#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ADAMTS12	81792	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	33881335	33881335	+	Silent	SNP	G	G	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:33881335G>C	ENST00000504830.1	-	2	713	c.378C>G	c.(376-378)ctC>ctG	p.L126L	ADAMTS12_ENST00000352040.3_Silent_p.L126L|ADAMTS12_ENST00000515401.1_Silent_p.L126L	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	126					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L126L(2)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TAACATGGGAGAGGTTCCCAT	0.502										HNSCC(64;0.19)																																							2	Substitution - coding silent(2)	kidney(2)											86.0	83.0	84.0					5																	33881335		2203	4300	6503	SO:0001819	synonymous_variant	81792			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.378C>G	5.37:g.33881335G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																				0.502	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2		NM_030955	
ADAMTS2	9509	broad.mit.edu;hgsc.bcm.edu	37	5	178548695	178548695	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:178548695C>G	ENST00000251582.7	-	21	3246	c.3145G>C	c.(3145-3147)Gac>Cac	p.D1049H		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1049					collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D1049H(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GAGTCGGGGTCCGGGCGGGAC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											182.0	194.0	190.0					5																	178548695		2203	4300	6503	SO:0001583	missense	9509			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3145G>C	5.37:g.178548695C>G	ENSP00000251582:p.Asp1049His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.598671	0.46318	.	.	ENSG00000087116	ENST00000251582	T	0.60040	0.22	5.74	4.87	0.63330	.	0.099352	0.43260	D	0.000584	T	0.61375	0.2342	M	0.62723	1.935	0.80722	D	1	P	0.39216	0.664	P	0.44772	0.46	T	0.62081	-0.6929	10	0.42905	T	0.14	.	13.6324	0.62202	0.0:0.9262:0.0:0.0738	.	1049	O95450	ATS2_HUMAN	H	1049	ENSP00000251582:D1049H	ENSP00000251582:D1049H	D	-	1	0	ADAMTS2	178481301	0.999000	0.42202	0.180000	0.23079	0.851000	0.48451	4.232000	0.58645	1.433000	0.47394	0.555000	0.69702	GAC		0.622	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1		NM_014244	
ADAMTS5	11096	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	28337626	28337626	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr21:28337626G>A	ENST00000284987.5	-	1	1206	c.1085C>T	c.(1084-1086)gCt>gTt	p.A362V		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	362	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A362V(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AAACAGGATAGCTGCATCGTA	0.552																																					Esophageal Squamous(53;683 1080 10100 14424 45938)												1	Substitution - Missense(1)	kidney(1)											144.0	124.0	131.0					21																	28337626		2203	4300	6503	SO:0001583	missense	11096			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1085C>T	21.37:g.28337626G>A	ENSP00000284987:p.Ala362Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	G	31	5.084995	0.94100	.	.	ENSG00000154736	ENST00000284987	T	0.69040	-0.37	5.1	5.1	0.69264	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.291176	0.31673	N	0.007245	D	0.86037	0.5837	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89008	0.3426	10	0.87932	D	0	.	18.7444	0.91787	0.0:0.0:1.0:0.0	.	362	Q9UNA0	ATS5_HUMAN	V	362	ENSP00000284987:A362V	ENSP00000284987:A362V	A	-	2	0	ADAMTS5	27259497	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.701000	0.84566	2.652000	0.90054	0.655000	0.94253	GCT		0.552	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			
ADCY8	114	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	131916170	131916170	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr8:131916170T>G	ENST00000286355.5	-	7	3851	c.1759A>C	c.(1759-1761)Att>Ctt	p.I587L	ADCY8_ENST00000377928.3_Missense_Mutation_p.I587L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	587					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|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)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|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)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.I587L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GGCTGCTTAATTAAGTAAGTT	0.488										HNSCC(32;0.087)																																							1	Substitution - Missense(1)	kidney(1)											142.0	129.0	133.0					8																	131916170		2203	4300	6503	SO:0001583	missense	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1759A>C	8.37:g.131916170T>G	ENSP00000286355:p.Ile587Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	T	36	5.614003	0.96637	.	.	ENSG00000155897	ENST00000286355;ENST00000377928;ENST00000522949	T;T;T	0.77877	-1.13;-1.13;-1.13	6.17	6.17	0.99709	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.67700	2.07	0.46954	D	0.999266	P;B	0.34522	0.455;0.164	D;P	0.72625	0.978;0.706	D	0.87291	0.2299	10	0.46703	T	0.11	.	16.0034	0.80327	0.0:0.0:0.0:1.0	.	587;587	E7EVL1;P40145	.;ADCY8_HUMAN	L	587;587;202	ENSP00000286355:I587L;ENSP00000367161:I587L;ENSP00000428010:I202L	ENSP00000286355:I587L	I	-	1	0	ADCY8	131985352	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.106000	0.64597	2.371000	0.80710	0.533000	0.62120	ATT		0.488	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			
ALDH8A1	64577	hgsc.bcm.edu;ucsc.edu	37	6	135254009	135254009	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr6:135254009G>T	ENST00000265605.2	-	5	822	c.754C>A	c.(754-756)Ctg>Atg	p.L252M	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.L202M|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.L252M	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	252				L -> P (in Ref. 3; BAD96568). {ECO:0000305}.	9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CCCAGCTCCAGGGAGAGCTTT	0.617																																																	0													81.0	84.0	83.0					6																	135254009		2203	4300	6503	SO:0001583	missense	64577			AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.754C>A	6.37:g.135254009G>T	ENSP00000265605:p.Leu252Met	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040374	0.35989	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	D;D;D	0.82984	-1.67;-1.67;-1.67	5.45	3.66	0.41972	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);Aldehyde dehydrogenase, conserved site (1);	0.069187	0.64402	D	0.000013	T	0.81621	0.4861	L	0.55834	1.745	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.79082	-0.1949	10	0.30078	T	0.28	.	8.1092	0.30905	0.3048:0.0:0.6952:0.0	.	202;252;252	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	M	252;252;202	ENSP00000265605:L252M;ENSP00000356819:L252M;ENSP00000356821:L202M	ENSP00000265605:L252M	L	-	1	2	ALDH8A1	135295702	1.000000	0.71417	0.635000	0.29338	0.005000	0.04900	3.857000	0.55972	0.665000	0.31066	0.557000	0.71058	CTG		0.617	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			
ANAPC16	119504	hgsc.bcm.edu	37	10	73992824	73992825	+	Frame_Shift_Ins	INS	-	-	G	rs147406330		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr10:73992824_73992825insG	ENST00000299381.4	+	4	401_402	c.283_284insG	c.(283-285)cggfs	p.R95fs	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	95					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						TGACGAGTGGCGGTTTAAGCCC	0.52																																																	0																																										SO:0001589	frameshift_variant	119504			BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"""Anaphase promoting complex subunits"""	26976	protein-coding gene	gene with protein product	"""centromere protein 27"""	613427	"""chromosome 10 open reading frame 104"""	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.285dupG	10.37:g.73992826_73992826dupG	ENSP00000299381:p.Arg95fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000299381.4	37	CCDS7314.1																																																																																				0.520	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2		NM_173473	
ANGPT4	51378	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	896633	896633	+	Silent	SNP	G	G	A	rs574115140		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr20:896633G>A	ENST00000381922.3	-	1	327	c.225C>T	c.(223-225)aaC>aaT	p.N75N	ANGPT4_ENST00000546022.1_Silent_p.N75N	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	75					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.N75N(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GGTGCAGTGGGTTGGCCAGTG	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19665	0.0		0.0	False		,,,				2504	0.0				Pancreas(181;481 2077 3259 31286 49856)												1	Substitution - coding silent(1)	kidney(1)											123.0	108.0	113.0					20																	896633		2203	4300	6503	SO:0001819	synonymous_variant	51378			AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.225C>T	20.37:g.896633G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																				0.607	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1		NM_015985	
ARL8B	55207	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	5215726	5215726	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:5215726G>C	ENST00000256496.3	+	5	643	c.397G>C	c.(397-399)Gat>Cat	p.D133H	ARL8B_ENST00000419534.2_Intron|ARL8B_ENST00000468010.1_Splice_Site|AC026202.3_ENST00000439325.1_RNA	NM_018184.2	NP_060654.1	Q9NVJ2	ARL8B_HUMAN	ADP-ribosylation factor-like 8B	133					cell cycle (GO:0007049)|cell division (GO:0051301)|chromosome segregation (GO:0007059)|GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)|midbody (GO:0030496)|spindle midzone (GO:0051233)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D133H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)		AAACAAGAGAGATCTTCCTAA	0.313																																																	1	Substitution - Missense(1)	kidney(1)											147.0	158.0	154.0					3																	5215726		2203	4300	6503	SO:0001583	missense	55207			AK001564	CCDS2566.1	3p26.1	2014-05-09	2005-11-03	2005-11-03	ENSG00000134108	ENSG00000134108		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25564	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 10C"""	ARL10C		12477932	Standard	NM_018184		Approved	FLJ10702, Gie1	uc003bqg.3	Q9NVJ2	OTTHUMG00000090463	ENST00000256496.3:c.397G>C	3.37:g.5215726G>C	ENSP00000256496:p.Asp133His	Somatic		WXS	Illumina HiSeq	Phase_I	B4DI85	Missense_Mutation	SNP	ENST00000256496.3	37	CCDS2566.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.718336	0.68844	.	.	ENSG00000134108	ENST00000256496;ENST00000438743	D	0.96856	-4.15	5.24	4.37	0.52481	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.99096	0.9689	H	0.99874	4.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	D	0.98411	1.0572	10	0.87932	D	0	-10.4929	14.0943	0.65010	0.0726:0.0:0.9274:0.0	.	124;133	B4DQT8;Q9NVJ2	.;ARL8B_HUMAN	H	133;185	ENSP00000256496:D133H	ENSP00000256496:D133H	D	+	1	0	ARL8B	5190726	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.507000	0.97996	1.354000	0.45846	0.650000	0.86243	GAT		0.313	ARL8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206910.2		NM_018184	
ATP6V0A4	50617	broad.mit.edu;ucsc.edu	37	7	138417832	138417832	+	Silent	SNP	G	G	A	rs367943974		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr7:138417832G>A	ENST00000310018.2	-	17	1980	c.1698C>T	c.(1696-1698)ttC>ttT	p.F566F	ATP6V0A4_ENST00000393054.1_Silent_p.F566F|ATP6V0A4_ENST00000353492.4_Silent_p.F566F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	566					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.F566F(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GAGTTCTTCTGAAGTATCTGG	0.378																																																	1	Substitution - coding silent(1)	kidney(1)											93.0	89.0	90.0					7																	138417832		2203	4300	6503	SO:0001819	synonymous_variant	50617			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1698C>T	7.37:g.138417832G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																				0.378	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1		NM_020632	
C20orf194	25943	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	3278767	3278767	+	Missense_Mutation	SNP	G	G	C	rs575069868		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr20:3278767G>C	ENST00000252032.9	-	22	1905	c.1838C>G	c.(1837-1839)cCt>cGt	p.P613R	C20orf194_ENST00000498079.1_5'UTR|C20orf194_ENST00000453730.2_Missense_Mutation_p.P351R	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	613								p.P613R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						TGGGAGGTGAGGAAGCAATGA	0.428																																																	1	Substitution - Missense(1)	kidney(1)											132.0	126.0	128.0					20																	3278767		1979	4176	6155	SO:0001583	missense	25943			AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1838C>G	20.37:g.3278767G>C	ENSP00000252032:p.Pro613Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.736988	0.69304	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.34667	2.15;1.35	5.65	4.7	0.59300	.	0.055632	0.64402	D	0.000001	T	0.49490	0.1560	L	0.59436	1.845	0.54753	D	0.999985	D;D	0.61080	0.989;0.989	P;P	0.61201	0.885;0.847	T	0.41502	-0.9505	10	0.26408	T	0.33	.	11.9944	0.53194	0.0816:0.0:0.9184:0.0	.	352;613	Q0IIP3;Q5TEA3	.;CT194_HUMAN	R	613;351	ENSP00000252032:P613R;ENSP00000407229:P351R	ENSP00000252032:P613R	P	-	2	0	C20orf194	3226767	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.030000	0.70903	1.528000	0.49103	0.563000	0.77884	CCT		0.428	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1		NM_001009984	
