		14111	0.2133		0.4364	False		,,,				2504	0.2311																0																																										SO:0001624	3_prime_UTR_variant	0				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.*7754G>-	2.37:g.206981155delC			B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	RNA	DEL	ENST00000233190.6	37	CCDS2366.1																																																																																				0.627	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4		NM_005006	
HMGB1P5	10354	broad.mit.edu	37	3	22424176	22424176	+	RNA	DEL	G	G	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:22424176delG	ENST00000451497.1	+	0	741									high mobility group box 1 pseudogene 5																		GGTACAGTATGGGGGTTGTAA	0.388																																																	0																																												0			AF076677		3p24	2011-09-21	2011-04-05	2010-10-15	ENSG00000132967	ENSG00000132967		"""High mobility group / HMG-box pseudogenes"""	4997	pseudogene	pseudogene			"""high-mobility group (nonhistone chromosomal) protein 1-like 5"", ""high-mobility group (nonhistone chromosomal) protein 1-like 5 pseudogene"", ""high-mobility group box 1-like 5 pseudogene"", ""high-mobility group box 1-like 15"", ""high-mobility group box 1 pseudogene 2"", ""high-mobility group box 1-like 5"", ""high-mobility group box 1 pseudogene 5"""	HMG1L5, HMGB1L15, HMGB1P2, HMGB1L5		9925949	Standard	NG_000897		Approved				OTTHUMG00000155591		3.37:g.22424176delG				RNA	DEL	ENST00000451497.1	37																																																																																					0.388	HMGB1P5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340803.1		NG_000897	
VCP	7415	broad.mit.edu;ucsc.edu	37	9	35068351	35068351	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr9:35068351C>A	ENST00000358901.6	-	2	921	c.26G>T	c.(25-27)gGt>gTt	p.G9V		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	9					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)	p.G9V(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TAGGTCATCACCTTTTGAACT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											205.0	187.0	193.0					9																	35068351		2203	4300	6503	SO:0001583	missense	7415			AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.26G>T	9.37:g.35068351C>A	ENSP00000351777:p.Gly9Val		B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	37	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.295742	0.40594	.	.	ENSG00000165280	ENST00000358901	D	0.94232	-3.38	6.06	5.14	0.70334	.	0.171224	0.51477	D	0.000088	D	0.88127	0.6353	N	0.22421	0.69	0.80722	D	1	B	0.20368	0.044	B	0.20184	0.028	T	0.83285	-0.0036	10	0.35671	T	0.21	-6.2354	15.0745	0.72066	0.0:0.7958:0.2041:0.0	.	9	P55072	TERA_HUMAN	V	9	ENSP00000351777:G9V	ENSP00000351777:G9V	G	-	2	0	VCP	35058351	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.664000	0.46783	2.882000	0.98803	0.655000	0.94253	GGT		0.448	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1		NM_007126	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188204	10188204	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:10188204delT	ENST00000256474.2	+	2	1187	c.347delT	c.(346-348)cttfs	p.L116fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	116	Involved in binding to CCT complex.		L -> V (in VHLD). {ECO:0000269|PubMed:8730290}.		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.?(2)|p.W117fs*14(2)|p.H115fs*15(1)|p.W117fs*42(1)|p.H115fs*41(1)|p.H115fs*42(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)		ATAGGTCACCTTTGGCTCTTC	0.527		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"""	8	Deletion - Frameshift(6)|Unknown(2)	kidney(8)											173.0	161.0	165.0					3																	10188204		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.347delT	3.37:g.10188204delT	ENSP00000256474:p.Leu116fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.527	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
CFAP44	55779	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	113127995	113127995	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b8480571-ee08-4fa1-b509-1331a8fbc075	c246767f-2df0-4836-b43f-a771f0782118	g.chr3:113127995T>G	ENST00000295868.2	-	7	1010	c.848A>C	c.(847-849)gAt>gCt	p.D283A	WDR52-AS1_ENST00000473329.1_RNA|WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.D283A	NM_018338.3	NP_060808.2												p.D283A(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						CTCTTCCTTATCAGGATTGAA	0.413																																																	1	Substitution - Missense(1)	kidney(1)											111.0	110.0	110.0					3																	113127995		2203	4300	6503	SO:0001583	missense	55779																														ENST00000295868.2:c.848A>C	3.37:g.113127995T>G	ENSP00000295868:p.Asp283Ala			Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	T	15.95	2.985325	0.53934	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.71698	-0.59;2.89	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.67268	0.2875	M	0.68317	2.08	0.80722	D	1	B	0.31910	0.346	B	0.25140	0.058	T	0.65269	-0.6209	9	0.25751	T	0.34	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	283	Q96MT7	WDR52_HUMAN	A	283	ENSP00000377428:D283A;ENSP00000295868:D283A	ENSP00000295868:D283A	D	-	2	0	WDR52	114610685	1.000000	0.71417	0.941000	0.38009	0.834000	0.47266	5.629000	0.67798	2.210000	0.71456	0.460000	0.39030	GAT		0.413	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			