C5orf28	64417	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	43446548	43446548	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:43446548A>T	ENST00000500337.2	-	5	755	c.424T>A	c.(424-426)Tgc>Agc	p.C142S	C5orf28_ENST00000397080.3_Missense_Mutation_p.C142S|C5orf28_ENST00000511525.1_5'UTR|C5orf28_ENST00000512085.1_Missense_Mutation_p.C142S|C5orf28_ENST00000510130.1_Missense_Mutation_p.C40S|C5orf28_ENST00000537319.1_Missense_Mutation_p.C11S			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	142						integral component of membrane (GO:0016021)		p.C142S(1)		breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					GGAAGAAAGCACCATGAGTCT	0.438																																																	1	Substitution - Missense(1)	kidney(1)											109.0	101.0	104.0					5																	43446548		2203	4300	6503	SO:0001583	missense	64417			AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881			26139	protein-coding gene	gene with protein product						12477932	Standard	NM_022483		Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.424T>A	5.37:g.43446548A>T	ENSP00000426067:p.Cys142Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RDA6|Q9H6Z2	Missense_Mutation	SNP	ENST00000500337.2	37	CCDS3945.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.226015	0.39300	.	.	ENSG00000151881	ENST00000500337;ENST00000537319;ENST00000397080;ENST00000512085;ENST00000510130;ENST00000506860	.	.	.	5.95	4.8	0.61643	.	0.166603	0.64402	N	0.000002	T	0.58104	0.2099	M	0.72118	2.19	0.58432	D	0.999996	B	0.06786	0.001	B	0.09377	0.004	T	0.52711	-0.8539	9	0.18276	T	0.48	-32.7975	11.229	0.48901	0.9278:0.0:0.0722:0.0	.	142	Q0VDI3	CE028_HUMAN	S	142;11;142;142;40;142	.	ENSP00000380270:C142S	C	-	1	0	C5orf28	43482305	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.127000	0.77210	1.082000	0.41137	0.533000	0.62120	TGC		0.438	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368003.1		NM_022483	
CABLES1	91768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	20814600	20814600	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr18:20814600T>C	ENST00000256925.7	+	5	1117	c.1117T>C	c.(1117-1119)Tca>Cca	p.S373P	CABLES1_ENST00000420687.2_Missense_Mutation_p.S108P|CABLES1_ENST00000400473.2_Missense_Mutation_p.S46P|CABLES1_ENST00000585061.1_Intron|TMEM241_ENST00000450466.2_Intron	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	373	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)	p.S373P(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGGAAGACAATCAACTGGTGC	0.502																																																	1	Substitution - Missense(1)	kidney(1)											81.0	84.0	83.0					18																	20814600		2005	4199	6204	SO:0001583	missense	91768			BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1117T>C	18.37:g.20814600T>C	ENSP00000256925:p.Ser373Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	37	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	T	13.70	2.316898	0.40996	.	.	ENSG00000134508	ENST00000400473;ENST00000256925;ENST00000420687	T;T;T	0.43294	0.97;0.95;0.97	5.81	5.81	0.92471	.	0.290166	0.22011	U	0.065876	T	0.21186	0.0510	N	0.02225	-0.63	0.80722	D	1	B;B	0.15930	0.001;0.015	B;B	0.09377	0.004;0.004	T	0.11842	-1.0571	10	0.21540	T	0.41	-22.9988	16.1668	0.81768	0.0:0.0:0.0:1.0	.	108;373	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	P	46;373;108	ENSP00000383321:S46P;ENSP00000256925:S373P;ENSP00000413851:S108P	ENSP00000256925:S373P	S	+	1	0	CABLES1	19068598	1.000000	0.71417	0.922000	0.36590	0.931000	0.56810	2.106000	0.41835	2.210000	0.71456	0.533000	0.62120	TCA		0.502	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2		NM_138375	
CARNS1	57571	broad.mit.edu	37	11	67191044	67191044	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr11:67191044C>A	ENST00000307823.3	+	9	1908	c.1456C>A	c.(1456-1458)Cag>Aag	p.Q486K	CARNS1_ENST00000423745.2_Missense_Mutation_p.Q486K|CARNS1_ENST00000531040.1_Missense_Mutation_p.Q583K|CARNS1_ENST00000445895.2_Missense_Mutation_p.Q609K|CARNS1_ENST00000524740.1_3'UTR	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	486					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)	p.Q44K(1)|p.Q609K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						CCTGCTCTGCCAGGAGCTAGG	0.652																																																	2	Substitution - Missense(2)	kidney(2)											30.0	39.0	36.0					11																	67191044		2145	4252	6397	SO:0001583	missense	57571				CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1456C>A	11.37:g.67191044C>A	ENSP00000308268:p.Gln486Lys	Somatic		WXS	Illumina GAIIx	Phase_I	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.634769	0.29068	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	T;T;T;T	0.30981	1.54;1.51;1.51;1.53	5.14	3.16	0.36331	.	0.174408	0.27249	N	0.020240	T	0.18593	0.0446	N	0.24115	0.695	0.22888	N	0.998602	B;B	0.19200	0.02;0.034	B;B	0.18561	0.01;0.022	T	0.09164	-1.0687	10	0.37606	T	0.19	-16.1512	8.5266	0.33309	0.2383:0.5469:0.2148:0.0	.	486;625	A5YM72;A5YM72-3	CRNS1_HUMAN;.	K	583;486;583;486;609	ENSP00000431670:Q583K;ENSP00000308268:Q486K;ENSP00000401519:Q486K;ENSP00000389009:Q609K	ENSP00000308268:Q486K	Q	+	1	0	CARNS1	66947620	0.998000	0.40836	1.000000	0.80357	0.938000	0.57974	0.463000	0.21972	2.397000	0.81536	0.549000	0.68633	CAG		0.652	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1		NM_020811	
CC2D1A	54862	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	14034594	14034594	+	Missense_Mutation	SNP	G	G	A	rs375346936		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr19:14034594G>A	ENST00000318003.7	+	17	2151	c.1910G>A	c.(1909-1911)cGc>cAc	p.R637H	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R637H	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	637					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|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 negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)	p.R637H(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CCCACCGCCCGCTTTGAGCAA	0.627																																																	1	Substitution - Missense(1)	kidney(1)						G	HIS/ARG	0,3988		0,0,1994	58.0	63.0	61.0		1910	2.3	1.0	19		61	1,8319		0,1,4159	no	missense	CC2D1A	NM_017721.4	29	0,1,6153	AA,AG,GG		0.012,0.0,0.0081	benign	637/952	14034594	1,12307	1994	4160	6154	SO:0001583	missense	54862			AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.1910G>A	19.37:g.14034594G>A	ENSP00000313601:p.Arg637His	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	2.688	-0.273892	0.05679	0.0	1.2E-4	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.17691	2.26	4.68	2.34	0.29019	.	0.123229	0.56097	D	0.000031	T	0.04907	0.0132	N	0.04297	-0.235	0.34797	D	0.736271	B;B;B	0.19583	0.003;0.023;0.037	B;B;B	0.09377	0.004;0.003;0.003	T	0.33624	-0.9861	10	0.02654	T	1	-11.9526	4.3915	0.11343	0.4929:0.0:0.5071:0.0	.	259;637;637	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	H	637;260	ENSP00000313601:R637H	ENSP00000254346:R260H	R	+	2	0	CC2D1A	13895594	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	1.443000	0.35057	0.955000	0.37878	0.561000	0.74099	CGC		0.627	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1		NM_017721	
CCDC81	60494	broad.mit.edu;ucsc.edu	37	11	86097136	86097137	+	Nonsense_Mutation	DNP	GC	GC	TT			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr11:86097136_86097137GC>TT	ENST00000445632.2	+	2	395_396	c.123_124GC>TT	c.(121-126)cgGCag>cgTTag	p.Q42*	CCDC81_ENST00000278487.3_5'UTR|CCDC81_ENST00000354755.1_Nonsense_Mutation_p.Q42*	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	42								p.R41R(2)|p.Q42*(2)		kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				TTGTGAGACGGCAGTTAACCCT	0.302																																																	4	Substitution - Nonsense(2)|Substitution - coding silent(2)	kidney(4)																																								SO:0001587	stop_gained	60494			AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	Exception_encountered	11.37:g.86097136_86097137delinsTT	ENSP00000415528:p.Gln42*	Somatic		WXS	Illumina GAIIx	Phase_I	A0AVL7|Q53FW3|Q9H5E5	Silent|Nonsense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1																																																																																				0.302	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1		NM_021827	
CDH11	1009	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	64981780	64981780	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr16:64981780G>A	ENST00000268603.4	-	13	2732	c.2117C>T	c.(2116-2118)cCt>cTt	p.P706L	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.P580L	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	706					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P706L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCGGAGCCCAGGTCTAGGCAT	0.517			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																														Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	1	Substitution - Missense(1)	kidney(1)											125.0	118.0	120.0					16																	64981780		2203	4300	6503	SO:0001583	missense	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2117C>T	16.37:g.64981780G>A	ENSP00000268603:p.Pro706Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	7.596	0.671733	0.14776	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76968	-1.06	6.17	6.17	0.99709	Cadherin, cytoplasmic domain (1);	0.206639	0.51477	D	0.000084	T	0.63827	0.2544	N	0.25201	0.72	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.57510	-0.7799	10	0.13108	T	0.6	.	13.0796	0.59107	0.0723:0.0:0.9277:0.0	.	706	P55287	CAD11_HUMAN	L	706;689	ENSP00000268603:P706L	ENSP00000268603:P706L	P	-	2	0	CDH11	63539281	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	6.519000	0.73768	2.941000	0.99782	0.655000	0.94253	CCT		0.517	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1		NM_033664	
CSMD2	114784	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	34238249	34238249	+	Silent	SNP	G	G	A	rs142181378		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:34238249G>A	ENST00000338325.1	-	7	1003	c.591C>T	c.(589-591)ccC>ccT	p.P197P	CSMD2_ENST00000373381.4_Silent_p.P589P			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	549	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P549P(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCTCAAAGGCGGGCTGGCACT	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		20022	0.0		0.001	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)						G		0,4406		0,0,2203	126.0	115.0	119.0		1647	-5.4	0.9	1	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CSMD2	NM_052896.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		549/3488	34238249	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114784			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.591C>T	1.37:g.34238249G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000338325.1	37																																																																																					0.577	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2		NM_052896	
CREB3L4	148327	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	153946103	153946103	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:153946103T>A	ENST00000368607.3	+	9	1171	c.905T>A	c.(904-906)cTt>cAt	p.L302H	CREB3L4_ENST00000405694.3_Missense_Mutation_p.L155H|CREB3L4_ENST00000368600.3_Missense_Mutation_p.L282H|CREB3L4_ENST00000271889.4_Missense_Mutation_p.L302H|CREB3L4_ENST00000468845.1_3'UTR|JTB_ENST00000471173.1_5'Flank|CREB3L4_ENST00000368603.1_Missense_Mutation_p.L302H	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	302					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)	p.L302H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGATTCTTCTTTTTTCCCTG	0.552																																																	1	Substitution - Missense(1)	kidney(1)											28.0	31.0	30.0					1																	153946103		2203	4300	6503	SO:0001583	missense	148327			AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"""basic leucine zipper proteins"""	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.905T>A	1.37:g.153946103T>A	ENSP00000357596:p.Leu302His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	37	CCDS1056.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276650	0.80580	.	.	ENSG00000143578	ENST00000405694;ENST00000368607;ENST00000271889;ENST00000368603;ENST00000368600	D;T;T;T;T	0.81659	-1.52;-0.61;-0.61;-0.61;-0.6	4.93	4.93	0.64822	.	0.157818	0.41605	D	0.000842	D	0.84588	0.5505	M	0.82323	2.585	0.58432	D	0.999999	D;D	0.65815	0.995;0.995	P;P	0.56700	0.804;0.804	D	0.87507	0.2437	10	0.87932	D	0	.	12.571	0.56337	0.0:0.0:0.0:1.0	.	282;302	Q5T4L0;Q8TEY5	.;CR3L4_HUMAN	H	155;302;302;302;282	ENSP00000385104:L155H;ENSP00000357596:L302H;ENSP00000271889:L302H;ENSP00000357592:L302H;ENSP00000357589:L282H	ENSP00000271889:L302H	L	+	2	0	CREB3L4	152212727	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.693000	0.74582	2.071000	0.62044	0.533000	0.62120	CTT		0.552	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1		NM_130898	
DHX29	54505	hgsc.bcm.edu;ucsc.edu	37	5	54569200	54569201	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:54569200_54569201insTA	ENST00000251636.5	-	17	2843_2844	c.2695_2696insTA	c.(2695-2697)aaafs	p.K899fs	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	899	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AGCTATCACTTTATATCTGAAA	0.351																																																	0																																										SO:0001589	frameshift_variant	54505			AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.2694_2695dupTA	5.37:g.54569203_54569204dupTA	ENSP00000251636:p.Lys899fs	Somatic		WXS	Illumina HiSeq	Phase_I	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Frame_Shift_Ins	INS	ENST00000251636.5	37	CCDS34158.1																																																																																				0.351	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1		NM_019030	
DIS3	22894	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	73336063	73336063	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr13:73336063T>G	ENST00000377767.4	-	17	2440	c.2340A>C	c.(2338-2340)agA>agC	p.R780S	DIS3_ENST00000545453.1_Missense_Mutation_p.R618S|DIS3_ENST00000377780.4_Missense_Mutation_p.R750S	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	780					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)	p.R780S(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		AAAAATACCTTCTAATGGGTG	0.318										Multiple Myeloma(4;0.011)																																							1	Substitution - Missense(1)	kidney(1)											57.0	57.0	57.0					13																	73336063		2203	4299	6502	SO:0001583	missense	22894			AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.2340A>C	13.37:g.73336063T>G	ENSP00000366997:p.Arg780Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939169	0.73557	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.74842	-0.88;-0.88;-0.88	5.69	5.69	0.88448	Ribonuclease II/R, conserved site (1);Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	D	0.93051	0.7788	H	0.99777	4.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.96286	0.9210	10	0.87932	D	0	.	15.9458	0.79792	0.0:0.0:0.0:1.0	.	750;780	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	S	780;750;618	ENSP00000366997:R780S;ENSP00000367011:R750S;ENSP00000440058:R618S	ENSP00000366997:R780S	R	-	3	2	DIS3	72234064	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.284000	0.51708	2.162000	0.67917	0.459000	0.35465	AGA		0.318	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2		NM_014953	
FAM83B	222584	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	54806400	54806400	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr6:54806400C>G	ENST00000306858.7	+	5	2747	c.2631C>G	c.(2629-2631)ttC>ttG	p.F877L	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	877								p.F877L(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					AAAGCAAGTTCTTGGAAAGGG	0.428																																																	1	Substitution - Missense(1)	kidney(1)											66.0	64.0	65.0					6																	54806400		2203	4300	6503	SO:0001583	missense	222584			AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.2631C>G	6.37:g.54806400C>G	ENSP00000304078:p.Phe877Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.445444	0.01089	.	.	ENSG00000168143	ENST00000306858	T	0.28895	1.59	5.34	2.58	0.30949	.	0.334169	0.30043	N	0.010560	T	0.05868	0.0153	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44081	-0.9351	10	0.02654	T	1	-5.4276	8.3491	0.32292	0.0:0.6126:0.2422:0.1452	.	877	Q5T0W9	FA83B_HUMAN	L	877	ENSP00000304078:F877L	ENSP00000304078:F877L	F	+	3	2	FAM83B	54914359	0.356000	0.24930	0.115000	0.21578	0.113000	0.19764	0.210000	0.17455	-0.000000	0.14550	-0.795000	0.03280	TTC		0.428	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1		XM_294139	
FBF1	85302	hgsc.bcm.edu;ucsc.edu	37	17	73927360	73927360	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr17:73927360C>A	ENST00000586717.1	-	5	409	c.136G>T	c.(136-138)Ggt>Tgt	p.G46C	FBF1_ENST00000319129.5_Missense_Mutation_p.G46C|FBF1_ENST00000389570.4_Missense_Mutation_p.G46C			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	46					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						ACATCATCACCCAGGAGGGAC	0.562																																																	0													31.0	35.0	33.0					17																	73927360		2049	4199	6248	SO:0001583	missense	85302			AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.136G>T	17.37:g.73927360C>A	ENSP00000465132:p.Gly46Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		.	.	.	.	.	.	.	.	.	.	C	12.22	1.873822	0.33069	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17691	2.26;2.26	5.22	3.22	0.36961	.	.	.	.	.	T	0.16811	0.0404	N	0.22421	0.69	0.21499	N	0.999665	P;D;P	0.53312	0.948;0.959;0.948	P;P;P	0.49708	0.517;0.62;0.517	T	0.08229	-1.0732	9	0.72032	D	0.01	-0.2651	8.9855	0.35992	0.0:0.8243:0.0:0.1757	.	60;46;46	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	C	46;46;46;59	ENSP00000374221:G46C;ENSP00000324292:G46C	ENSP00000324292:G46C	G	-	1	0	FBF1	71438955	0.732000	0.28121	0.855000	0.33649	0.046000	0.14306	1.335000	0.33839	0.568000	0.29311	-0.258000	0.10820	GGT		0.562	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2		NM_001080542	
FBXO42	54455	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	16577186	16577186	+	Nonsense_Mutation	SNP	G	G	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:16577186G>C	ENST00000375592.3	-	10	2349	c.2133C>G	c.(2131-2133)taC>taG	p.Y711*		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	711								p.Y711*(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CTCGTACAAAGTACAAGGCGT	0.403																																																	1	Substitution - Nonsense(1)	kidney(1)											142.0	137.0	138.0					1																	16577186		2203	4300	6503	SO:0001587	stop_gained	54455			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.2133C>G	1.37:g.16577186G>C	ENSP00000364742:p.Tyr711*	Somatic		WXS	Illumina HiSeq	Phase_I	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Nonsense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	G	38	7.023747	0.98010	.	.	ENSG00000037637	ENST00000375592	.	.	.	5.52	4.6	0.57074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4342	10.015	0.42010	0.1536:0.0:0.8464:0.0	.	.	.	.	X	711	.	ENSP00000364742:Y711X	Y	-	3	2	FBXO42	16449773	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.377000	0.52425	1.478000	0.48253	0.655000	0.94253	TAC		0.403	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			
FCGBP	8857	broad.mit.edu;hgsc.bcm.edu	37	19	40376809	40376809	+	Silent	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr19:40376809C>T	ENST00000221347.6	-	24	11620	c.11613G>A	c.(11611-11613)ggG>ggA	p.G3871G	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3871	VWFD 9. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G3871G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGACAGTGGCCCTGTGGGGC	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											9.0	14.0	12.0					19																	40376809		2101	4122	6223	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.11613G>A	19.37:g.40376809C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1		NM_003890	
GGTLC1	92086	broad.mit.edu;hgsc.bcm.edu	37	20	23966339	23966339	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr20:23966339G>A	ENST00000335694.4	-	5	700	c.496C>T	c.(496-498)Ccc>Tcc	p.P166S	GGTLC1_ENST00000286890.4_Missense_Mutation_p.P166S|GGTLC1_ENST00000278765.4_Missense_Mutation_p.P166S	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	166					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)	p.P166S(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GTGACGTTGGGCAGAAGCTGG	0.617																																																	2	Substitution - Missense(2)	kidney(2)											53.0	58.0	57.0					20																	23966339		2203	4296	6499	SO:0001583	missense	92086			AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.496C>T	20.37:g.23966339G>A	ENSP00000337587:p.Pro166Ser	Somatic		WXS	Illumina HiSeq	Phase_I	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	37	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	g	16.99	3.275029	0.59649	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.12984	2.63;2.63;2.63	0.844	0.844	0.18943	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	H	0.94222	3.51	0.43693	D	0.996141	D	0.89917	1.0	D	0.78314	0.991	T	0.36114	-0.9761	10	0.87932	D	0	-25.7784	7.477	0.27382	1.0E-4:0.0:0.9999:0.0	.	166	Q9BX51	GGTL1_HUMAN	S	166	ENSP00000286890:P166S;ENSP00000278765:P166S;ENSP00000337587:P166S	ENSP00000278765:P166S	P	-	1	0	GGTLC1	23914339	1.000000	0.71417	0.361000	0.25849	0.364000	0.29643	4.500000	0.60387	0.088000	0.17205	0.089000	0.15464	CCC		0.617	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2		NM_178311.2	
GPR37L1	9283	broad.mit.edu;hgsc.bcm.edu	37	1	202097558	202097558	+	Silent	SNP	C	C	T	rs200746512		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:202097558C>T	ENST00000367282.5	+	2	1426	c.1320C>T	c.(1318-1320)ggC>ggT	p.G440G		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	440					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.G440G(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						AGGAGTGCGGCGGGGCTTCGG	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17044	0.0		0.001	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											29.0	32.0	31.0					1																	202097558		2203	4298	6501	SO:0001819	synonymous_variant	9283			AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1320C>T	1.37:g.202097558C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7M9|Q5SXP7|Q86VP7	Silent	SNP	ENST00000367282.5	37	CCDS1420.1																																																																																				0.637	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2		NM_004767	
ITIH6	347365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	54785277	54785277	+	Silent	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chrX:54785277G>A	ENST00000218436.6	-	8	1259	c.1230C>T	c.(1228-1230)atC>atT	p.I410I		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	410	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.I410I(1)									CATTGGAGAGGATCACACTGG	0.627																																																	1	Substitution - coding silent(1)	kidney(1)											70.0	53.0	59.0					X																	54785277		2203	4300	6503	SO:0001819	synonymous_variant	0			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1230C>T	X.37:g.54785277G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NN03	Silent	SNP	ENST00000218436.6	37	CCDS14361.1																																																																																				0.627	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2		NM_198510	
KBTBD6	89890	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	41706026	41706026	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr13:41706026A>C	ENST00000379485.1	-	1	856	c.622T>G	c.(622-624)Tca>Gca	p.S208A	KBTBD6_ENST00000499385.2_Missense_Mutation_p.S142A	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	208								p.S208A(1)		NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		TCCCGAATTGAACCCATGTGG	0.562																																																	1	Substitution - Missense(1)	kidney(1)											82.0	80.0	81.0					13																	41706026		2203	4300	6503	SO:0001583	missense	89890			AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"""BTB/POZ domain containing"""	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.622T>G	13.37:g.41706026A>C	ENSP00000368799:p.Ser208Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	a	0.007	-1.989012	0.00439	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.75938	-0.87;-0.98	3.69	-1.7	0.08159	BTB/Kelch-associated (2);	0.239217	0.21672	N	0.070844	T	0.42200	0.1192	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.14023	0.01;0.005	T	0.21724	-1.0237	10	0.37606	T	0.19	.	3.0357	0.06121	0.4343:0.0:0.3632:0.2025	.	142;208	F5GZN7;Q86V97	.;KBTB6_HUMAN	A	208;142	ENSP00000368799:S208A;ENSP00000444326:S142A	ENSP00000368799:S208A	S	-	1	0	KBTBD6	40604026	0.127000	0.22367	0.084000	0.20598	0.330000	0.28571	0.854000	0.27791	-0.141000	0.11374	0.379000	0.24179	TCA		0.562	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1		NM_152903	
KCNQ3	3786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	133141908	133141908	+	Silent	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr8:133141908C>T	ENST00000388996.4	-	15	2640	c.2220G>A	c.(2218-2220)acG>acA	p.T740T	KCNQ3_ENST00000519445.1_Silent_p.T728T|KCNQ3_ENST00000521134.1_Silent_p.T620T	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	740					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.T740T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCTCCACATACGTTGTTGCTG	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											39.0	40.0	40.0					8																	133141908		2203	4300	6503	SO:0001819	synonymous_variant	3786			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2220G>A	8.37:g.133141908C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																				0.592	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2		NM_004519	
KCTD7	154881	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	66103318	66103318	+	Nonsense_Mutation	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr7:66103318C>G	ENST00000275532.3	+	3	577	c.393C>G	c.(391-393)taC>taG	p.Y131*	KCTD7_ENST00000443322.1_Nonsense_Mutation_p.Y131*	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	131	BTB.				cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.Y131*(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						AGGCCCAGTACTATGCCATCG	0.572																																																	1	Substitution - Nonsense(1)	kidney(1)											84.0	77.0	79.0					7																	66103318		2203	4300	6503	SO:0001587	stop_gained	154881			AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.393C>G	7.37:g.66103318C>G	ENSP00000275532:p.Tyr131*	Somatic		WXS	Illumina HiSeq	Phase_I	A4D2M4|Q8IVR0	Nonsense_Mutation	SNP	ENST00000275532.3	37	CCDS5534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	28.2|28.2	4.898639|4.898639	0.91962|0.91962	.|.	.|.	ENSG00000243335|ENSG00000243335	ENST00000449064|ENST00000275532;ENST00000443322	.|.	.|.	.|.	5.8|5.8	3.98|3.98	0.46160|0.46160	.|.	0.000000|.	0.33272|.	N|.	0.005083|.	T|.	0.31544|.	0.0800|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.13176|.	-1.0519|.	6|.	0.34782|0.02654	T|T	0.22|1	-4.409|-4.409	10.3553|10.3553	0.43960|0.43960	0.0:0.7827:0.0:0.2173|0.0:0.7827:0.0:0.2173	.|.	.|.	.|.	.|.	V|X	75|131	.|.	ENSP00000388463:L75V|ENSP00000275532:Y131X	L|Y	+|+	1|3	2|2	KCTD7|KCTD7	65740753|65740753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	1.797000|1.797000	0.38804|0.38804	1.469000|1.469000	0.48083|0.48083	0.561000|0.561000	0.74099|0.74099	CTA|TAC		0.572	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2		NM_153033	
LEF1	51176	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	109004590	109004590	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr4:109004590T>G	ENST00000265165.1	-	5	1214	c.560A>C	c.(559-561)cAt>cCt	p.H187P	LEF1_ENST00000438313.2_Missense_Mutation_p.H187P|LEF1_ENST00000379951.2_Missense_Mutation_p.H187P|LEF1_ENST00000510624.1_Missense_Mutation_p.H119P|LEF1_ENST00000512172.1_Missense_Mutation_p.H119P	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	187	Pro-rich.				alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.H119P(1)|p.H187P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		AGCTGGAGGATGTCTGGACAT	0.438																																																	2	Substitution - Missense(2)	kidney(2)											124.0	109.0	114.0					4																	109004590		2203	4300	6503	SO:0001583	missense	51176				CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.560A>C	4.37:g.109004590T>G	ENSP00000265165:p.His187Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Missense_Mutation	SNP	ENST00000265165.1	37	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	T	5.470	0.271692	0.10349	.	.	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624;ENST00000515500;ENST00000512172	D;D;D;D	0.99121	-5.38;-5.45;-5.4;-5.36	5.64	5.64	0.86602	CTNNB1 binding, N-teminal (1);	0.046000	0.85682	D	0.000000	D	0.95598	0.8569	N	0.11313	0.125	0.51233	D	0.999911	B;B;B;B;B	0.30889	0.001;0.299;0.255;0.0;0.0	B;B;B;B;B	0.35278	0.001;0.199;0.095;0.001;0.002	D	0.95015	0.8155	10	0.02654	T	1	-21.1852	15.8595	0.79012	0.0:0.0:0.0:1.0	.	119;72;187;187;187	E9PDK3;B4DZY5;Q9UJU2-6;Q9UJU2-5;Q9UJU2	.;.;.;.;LEF1_HUMAN	P	187;187;187;119;119;119	ENSP00000265165:H187P;ENSP00000369284:H187P;ENSP00000406176:H187P;ENSP00000422840:H119P	ENSP00000265165:H187P	H	-	2	0	LEF1	109224039	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.793000	0.55484	2.144000	0.66660	0.533000	0.62120	CAT		0.438	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			
LHX1	3975	hgsc.bcm.edu;ucsc.edu	37	17	35295520	35295520	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr17:35295520delG	ENST00000254457.5	+	1	1437	c.26delG	c.(25-27)aggfs	p.R9fs	RP11-445F12.1_ENST00000529264.1_RNA|RP11-445F12.1_ENST00000528383.1_RNA|RP11-445F12.1_ENST00000532387.2_RNA|RP11-445F12.1_ENST00000525111.1_RNA|RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	9	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				GGCTGCAAAAGGCCCATCCTG	0.562																																																	0													92.0	85.0	87.0					17																	35295520		2203	4300	6503	SO:0001589	frameshift_variant	3975			U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"""Homeoboxes / LIM class"""	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.26delG	17.37:g.35295520delG	ENSP00000254457:p.Arg9fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MIW0	Frame_Shift_Del	DEL	ENST00000254457.5	37	CCDS11316.1																																																																																				0.562	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3		NM_005568	
LILRA6	79168	broad.mit.edu	37	19	54744735	54744735	+	Silent	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr19:54744735G>A	ENST00000396365.2	-	5	966	c.927C>T	c.(925-927)ccC>ccT	p.P309P	LILRA6_ENST00000419410.2_Silent_p.P309P|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000245621.5_Silent_p.P309P|LILRA6_ENST00000440558.2_Silent_p.P309P	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	309	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.P309P(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGGGTCGCTGGGGGCCGACC	0.677																																																	2	Substitution - coding silent(2)	lung(1)|kidney(1)											31.0	42.0	38.0					19																	54744735		2201	4298	6499	SO:0001819	synonymous_variant	79168			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.927C>T	19.37:g.54744735G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																				0.677	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1		NM_024318	
MADD	8567	hgsc.bcm.edu;ucsc.edu	37	11	47299728	47299730	+	In_Frame_Del	DEL	CCA	CCA	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr11:47299728_47299730delCCA	ENST00000311027.5	+	6	1273_1275	c.1108_1110delCCA	c.(1108-1110)ccadel	p.P370del	MADD_ENST00000402192.2_In_Frame_Del_p.P370del|MADD_ENST00000342922.4_In_Frame_Del_p.P370del|MADD_ENST00000406482.1_In_Frame_Del_p.P370del|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000407859.3_In_Frame_Del_p.P370del|MADD_ENST00000349238.3_In_Frame_Del_p.P370del|MADD_ENST00000395336.3_In_Frame_Del_p.P370del|MADD_ENST00000395344.3_In_Frame_Del_p.P370del|MADD_ENST00000402799.1_In_Frame_Del_p.P370del	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GCTGTTGGCTCCAACCCCGTACA	0.443																																																	0																																										SO:0001651	inframe_deletion	8567			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1108_1110delCCA	11.37:g.47299728_47299730delCCA	ENSP00000310933:p.Pro370del	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Del	DEL	ENST00000311027.5	37	CCDS7930.1																																																																																				0.443	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			
MAST4	375449	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	66460450	66460450	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:66460450G>A	ENST00000403625.2	+	29	5738	c.5443G>A	c.(5443-5445)Gcc>Acc	p.A1815T	MAST4_ENST00000404260.3_Missense_Mutation_p.A1818T|MAST4_ENST00000405643.1_Missense_Mutation_p.A1636T|MAST4_ENST00000261569.7_Missense_Mutation_p.A1621T|MAST4_ENST00000403666.1_Missense_Mutation_p.A1626T	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1818						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.A1818T(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CGGACCTCAGGCCTCCAAGAC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											86.0	92.0	90.0					5																	66460450		1996	4172	6168	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.5443G>A	5.37:g.66460450G>A	ENSP00000385727:p.Ala1815Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.247481|5.247481	0.95305|0.95305	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808	T;T;T;T;T|.	0.69806|.	-0.41;-0.41;-0.43;-0.43;-0.4|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.110832|.	0.40908|.	D|.	0.000988|.	T|T	0.59770|0.59770	0.2218|0.2218	L|L	0.34521|0.34521	1.04|1.04	0.39328|0.39328	D|D	0.965364|0.965364	P;D|.	0.55605|.	0.953;0.972|.	P;P|.	0.49752|.	0.556;0.621|.	T|T	0.56183|0.56183	-0.8021|-0.8021	10|5	0.56958|.	D|.	0.05|.	-16.916|-16.916	18.8046|18.8046	0.92032|0.92032	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1818;1626|.	O15021;O15021-3|.	MAST4_HUMAN;.|.	T|D	1818;1815;1626;1636;1636;1621|871	ENSP00000385048:A1818T;ENSP00000385727:A1815T;ENSP00000384313:A1626T;ENSP00000384099:A1636T;ENSP00000261569:A1621T|.	ENSP00000261569:A1621T|.	A|G	+|+	1|2	0|0	MAST4|MAST4	66496206|66496206	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	2.866000|2.866000	0.48420|0.48420	2.659000|2.659000	0.90383|0.90383	0.655000|0.655000	0.94253|0.94253	GCC|GGC		0.602	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			
MDGA1	266727	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	37606075	37606075	+	Silent	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr6:37606075C>T	ENST00000434837.3	-	16	3860	c.2682G>A	c.(2680-2682)ggG>ggA	p.G894G	MDGA1_ENST00000505425.1_Silent_p.G894G|MDGA1_ENST00000297153.7_Silent_p.G898G	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	894	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.G896G(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GGCCTCGAACCCCCTCAAAAA	0.567																																																	1	Substitution - coding silent(1)	kidney(1)											46.0	46.0	46.0					6																	37606075		1845	4099	5944	SO:0001819	synonymous_variant	266727			AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2682G>A	6.37:g.37606075C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																				0.567	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			
MOSPD3	64598	broad.mit.edu;hgsc.bcm.edu	37	7	100211260	100211260	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr7:100211260C>T	ENST00000393950.2	+	3	724	c.442C>T	c.(442-444)Cca>Tca	p.P148S	MOSPD3_ENST00000424091.2_Missense_Mutation_p.P138S|MOSPD3_ENST00000223054.4_Missense_Mutation_p.P148S|MOSPD3_ENST00000379527.2_Missense_Mutation_p.P148S	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	148					heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)	p.P148S(1)		breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					TCAGGGACAGCCAGATCCAGC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											56.0	53.0	54.0					7																	100211260		2203	4300	6503	SO:0001583	missense	64598			BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.442C>T	7.37:g.100211260C>T	ENSP00000377522:p.Pro148Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Missense_Mutation	SNP	ENST00000393950.2	37	CCDS5701.1	.	.	.	.	.	.	.	.	.	.	C	5.031	0.191432	0.09547	.	.	ENSG00000106330	ENST00000223054;ENST00000493970;ENST00000379527;ENST00000393950;ENST00000424091;ENST00000393953	.	.	.	4.12	0.286	0.15710	.	0.738322	0.11866	N	0.521852	T	0.13030	0.0316	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23190	-1.0195	9	0.38643	T	0.18	-0.0023	6.2728	0.20963	0.0:0.5487:0.0:0.4513	.	138;148	C9JE89;O75425	.;MSPD3_HUMAN	S	148;148;148;148;138;134	.	ENSP00000223054:P148S	P	+	1	0	MOSPD3	100049196	0.000000	0.05858	0.024000	0.17045	0.604000	0.37047	-0.270000	0.08584	0.034000	0.15491	0.563000	0.77884	CCA		0.622	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1		NM_023948	
Unknown	0	broad.mit.edu	37	1	16973855	16973855	+	IGR	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:16973855G>A								CROCCP2 (12801 upstream) : RNU1-3 (19424 downstream)																							CCGGGCTAGGGAAGGTCCAGG	0.692																																																	0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16973855G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.692									
MUC4	4585	hgsc.bcm.edu	37	3	195507215	195507262	+	In_Frame_Del	DEL	GAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	GAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	-	rs553645209|rs74187968|rs375915811|rs201269328|rs569772156|rs199994331|rs200315207|rs201456607|rs567957149|rs370997210|rs535035384|rs367631576|rs532961620|rs537603063|rs199776180	byFrequency	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	GAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	GAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:195507215_195507262delGAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	ENST00000463781.3	-	2	11648_11695	c.11189_11236delATGTCACCAGCCCTTCCTCAGCATCCACAGGTCACGTCACCCCTCTTC	c.(11188-11238)catgtcaccagcccttcctcagcatccacaggtcacgtcacccctcttcct>cct	p.HVTSPSSASTGHVTPL3730del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.HVTSPSSASTGHVTPL3730del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H3741Q(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)		CTGGTGACAGGAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACATGAAGAGGGGT	0.577																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11189_11236delATGTCACCAGCCCTTCCTCAGCATCCACAGGTCACGTCACCCCTCTTC	3.37:g.195507215_195507262delGAAGAGGGGTGACGTGACCTGTGGATGCTGAGGAAGGGCTGGTGACAT	ENSP00000417498:p.His3730_Leu3745del	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195509031	195509078	+	In_Frame_Del	DEL	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	-	rs540650529|rs78565605|rs559337249|rs75721951|rs35479616|rs35658525|rs201338210|rs371017154|rs75309583|rs77818558|rs71634715|rs185913520|rs35533324	byFrequency	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	GGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENST00000463781.3	-	2	9832_9879	c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	c.(9373-9420)gacacttcctcagcatccacaggtcaggccaccgctcttcctgtcaccdel	p.DTSSASTGQATALPVT3125del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.DTSSASTGQATALPVT3125del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			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)		AGGAAGTGCTGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGGTGACAGGA	0.593																																																	0																																										SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9373_9420delGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACC	3.37:g.195509031_195509078delGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTC	ENSP00000417498:p.Asp3125_Thr3140del	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.593	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYO10	4651	broad.mit.edu	37	5	16674991	16674991	+	Silent	SNP	A	A	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr5:16674991A>G	ENST00000513610.1	-	35	5389	c.4935T>C	c.(4933-4935)atT>atC	p.I1645I	MYO10_ENST00000274203.9_Silent_p.I1002I|MYO10_ENST00000505695.1_Silent_p.I984I|MYO10_ENST00000515803.1_Silent_p.I984I|MYO10_ENST00000427430.2_Silent_p.I1002I	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1645	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.I1645I(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GATACTTGAGAATCCCTCGAC	0.572																																																	1	Substitution - coding silent(1)	kidney(1)											112.0	114.0	114.0					5																	16674991		2062	4212	6274	SO:0001819	synonymous_variant	4651			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4935T>C	5.37:g.16674991A>G		Somatic		WXS	Illumina GAIIx	Phase_I	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																				0.572	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1		NM_012334	
NCOA2	10499	hgsc.bcm.edu;ucsc.edu	37	8	71068322	71068322	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr8:71068322G>T	ENST00000452400.2	-	11	2459	c.2278C>A	c.(2278-2280)Cca>Aca	p.P760T	NCOA2_ENST00000524223.1_5'UTR	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	760					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GTTATTTCTGGTAAACCAATA	0.393			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													121.0	121.0	121.0					8																	71068322		1857	4109	5966	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2278C>A	8.37:g.71068322G>T	ENSP00000399968:p.Pro760Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.625634	0.28889	.	.	ENSG00000140396	ENST00000452400	T	0.01495	4.83	5.65	4.77	0.60923	.	0.209202	0.50627	D	0.000116	T	0.01189	0.0039	N	0.17082	0.46	0.80722	D	1	P	0.44627	0.839	B	0.36134	0.218	T	0.71451	-0.4589	10	0.12766	T	0.61	.	10.2537	0.43383	0.0713:0.1351:0.7936:0.0	.	760	Q15596	NCOA2_HUMAN	T	760	ENSP00000399968:P760T	ENSP00000399968:P760T	P	-	1	0	NCOA2	71230876	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.702000	0.54800	1.389000	0.46526	0.563000	0.77884	CCA		0.393	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			
NCOA5	57727	broad.mit.edu;hgsc.bcm.edu	37	20	44692013	44692013	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr20:44692013G>A	ENST00000290231.6	-	7	1300	c.1136C>T	c.(1135-1137)aCc>aTc	p.T379I		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T379I(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				CAGAGAGTCGGTGCTGCTCCT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											58.0	53.0	55.0					20																	44692013		2203	4300	6503	SO:0001583	missense	57727				CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"""coactivator independent of AF-2"""					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.1136C>T	20.37:g.44692013G>A	ENSP00000290231:p.Thr379Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.683113	0.29872	.	.	ENSG00000124160	ENST00000290231	T	0.47177	0.85	5.41	3.39	0.38822	.	0.517851	0.23624	N	0.046201	T	0.31451	0.0797	N	0.19112	0.55	0.30418	N	0.778412	B	0.02656	0.0	B	0.04013	0.001	T	0.29941	-0.9995	10	0.51188	T	0.08	-14.5582	10.5689	0.45188	0.0713:0.2306:0.6982:0.0	.	379	Q9HCD5	NCOA5_HUMAN	I	379	ENSP00000290231:T379I	ENSP00000290231:T379I	T	-	2	0	NCOA5	44125420	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	2.792000	0.47837	1.524000	0.49035	-0.258000	0.10820	ACC		0.572	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1		NM_020967	
NDST2	8509	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	75567375	75567375	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr10:75567375G>A	ENST00000309979.6	-	3	1328	c.772C>T	c.(772-774)Cgt>Tgt	p.R258C	RP11-574K11.31_ENST00000603027.1_Missense_Mutation_p.R258C|NDST2_ENST00000299641.4_Missense_Mutation_p.R135C			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	258	Heparan sulfate N-deacetylase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)	p.R258C(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					CGGGCCCGACGAAGAACTGGT	0.562																																																	1	Substitution - Missense(1)	kidney(1)											52.0	52.0	52.0					10																	75567375		2203	4300	6503	SO:0001583	missense	8509			U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"""Sulfotransferases, membrane-bound"""	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.772C>T	10.37:g.75567375G>A	ENSP00000310657:p.Arg258Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q2TB32|Q59H89	Missense_Mutation	SNP	ENST00000309979.6	37	CCDS7335.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895387	0.72639	.	.	ENSG00000166507	ENST00000309979;ENST00000299641	T;T	0.44881	1.23;0.91	5.75	5.75	0.90469	.	0.144197	0.51477	D	0.000086	T	0.45875	0.1364	N	0.14661	0.345	0.52501	D	0.999951	P;D	0.69078	0.939;0.997	P;P	0.57548	0.759;0.823	T	0.50021	-0.8876	10	0.59425	D	0.04	.	19.9417	0.97165	0.0:0.0:1.0:0.0	.	135;258	B4E139;P52849	.;NDST2_HUMAN	C	258;135	ENSP00000310657:R258C;ENSP00000299641:R135C	ENSP00000299641:R135C	R	-	1	0	NDST2	75237381	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	4.654000	0.61469	2.720000	0.93068	0.655000	0.94253	CGT		0.562	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1		NM_003635	
NKTR	4820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	42680080	42680080	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:42680080G>T	ENST00000232978.8	+	13	3072	c.2884G>T	c.(2884-2886)Ggg>Tgg	p.G962W	RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	962					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.G962W(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TGACTCTGAGGGGTCCTGTTC	0.423																																																	1	Substitution - Missense(1)	kidney(1)											87.0	89.0	88.0					3																	42680080		2203	4300	6503	SO:0001583	missense	4820				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2884G>T	3.37:g.42680080G>T	ENSP00000232978:p.Gly962Trp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	G	8.212	0.800554	0.16397	.	.	ENSG00000114857	ENST00000232978	T	0.12255	2.7	5.51	3.46	0.39613	.	0.454353	0.25352	N	0.031294	T	0.13500	0.0327	L	0.36672	1.1	0.80722	D	1	D;P	0.55800	0.973;0.948	P;B	0.49528	0.614;0.41	T	0.03249	-1.1056	10	0.87932	D	0	-1.2172	4.0369	0.09733	0.4089:0.0:0.5911:0.0	.	662;962	Q6M1B8;P30414	.;NKTR_HUMAN	W	962	ENSP00000232978:G962W	ENSP00000232978:G962W	G	+	1	0	NKTR	42655084	0.999000	0.42202	0.834000	0.33040	0.196000	0.23810	2.308000	0.43690	1.329000	0.45376	0.650000	0.86243	GGG		0.423	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2		NM_005385	
NMT1	4836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	43173564	43173564	+	Silent	SNP	A	A	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr17:43173564A>C	ENST00000592782.1	+	6	638	c.507A>C	c.(505-507)ctA>ctC	p.L169L	NMT1_ENST00000258960.2_Silent_p.L169L|NMT1_ENST00000590114.1_3'UTR			P30419	NMT1_HUMAN	N-myristoyltransferase 1	169					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)	p.L169L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				CTTTACAGCTAAAAGAACTGT	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											145.0	136.0	139.0					17																	43173564		2203	4300	6503	SO:0001819	synonymous_variant	4836				CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.507A>C	17.37:g.43173564A>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.763062	0.31228	.	.	ENSG00000136448	ENST00000543908	T	0.42900	0.96	5.65	0.127	0.14727	.	.	.	.	.	T	0.47619	0.1455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46679	-0.9174	6	0.87932	D	0	-13.6584	7.7356	0.28812	0.1842:0.3212:0.4946:0.0	.	.	.	.	Q	130	ENSP00000439263:K130Q	ENSP00000439263:K130Q	K	+	1	0	NMT1	40529090	0.999000	0.42202	0.997000	0.53966	0.331000	0.28603	0.436000	0.21526	-0.041000	0.13558	-0.798000	0.03219	AAA		0.433	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1		NM_021079	
NPHP3	27031	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	132409424	132409424	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:132409424T>G	ENST00000337331.5	-	19	2727	c.2641A>C	c.(2641-2643)Aag>Cag	p.K881Q	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	881					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)		p.K881Q(1)		NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCATGCAGCTTCTGTTTACTT	0.383																																																	1	Substitution - Missense(1)	kidney(1)											93.0	96.0	95.0					3																	132409424		2203	4300	6503	SO:0001583	missense	27031			AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.2641A>C	3.37:g.132409424T>G	ENSP00000338766:p.Lys881Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.532392	0.45073	.	.	ENSG00000113971	ENST00000393144;ENST00000337331	D	0.91843	-2.92	5.62	3.24	0.37175	.	0.093373	0.64402	N	0.000001	D	0.89329	0.6684	M	0.66939	2.045	0.80722	D	1	B	0.15719	0.014	B	0.14023	0.01	D	0.83726	0.0195	10	0.59425	D	0.04	-10.9007	8.1344	0.31046	0.0:0.0709:0.147:0.7821	.	881	Q7Z494	NPHP3_HUMAN	Q	161;881	ENSP00000338766:K881Q	ENSP00000338766:K881Q	K	-	1	0	NPHP3	133892114	1.000000	0.71417	0.933000	0.37362	0.667000	0.39255	3.902000	0.56310	0.412000	0.25729	0.482000	0.46254	AAG		0.383	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2		NM_153240	
NR4A1	3164	broad.mit.edu	37	12	52452615	52452615	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr12:52452615C>A	ENST00000243050.1	+	8	1998	c.1684C>A	c.(1684-1686)Ctg>Atg	p.L562M	NR4A1_ENST00000545748.1_Missense_Mutation_p.L616M|NR4A1_ENST00000394825.1_Missense_Mutation_p.L562M|NR4A1_ENST00000550082.1_Missense_Mutation_p.L575M|RP11-1100L3.8_ENST00000564363.1_lincRNA|NR4A1_ENST00000394824.2_Missense_Mutation_p.L562M|NR4A1_ENST00000360284.3_Missense_Mutation_p.L575M	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	562					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.L562M(2)		endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACTGCCCGAGCTGCGGACCCT	0.637																																																	2	Substitution - Missense(2)	endometrium(1)|kidney(1)											58.0	51.0	53.0					12																	52452615		2203	4300	6503	SO:0001583	missense	3164			L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"""Nuclear hormone receptors"""	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.1684C>A	12.37:g.52452615C>A	ENSP00000243050:p.Leu562Met	Somatic		WXS	Illumina GAIIx	Phase_I	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	37	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165339	0.78339	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000394824	T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.06	4.17	0.49024	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.87489	0.6190	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.90516	0.4485	10	0.87932	D	0	.	12.8189	0.57681	0.0:0.9197:0.0:0.0803	.	575;562	B4DML7;P22736	.;NR4A1_HUMAN	M	575;616;575;562;562;562	ENSP00000353427:L575M;ENSP00000440864:L616M;ENSP00000449539:L575M;ENSP00000243050:L562M;ENSP00000378302:L562M;ENSP00000378301:L562M	ENSP00000243050:L562M	L	+	1	2	NR4A1	50738882	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.791000	0.62460	1.524000	0.49035	0.655000	0.94253	CTG		0.637	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2			
NT5M	56953	broad.mit.edu	37	17	17250185	17250185	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr17:17250185T>C	ENST00000389022.4	+	5	827	c.611T>C	c.(610-612)cTg>cCg	p.L204P	NT5M_ENST00000582909.1_3'UTR	NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	204					dephosphorylation (GO:0016311)|DNA replication (GO:0006260)|dUMP catabolic process (GO:0046079)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|nucleotide binding (GO:0000166)	p.L204P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						CACCTGCAGCTGCAGCCCCCC	0.672																																																	1	Substitution - Missense(1)	kidney(1)											30.0	36.0	34.0					17																	17250185		2202	4298	6500	SO:0001583	missense	56953			AF210652	CCDS32581.1	17p11.2	2007-08-01	2002-05-23		ENSG00000205309	ENSG00000205309	3.1.3.5		15769	protein-coding gene	gene with protein product		605292	"""5' nucleotidase, mitochondrial"""			10899995	Standard	XM_005256731		Approved	dNT-2, dNT2, mdN	uc002grf.3	Q9NPB1	OTTHUMG00000059277	ENST00000389022.4:c.611T>C	17.37:g.17250185T>C	ENSP00000373674:p.Leu204Pro	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000389022.4	37	CCDS32581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.08|17.08	3.297044|3.297044	0.60086|0.60086	.|.	.|.	ENSG00000205309|ENSG00000205309	ENST00000446264|ENST00000389022	.|T	.|0.49139	.|0.79	5.79|5.79	4.72|4.72	0.59763|0.59763	.|HAD-like domain (2);	0.043809|.	0.85682|.	D|.	0.000000|.	T|T	0.48660|0.48660	0.1512|0.1512	M|M	0.61703|0.61703	1.905|1.905	0.47214|0.47214	D|D	0.999351|0.999351	B|B;B	0.32350|0.28439	0.366|0.212;0.212	B|B;B	0.27796|0.36030	0.083|0.216;0.216	T|T	0.52230|0.52230	-0.8603|-0.8603	9|9	0.72032|0.54805	D|T	0.01|0.06	-30.5484|-30.5484	10.2483|10.2483	0.43354|0.43354	0.0:0.0778:0.0:0.9222|0.0:0.0778:0.0:0.9222	.|.	203|210;204	F6S3X3|Q2I378;Q9NPB1	.|.;NT5M_HUMAN	R|P	203|204	.|ENSP00000373674:L204P	ENSP00000390695:C203R|ENSP00000373674:L204P	C|L	+|+	1|2	0|0	NT5M|NT5M	17190910|17190910	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	3.300000|3.300000	0.51834|0.51834	2.203000|2.203000	0.70933|0.70933	0.459000|0.459000	0.35465|0.35465	TGC|CTG		0.672	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			
OLFML2B	25903	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	161953786	161953786	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:161953786C>G	ENST00000294794.3	-	8	2355	c.1932G>C	c.(1930-1932)gaG>gaC	p.E644D	OLFML2B_ENST00000367938.1_Missense_Mutation_p.E127D|OLFML2B_ENST00000367940.2_Missense_Mutation_p.E645D	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	644	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.E644D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GGACAATGACCTCCTGGCTGA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											84.0	75.0	78.0					1																	161953786		2203	4300	6503	SO:0001583	missense	25903			BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.1932G>C	1.37:g.161953786C>G	ENSP00000294794:p.Glu644Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	37	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.543468	0.65198	.	.	ENSG00000162745	ENST00000294794;ENST00000367940;ENST00000367938	D;D;D	0.88277	-2.36;-2.36;-2.23	5.36	4.44	0.53790	Olfactomedin-like (3);	.	.	.	.	D	0.89760	0.6808	L	0.60012	1.86	0.41904	D	0.990435	D;D	0.89917	1.0;0.996	D;D	0.87578	0.998;0.965	D	0.90557	0.4513	8	0.87932	D	0	.	8.605	0.33767	0.0:0.8227:0.0:0.1773	.	645;644	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	D	644;645;127	ENSP00000294794:E644D;ENSP00000356917:E645D;ENSP00000356915:E127D	ENSP00000294794:E644D	E	-	3	2	OLFML2B	160220410	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.406000	0.34646	1.216000	0.43427	0.561000	0.74099	GAG		0.607	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2		NM_015441	
PARP9	83666	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	122247559	122247559	+	Silent	SNP	G	G	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:122247559G>C	ENST00000360356.2	-	11	2444	c.2217C>G	c.(2215-2217)acC>acG	p.T739T	PARP9_ENST00000477522.2_Silent_p.T704T|PARP9_ENST00000492382.1_Silent_p.T284T|PARP9_ENST00000471785.1_Silent_p.T704T	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	739	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.T739T(1)		endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		TGAGGTTCTTGGTGAAGTATA	0.383																																																	1	Substitution - coding silent(1)	kidney(1)											98.0	95.0	96.0					3																	122247559		2203	4300	6503	SO:0001819	synonymous_variant	83666			AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.2217C>G	3.37:g.122247559G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Silent	SNP	ENST00000360356.2	37	CCDS3014.1																																																																																				0.383	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1		NM_031458	
PCSK9	255738	broad.mit.edu;hgsc.bcm.edu	37	1	55529175	55529175	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:55529175G>A	ENST00000302118.5	+	12	2287	c.1997G>A	c.(1996-1998)aGc>aAc	p.S666N	PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	666	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.S666N(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						ACTACAGGCAGCACCAGCGAA	0.677																																					Pancreas(137;1454 1827 5886 22361 42375)												1	Substitution - Missense(1)	kidney(1)											49.0	49.0	49.0					1																	55529175		2203	4300	6503	SO:0001583	missense	255738			AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1997G>A	1.37:g.55529175G>A	ENSP00000303208:p.Ser666Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	8.377	0.836585	0.16891	.	.	ENSG00000169174	ENST00000302118	T	0.70986	-0.53	3.38	3.38	0.38709	.	0.731439	0.11551	N	0.552830	T	0.50274	0.1606	N	0.08118	0	0.31521	N	0.662415	B	0.02656	0.0	B	0.01281	0.0	T	0.52049	-0.8627	10	0.34782	T	0.22	-2.8182	11.2526	0.49034	0.0:0.1843:0.8157:0.0	.	666	Q8NBP7	PCSK9_HUMAN	N	666	ENSP00000303208:S666N	ENSP00000303208:S666N	S	+	2	0	PCSK9	55301763	0.113000	0.22115	0.002000	0.10522	0.013000	0.08279	3.458000	0.53014	1.869000	0.54173	0.455000	0.32223	AGC		0.677	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1		NM_174936	
PLEC	5339	broad.mit.edu	37	8	144995868	144995868	+	Silent	SNP	A	A	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr8:144995868A>G	ENST00000322810.4	-	32	8701	c.8532T>C	c.(8530-8532)aaT>aaC	p.N2844N	PLEC_ENST00000527096.1_Silent_p.N2730N|PLEC_ENST00000354589.3_Silent_p.N2707N|PLEC_ENST00000398774.2_Silent_p.N2675N|PLEC_ENST00000356346.3_Silent_p.N2693N|PLEC_ENST00000436759.2_Silent_p.N2734N|PLEC_ENST00000357649.2_Silent_p.N2711N|PLEC_ENST00000354958.2_Silent_p.N2685N|PLEC_ENST00000345136.3_Silent_p.N2707N	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2844	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.N2844N(1)|p.N2707N(1)|p.N2734N(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TCAGCTTCTCATTGGTGGCCT	0.672																																																	3	Substitution - coding silent(3)	kidney(3)											43.0	47.0	46.0					8																	144995868		2174	4268	6442	SO:0001819	synonymous_variant	5339			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8532T>C	8.37:g.144995868A>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																				0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1		NM_000445	
PLXNA1	5361	broad.mit.edu	37	3	126733641	126733641	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:126733641C>A	ENST00000393409.2	+	13	2844	c.2844C>A	c.(2842-2844)taC>taA	p.Y948*	PLXNA1_ENST00000251772.4_Nonsense_Mutation_p.Y925*	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	948	IPT/TIG 1.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.Y925*(1)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CACCACACTACCGCGCCCTGT	0.647																																																	1	Substitution - Nonsense(1)	kidney(1)											68.0	49.0	55.0					3																	126733641		2202	4298	6500	SO:0001587	stop_gained	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2844C>A	3.37:g.126733641C>A	ENSP00000377061:p.Tyr948*	Somatic		WXS	Illumina GAIIx	Phase_I		Nonsense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	C	38	6.890525	0.97912	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	.	.	.	4.21	4.21	0.49690	.	0.652496	0.14083	N	0.342524	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	16.7531	0.85492	0.0:1.0:0.0:0.0	.	.	.	.	X	948;925	.	ENSP00000251772:Y925X	Y	+	3	2	PLXNA1	128216331	1.000000	0.71417	0.998000	0.56505	0.204000	0.24138	4.789000	0.62446	2.184000	0.69523	0.484000	0.47621	TAC		0.647	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1		NM_032242	
GALNT4	8693	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	89917147	89917147	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr12:89917147A>T	ENST00000529983.2	-	1	1436	c.1180T>A	c.(1180-1182)Ttc>Atc	p.F394I	GALNT4_ENST00000413530.1_Missense_Mutation_p.F222I|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000549504.1_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.F391I|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000393179.4_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	394					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.F394I(1)		endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CTATTGTAGAAGTGCTCTTTG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											83.0	77.0	79.0					12																	89917147		1860	4096	5956	SO:0001583	missense	100528030			Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1180T>A	12.37:g.89917147A>T	ENSP00000436604:p.Phe394Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296528	0.81025	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.70399	-0.48;-0.48;-0.48	5.66	5.66	0.87406	.	.	.	.	.	T	0.70718	0.3256	M	0.63428	1.95	0.51482	D	0.999922	B;B	0.28055	0.199;0.126	B;B	0.34180	0.177;0.086	T	0.67848	-0.5564	9	0.33141	T	0.24	.	15.0588	0.71936	1.0:0.0:0.0:0.0	.	391;394	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	I	391;222;394	ENSP00000447852:F391I;ENSP00000389686:F222I;ENSP00000436604:F394I	ENSP00000436604:F394I	F	-	1	0	GALNT4;RP11-1109F11.4	88441278	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.268000	0.95675	2.151000	0.67156	0.482000	0.46254	TTC		0.458	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2		NM_003774	
PPP1R9A	55607	hgsc.bcm.edu;ucsc.edu	37	7	94919499	94919499	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr7:94919499delA	ENST00000433881.1	+	16	3713	c.3181delA	c.(3181-3183)aaafs	p.K1061fs	PPP1R9A_ENST00000289495.5_Frame_Shift_Del_p.K1259fs|PPP1R9A_ENST00000456331.2_Frame_Shift_Del_p.K1216fs|PPP1R9A_ENST00000433360.1_Frame_Shift_Del_p.K1337fs|PPP1R9A_ENST00000424654.1_Frame_Shift_Del_p.K1216fs|PPP1R9A_ENST00000340694.4_Frame_Shift_Del_p.K1061fs			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	1061	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			GGCCCAAGAGAAAATGGAAAA	0.453										HNSCC(28;0.073)																																							0													91.0	89.0	90.0					7																	94919499		2203	4300	6503	SO:0001589	frameshift_variant	55607			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.3181delA	7.37:g.94919499delA	ENSP00000398870:p.Lys1061fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Frame_Shift_Del	DEL	ENST00000433881.1	37	CCDS34683.1																																																																																				0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1		NM_001166160	
PPP2R3B	28227	hgsc.bcm.edu;ucsc.edu	37	X	322172	322172	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chrX:322172delC	ENST00000390665.3	-	2	496	c.478delG	c.(478-480)gccfs	p.A160fs		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	160					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|phosphoprotein phosphatase activity (GO:0004721)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(5)|lung(5)|skin(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCCATGGTGGCCCTCTCGTGG	0.647																																																	0													157.0	186.0	176.0					X																	322172		2182	4262	6444	SO:0001589	frameshift_variant	28227			AF215840	CCDS14104.1	Xp22.3 and Yp11.3	2013-01-10	2010-06-18		ENSG00000167393	ENSG00000167393		"""Pseudoautosomal regions / PAR1"", ""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	13417	protein-coding gene	gene with protein product		300339	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'', beta"""	PPP2R3L		11173861	Standard	NM_013239		Approved	PPP2R3LY, PR48	uc004cpg.3	Q9Y5P8	OTTHUMG00000021052	ENST00000390665.3:c.478delG	X.37:g.322172delC	ENSP00000375080:p.Ala160fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P4G9|Q7RTT1|Q96H01	Frame_Shift_Del	DEL	ENST00000390665.3	37	CCDS14104.1																																																																																				0.647	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2		NM_013239	
PRR23A	729627	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	138724479	138724479	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr3:138724479G>A	ENST00000383163.2	-	1	631	c.632C>T	c.(631-633)tCt>tTt	p.S211F	MRPS22_ENST00000495075.1_5'Flank	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	211	Pro-rich.							p.S211F(1)		endometrium(3)|kidney(1)|lung(7)	11						GGGGCCTGGAGAGTGTCCCTC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											33.0	39.0	37.0					3																	138724479		692	1591	2283	SO:0001583	missense	729627				CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.632C>T	3.37:g.138724479G>A	ENSP00000372649:p.Ser211Phe	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000383163.2	37	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918681	0.33908	.	.	ENSG00000206260	ENST00000383163	.	.	.	2.59	1.68	0.24146	.	1.264620	0.05719	N	0.597369	T	0.59838	0.2223	M	0.63843	1.955	0.09310	N	1	D	0.69078	0.997	D	0.81914	0.995	T	0.36553	-0.9743	9	0.66056	D	0.02	.	6.7946	0.23719	0.0:0.0:0.7248:0.2752	.	211	A6NEV1	PR23A_HUMAN	F	211	.	ENSP00000372649:S211F	S	-	2	0	PRR23A	140207169	0.002000	0.14202	0.001000	0.08648	0.014000	0.08584	0.855000	0.27805	0.624000	0.30286	0.491000	0.48974	TCT		0.647	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1		NM_001134659	
PRRC2A	7916	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	31598498	31598498	+	Silent	SNP	C	C	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr6:31598498C>A	ENST00000376033.2	+	15	2619	c.2385C>A	c.(2383-2385)gtC>gtA	p.V795V	PRRC2A_ENST00000376007.4_Silent_p.V795V	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	795	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.V795V(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TAGGAGATGTCTTCACCGCCA	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											78.0	68.0	72.0					6																	31598498		2203	4300	6503	SO:0001819	synonymous_variant	7916			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.2385C>A	6.37:g.31598498C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																				0.592	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1		NM_080686	
RAI2	10742	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	17819773	17819773	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chrX:17819773C>T	ENST00000545871.1	-	3	818	c.358G>A	c.(358-360)Gtg>Atg	p.V120M	RAI2_ENST00000331511.1_Missense_Mutation_p.V120M|RAI2_ENST00000451717.1_Missense_Mutation_p.V120M|RAI2_ENST00000360011.1_Missense_Mutation_p.V120M|RAI2_ENST00000415486.3_Missense_Mutation_p.V70M	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	120					embryo development (GO:0009790)			p.V120M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					GGCAGTTGCACGGGGCCCTGG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											58.0	61.0	60.0					X																	17819773		2203	4296	6499	SO:0001583	missense	10742			Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.358G>A	X.37:g.17819773C>T	ENSP00000444210:p.Val120Met	Somatic		WXS	Illumina HiSeq	Phase_I	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	37	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289640	0.40494	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.84	5.63	3.88	0.44766	.	0.000000	0.64402	D	0.000002	T	0.33760	0.0874	L	0.32530	0.975	0.45439	D	0.998411	P;P	0.48294	0.908;0.796	B;B	0.36959	0.237;0.237	T	0.10917	-1.0609	10	0.62326	D	0.03	-10.2203	11.5497	0.50713	0.0:0.8517:0.0:0.1483	.	70;120	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	M	120;120;120;120;70	ENSP00000333456:V120M;ENSP00000353106:V120M;ENSP00000444210:V120M;ENSP00000401323:V120M;ENSP00000392578:V70M	ENSP00000333456:V120M	V	-	1	0	RAI2	17729694	0.996000	0.38824	0.998000	0.56505	0.964000	0.63967	3.496000	0.53288	0.562000	0.29204	-0.191000	0.12829	GTG		0.617	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1		NM_021785	
RNLS	55328	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	90122392	90122392	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr10:90122392A>G	ENST00000331772.4	-	5	639	c.617T>C	c.(616-618)aTt>aCt	p.I206T	RNLS_ENST00000466945.1_5'UTR|RNLS_ENST00000437752.1_Missense_Mutation_p.I123T|RNLS_ENST00000371947.3_Missense_Mutation_p.I206T	NM_001031709.2	NP_001026879.2	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	206					cardiac left ventricle morphogenesis (GO:0003214)|dopamine metabolic process (GO:0042417)|epinephrine metabolic process (GO:0042414)|heart contraction (GO:0060047)|norepinephrine metabolic process (GO:0042415)|phosphate ion homeostasis (GO:0055062)|regulation of systemic arterial blood pressure (GO:0003073)|response to epinephrine (GO:0071871)|response to ischemia (GO:0002931)|response to norepinephrine (GO:0071873)|response to salt (GO:1902074)	extracellular space (GO:0005615)	oxidoreductase activity (GO:0016491)	p.I206T(1)		breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						AGGGACATCAATCTTCGTACC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											145.0	134.0	138.0					10																	90122392		2203	4300	6503	SO:0001583	missense	55328			BC005364	CCDS7388.1, CCDS31239.1	10q23.31	2009-04-22	2009-04-22	2009-04-22	ENSG00000184719	ENSG00000184719			25641	protein-coding gene	gene with protein product		609360	"""chromosome 10 open reading frame 59"""	C10orf59		15841207, 17565281	Standard	NM_001031709		Approved	FLJ11218, renalase	uc001kfe.3	Q5VYX0	OTTHUMG00000018692	ENST00000331772.4:c.617T>C	10.37:g.90122392A>G	ENSP00000332530:p.Ile206Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BS33|Q9NUP8	Missense_Mutation	SNP	ENST00000331772.4	37	CCDS31239.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.027487	0.75390	.	.	ENSG00000184719	ENST00000371947;ENST00000437752;ENST00000331772	D;T;D	0.92249	-3.0;0.83;-3.0	6.07	4.94	0.65067	Amine oxidase (1);	0.048062	0.85682	D	0.000000	D	0.94863	0.8340	M	0.74881	2.28	0.54753	D	0.999981	D;P;D	0.76494	0.999;0.952;0.982	D;P;P	0.83275	0.996;0.845;0.888	D	0.92994	0.6417	10	0.24483	T	0.36	.	11.2306	0.48910	0.9276:0.0:0.0724:0.0	.	123;206;206	B4DJW3;Q5VYX0;Q5VYX0-2	.;RNLS_HUMAN;.	T	206;123;206	ENSP00000361015:I206T;ENSP00000387577:I123T;ENSP00000332530:I206T	ENSP00000332530:I206T	I	-	2	0	RNLS	90112372	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.306000	0.72810	1.117000	0.41842	0.477000	0.44152	ATT		0.468	RNLS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049250.1		NM_018363	
SARDH	1757	broad.mit.edu	37	9	136577831	136577831	+	Splice_Site	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr9:136577831C>G	ENST00000371872.4	-	10	1495	c.1238G>C	c.(1237-1239)gGa>gCa	p.G413A	SARDH_ENST00000422262.2_Splice_Site_p.G245A|SARDH_ENST00000439388.1_Splice_Site_p.G413A	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	413					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.G413A(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CAGCATCATTCCTGGCAGGAA	0.627																																																	1	Substitution - Missense(1)	kidney(1)											47.0	48.0	48.0					9																	136577831		2203	4300	6503	SO:0001630	splice_region_variant	1757				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1238-1G>C	9.37:g.136577831C>G		Somatic		WXS	Illumina GAIIx	Phase_I	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.643075	0.87859	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227	D;D;D	0.94758	-3.51;-3.51;-3.51	4.3	4.3	0.51218	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.98242	0.9418	H	0.96861	3.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99870	1.1095	10	0.87932	D	0	.	16.7838	0.85569	0.0:1.0:0.0:0.0	.	413	Q9UL12	SARDH_HUMAN	A	413;413;245;413;413	ENSP00000360938:G413A;ENSP00000403084:G413A;ENSP00000415537:G245A	ENSP00000360938:G413A	G	-	2	0	SARDH	135567652	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.488000	0.81441	1.947000	0.56498	0.491000	0.48974	GGA		0.627	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			Missense_Mutation
SCN3A	6328	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	165948825	165948825	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr2:165948825G>C	ENST00000360093.3	-	27	5237	c.4746C>G	c.(4744-4746)caC>caG	p.H1582Q	AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000283254.7_Missense_Mutation_p.H1582Q|SCN3A_ENST00000465043.1_5'UTR|SCN3A_ENST00000540861.1_Missense_Mutation_p.H65Q|SCN3A_ENST00000409101.3_Missense_Mutation_p.H1533Q	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1582					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.H1533Q(1)|p.H1582Q(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGAAGTAGTAGTGTCTGAGGG	0.433																																																	2	Substitution - Missense(2)	kidney(2)											141.0	124.0	130.0					2																	165948825		2203	4300	6503	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4746C>G	2.37:g.165948825G>C	ENSP00000353206:p.His1582Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	G	11.51	1.661399	0.29515	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.98345	-4.88;-4.88;-4.88;-4.88	5.78	1.47	0.22746	.	0.219831	0.34386	N	0.004011	D	0.93012	0.7776	N	0.04320	-0.23	0.39741	D	0.971741	B;B;P	0.38078	0.429;0.134;0.617	B;B;B	0.43478	0.326;0.059;0.421	D	0.88870	0.3332	10	0.32370	T	0.25	.	6.6468	0.22939	0.5774:0.0:0.4226:0.0	.	1533;1533;1582	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	Q	1582;1582;1533;65	ENSP00000353206:H1582Q;ENSP00000283254:H1582Q;ENSP00000386726:H1533Q;ENSP00000439920:H65Q	ENSP00000283254:H1582Q	H	-	3	2	SCN3A	165657071	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.956000	0.49129	0.477000	0.27464	-0.229000	0.12294	CAC		0.433	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_006922	
SCN9A	6335	hgsc.bcm.edu;ucsc.edu	37	2	167137006	167137006	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr2:167137006delT	ENST00000409435.1	-	13	2203	c.2204delA	c.(2203-2205)aagfs	p.K735fs	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.K724fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.K736fs|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.K736fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	735					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATAGATACACTTTTTGAATTT	0.343																																																	0													56.0	54.0	54.0					2																	167137006		1806	4083	5889	SO:0001589	frameshift_variant	6335			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.2204delA	2.37:g.167137006delT	ENSP00000386330:p.Lys735fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	CCDS46441.1																																																																																				0.343	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1		NM_002977	
SDC3	9672	hgsc.bcm.edu;ucsc.edu	37	1	31347255	31347255	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr1:31347255G>A	ENST00000339394.6	-	4	1225	c.1051C>T	c.(1051-1053)Ccc>Tcc	p.P351S	SDC3_ENST00000471567.1_5'Flank|SDC3_ENST00000336798.7_Missense_Mutation_p.P293S	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	351					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GCACCCTTGGGCAGTGTCCCA	0.632																																																	0													80.0	87.0	85.0					1																	31347255		2203	4300	6503	SO:0001583	missense	9672			AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.1051C>T	1.37:g.31347255G>A	ENSP00000344468:p.Pro351Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876360	0.72180	.	.	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.25414	1.8;1.8	4.84	4.84	0.62591	.	0.215329	0.30742	N	0.008963	T	0.27524	0.0676	N	0.19112	0.55	0.34810	D	0.737585	D;D	0.61697	0.99;0.975	P;P	0.57846	0.828;0.766	T	0.22521	-1.0214	10	0.38643	T	0.18	-17.9559	10.3322	0.43829	0.0:0.1541:0.7057:0.1402	.	351;293	O75056;D3DPN2	SDC3_HUMAN;.	S	293;351	ENSP00000338346:P293S;ENSP00000344468:P351S	ENSP00000338346:P293S	P	-	1	0	SDC3	31119842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.303000	0.43646	2.535000	0.85469	0.563000	0.77884	CCC		0.632	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1		NM_014654	
SDK1	221935	hgsc.bcm.edu	37	7	4007044	4007045	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr7:4007044_4007045insC	ENST00000404826.2	+	10	1663_1664	c.1524_1525insC	c.(1525-1527)cccfs	p.P509fs	SDK1_ENST00000389531.3_Frame_Shift_Ins_p.P509fs	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	509	Ig-like C2-type 5.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGGCTCCCAAACCCGCCATCAC	0.55																																																	0																																										SO:0001589	frameshift_variant	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1527dupC	7.37:g.4007047_4007047dupC	ENSP00000385899:p.Pro509fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TEN9|Q8TEP5|Q96N44	Frame_Shift_Ins	INS	ENST00000404826.2	37	CCDS34590.1																																																																																				0.550	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1		NM_152744	
SNX21	90203	broad.mit.edu	37	20	44463023	44463037	+	In_Frame_Del	DEL	GACGAGGACGACGAG	GACGAGGACGACGAG	-	rs547874769	byFrequency	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	GACGAGGACGACGAG	GACGAGGACGACGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr20:44463023_44463037delGACGAGGACGACGAG	ENST00000491381.1	+	2	273_287	c.205_219delGACGAGGACGACGAG	c.(205-219)gacgaggacgacgagdel	p.DEDDE74del	SNX21_ENST00000372542.1_In_Frame_Del_p.DEDDE65del|TNNC2_ENST00000372557.1_5'Flank|SNX21_ENST00000372541.1_In_Frame_Del_p.DEDDE65del|SNX21_ENST00000342644.5_In_Frame_Del_p.DEDDE74del|SNX21_ENST00000462307.1_In_Frame_Del_p.DEDDE74del|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	74					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				CGCcgaggacgacgaggacgacgaggacgaggacg	0.693																																																	0									,,,	30,4214		13,4,2105					,,,	1.3	1.0			26	50,8182		15,20,4081	no	coding,coding,coding,coding	SNX21	NM_152897.1,NM_033421.2,NM_001042633.1,NM_001042632.1	,,,	28,24,6186	A1A1,A1R,RR		0.6074,0.7069,0.6412	,,,	,,,		80,12396				SO:0001651	inframe_deletion	90203			AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.205_219delGACGAGGACGACGAG	20.37:g.44463023_44463037delGACGAGGACGACGAG	ENSP00000418593:p.Asp74_Glu78del	Somatic		WXS	Illumina GAIIx	Phase_I	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	In_Frame_Del	DEL	ENST00000491381.1	37	CCDS13377.1																																																																																				0.693	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1		NM_033421	
SRRM2	23524	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	2809006	2809006	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr16:2809006C>T	ENST00000301740.8	+	6	1163	c.614C>T	c.(613-615)cCt>cTt	p.P205L		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	205	Lys-rich.|Ser-rich.|Sufficient for RNA-binding.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.P205L(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AGCAGCTCTCCTCGACGGGAG	0.473																																																	1	Substitution - Missense(1)	kidney(1)											102.0	100.0	101.0					16																	2809006		2198	4300	6498	SO:0001583	missense	23524			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.614C>T	16.37:g.2809006C>T	ENSP00000301740:p.Pro205Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498974	0.64298	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000396975;ENST00000426305	T	0.26660	1.72	4.59	4.59	0.56863	.	0.000000	0.49916	D	0.000140	T	0.46464	0.1394	L	0.58810	1.83	0.51767	D	0.999935	D	0.89917	1.0	D	0.80764	0.994	T	0.40776	-0.9545	10	0.48119	T	0.1	-12.7588	14.8866	0.70572	0.0:1.0:0.0:0.0	.	205	Q9UQ35	SRRM2_HUMAN	L	205;205;109;170	ENSP00000301740:P205L	ENSP00000301740:P205L	P	+	2	0	SRRM2	2749007	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.563000	0.45922	2.077000	0.62373	0.561000	0.74099	CCT		0.473	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			
TJP1	7082	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	30064288	30064288	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr15:30064288T>G	ENST00000346128.6	-	4	765	c.291A>C	c.(289-291)aaA>aaC	p.K97N	TJP1_ENST00000400011.2_Missense_Mutation_p.K101N|TJP1_ENST00000545208.2_Missense_Mutation_p.K97N|TJP1_ENST00000356107.6_Missense_Mutation_p.K97N|TJP1_ENST00000495972.2_Missense_Mutation_p.K97N	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	97	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.K97N(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TTTTCCCACTTTTCCTTAGTT	0.353																																					Melanoma(77;681 1843 6309 6570)												1	Substitution - Missense(1)	kidney(1)											69.0	62.0	64.0					15																	30064288		1813	4078	5891	SO:0001583	missense	7082				CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.291A>C	15.37:g.30064288T>G	ENSP00000281537:p.Lys97Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630482	0.46944	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	5.22	2.82	0.32997	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.35068	0.0919	L	0.33710	1.025	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.992	D;D;D;P	0.97110	0.999;0.999;1.0;0.856	T	0.01688	-1.1295	9	.	.	.	.	10.0095	0.41977	0.0:0.1377:0.0:0.8623	.	90;97;97;101	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	N	97;101;97;97;97	ENSP00000281537:K97N;ENSP00000382890:K101N;ENSP00000441202:K97N;ENSP00000348416:K97N	.	K	-	3	2	TJP1	27851580	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	3.401000	0.52601	0.367000	0.24454	0.477000	0.44152	AAA		0.353	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3		NM_003257	
TLCD1	116238	broad.mit.edu;hgsc.bcm.edu	37	17	27052361	27052361	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr17:27052361C>G	ENST00000292090.3	-	3	431	c.321G>C	c.(319-321)caG>caC	p.Q107H	AC010761.8_ENST00000582718.1_RNA|SNORD4B_ENST00000459083.1_RNA|AC010761.14_ENST00000587898.1_RNA|TLCD1_ENST00000394933.3_Missense_Mutation_p.Q60H|SNORD42A_ENST00000459584.1_RNA|SNORD4A_ENST00000459174.1_RNA	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	107	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Q107H(1)		breast(2)|endometrium(1)|kidney(2)|lung(2)	7	Lung NSC(42;0.00431)					AGGCTCGCGTCTGTCCGCTAG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											78.0	67.0	71.0					17																	27052361		2203	4300	6503	SO:0001583	missense	116238			BC014072	CCDS11242.1, CCDS54102.1	17q11.2	2007-03-23			ENSG00000160606	ENSG00000160606			25177	protein-coding gene	gene with protein product						12151215	Standard	NM_138463		Approved		uc002hco.3	Q96CP7	OTTHUMG00000132683	ENST00000292090.3:c.321G>C	17.37:g.27052361C>G	ENSP00000292090:p.Gln107His	Somatic		WXS	Illumina HiSeq	Phase_I	A8MYP9	Missense_Mutation	SNP	ENST00000292090.3	37	CCDS11242.1	.	.	.	.	.	.	.	.	.	.	C	8.139	0.784768	0.16189	.	.	ENSG00000160606	ENST00000292090;ENST00000394933	D;D	0.85171	-1.95;-1.95	5.62	2.55	0.30701	TRAM/LAG1/CLN8 homology domain (3);	0.054643	0.85682	D	0.000000	D	0.86744	0.6006	L	0.51422	1.61	0.41020	D	0.985074	D;D	0.69078	0.996;0.997	D;D	0.66084	0.941;0.938	T	0.82378	-0.0487	10	0.28530	T	0.3	-14.1051	8.4745	0.33005	0.0:0.7567:0.0:0.2433	.	60;107	A8MYP9;Q96CP7	.;TLCD1_HUMAN	H	107;60	ENSP00000292090:Q107H;ENSP00000378391:Q60H	ENSP00000292090:Q107H	Q	-	3	2	TLCD1	24076488	0.016000	0.18221	0.066000	0.19879	0.065000	0.16274	-0.027000	0.12371	0.403000	0.25479	0.555000	0.69702	CAG		0.517	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1		NM_138463	
LINC01182	101929071	broad.mit.edu	37	4	13659429	13659429	+	lincRNA	DEL	A	A	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr4:13659429delA	ENST00000510907.1	+	0	232				AC098830.1_ENST00000516283.1_RNA																							AGATATTGGCAATTTGGAGCA	0.433																																																	0																																												0																															4.37:g.13659429delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000510907.1	37																																																																																					0.433	RP11-341G5.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000360404.1			
TSPAN5	10098	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	99397581	99397581	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr4:99397581C>T	ENST00000305798.3	-	6	1009	c.607G>A	c.(607-609)Gat>Aat	p.D203N	TSPAN5_ENST00000509168.1_5'Flank|TSPAN5_ENST00000505184.1_Missense_Mutation_p.D132N	NM_005723.3	NP_005714.2	P62079	TSN5_HUMAN	tetraspanin 5	203					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)	p.D203N(1)		kidney(2)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		TGCCTGGCATCATAGCCACAC	0.448																																																	1	Substitution - Missense(1)	kidney(1)											168.0	141.0	150.0					4																	99397581		2203	4300	6503	SO:0001583	missense	10098				CCDS3646.1	4q22.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000168785	ENSG00000168785		"""Tetraspanins"""	17753	protein-coding gene	gene with protein product		613136	"""transmembrane 4 superfamily member 9"""	TM4SF9			Standard	NM_005723		Approved	Tspan-5, NET-4	uc003hub.3	P62079	OTTHUMG00000131008	ENST00000305798.3:c.607G>A	4.37:g.99397581C>T	ENSP00000307701:p.Asp203Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RDY2|O60628|O60746|Q6FHE5|Q9JLY1	Missense_Mutation	SNP	ENST00000305798.3	37	CCDS3646.1	.	.	.	.	.	.	.	.	.	.	C	34	5.340573	0.95783	.	.	ENSG00000168785	ENST00000305798;ENST00000505184	T;T	0.80304	-1.36;-1.36	5.61	5.61	0.85477	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.88573	0.6473	L	0.58354	1.805	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.88058	0.2792	10	0.52906	T	0.07	.	19.6278	0.95687	0.0:1.0:0.0:0.0	.	203	P62079	TSN5_HUMAN	N	203;132	ENSP00000307701:D203N;ENSP00000423916:D132N	ENSP00000307701:D203N	D	-	1	0	TSPAN5	99616604	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.620000	0.83070	2.646000	0.89796	0.585000	0.79938	GAT		0.448	TSPAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253641.2		NM_005723	
VHL	7428	hgsc.bcm.edu	37	3	10183864	10183864	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5675-01A-11W-1584-10	TCGA-CJ-5675-11A-01W-1585-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6b33ad1e-6eed-4a96-b8e3-360f12c58ea7	c5a65315-0c2c-46a1-b8b9-ea114ce12fec	g.chr3:10183864C>A	ENST00000256474.2	+	1	1173	c.333C>A	c.(331-333)agC>agA	p.S111R	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Missense_Mutation_p.S111R	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	111	Involved in binding to CCT complex.		S -> C (in VHLD; type II).|S -> N (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911}.|S -> R (in VHLD; type I). {ECO:0000269|PubMed:8956040}.		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.S111R(3)|p.S111S(2)|p.?(1)|p.I109_R113del(1)|p.S111fs*45(1)|p.H110_S111del(1)|p.S111_Y112del(1)|p.Y112fs*47(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)		GCATCCACAGCTACCGAGGTA	0.692		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	11	Substitution - Missense(3)|Deletion - In frame(3)|Deletion - Frameshift(2)|Substitution - coding silent(2)|Unknown(1)	kidney(11)	GRCh37	CM951281	VHL	M							10.0	11.0	11.0					3																	10183864		1807	3766	5573	SO:0001583	missense	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.333C>A	3.37:g.10183864C>A	ENSP00000256474:p.Ser111Arg	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.980286	0.92982	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99773	-6.72;-6.72	5.17	4.3	0.51218	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.096185	0.64402	D	0.000001	D	0.99510	0.9825	L	0.46157	1.445	0.25288	N	0.989387	D;D	0.89917	0.991;1.0	P;D	0.85130	0.858;0.997	D	0.98010	1.0365	10	0.87932	D	0	-5.879	11.6184	0.51102	0.0:0.9134:0.0:0.0866	.	111;111	P40337-2;P40337	.;VHL_HUMAN	R	111;111;29	ENSP00000256474:S111R;ENSP00000344757:S111R	ENSP00000256474:S111R	S	+	3	2	VHL	10158864	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.672000	0.37523	1.199000	0.43173	0.479000	0.44913	AGC		0.692	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WDR35	57539	broad.mit.edu;ucsc.edu	37	2	20138115	20138115	+	Silent	SNP	C	C	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr2:20138115C>G	ENST00000345530.3	-	19	2122	c.2007G>C	c.(2005-2007)cgG>cgC	p.R669R	WDR35_ENST00000416055.2_Silent_p.R234R|WDR35_ENST00000281405.4_Silent_p.R658R	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	669					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.R669R(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGCAGAGACCGAATCTCAA	0.368																																																	1	Substitution - coding silent(1)	kidney(1)											90.0	91.0	91.0					2																	20138115		2203	4300	6503	SO:0001819	synonymous_variant	57539			AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2007G>C	2.37:g.20138115C>G		Somatic		WXS	Illumina GAIIx	Phase_I	B3KVI5|Q4ZG01|Q8NE11	Silent	SNP	ENST00000345530.3	37	CCDS33152.1																																																																																				0.368	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2		NM_020779	
ZBTB49	166793	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	4303969	4303969	+	Silent	SNP	C	C	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr4:4303969C>T	ENST00000337872.4	+	3	527	c.406C>T	c.(406-408)Cta>Tta	p.L136L	ZBTB49_ENST00000355834.3_Silent_p.L136L|ZBTB49_ENST00000538529.1_5'UTR	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L136L(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						TACATTGTCTCTACAAAGCAC	0.438																																																	1	Substitution - coding silent(1)	kidney(1)											131.0	123.0	126.0					4																	4303969		2203	4300	6503	SO:0001819	synonymous_variant	166793			AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.406C>T	4.37:g.4303969C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																				0.438	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3		NM_145291	
ZFHX3	463	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	72993014	72993014	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr16:72993014T>A	ENST00000268489.5	-	2	1703	c.1031A>T	c.(1030-1032)aAc>aTc	p.N344I	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	344					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.N344I(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AAAGTTTTTGTTTTTTGGTTC	0.428																																																	1	Substitution - Missense(1)	kidney(1)											63.0	70.0	68.0					16																	72993014		2198	4300	6498	SO:0001583	missense	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1031A>T	16.37:g.72993014T>A	ENSP00000268489:p.Asn344Ile	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	T	4.633	0.117698	0.08881	.	.	ENSG00000140836	ENST00000268489	T	0.74209	-0.82	4.92	3.81	0.43845	.	0.000000	0.53938	D	0.000058	T	0.73241	0.3562	L	0.36672	1.1	0.80722	D	1	D	0.62365	0.991	P	0.54060	0.741	T	0.73151	-0.4073	10	0.52906	T	0.07	.	11.5036	0.50451	0.0:0.0:0.2844:0.7156	.	344	Q15911	ZFHX3_HUMAN	I	344	ENSP00000268489:N344I	ENSP00000268489:N344I	N	-	2	0	ZFHX3	71550515	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.227000	0.32576	0.814000	0.34374	0.482000	0.46254	AAC		0.428	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1		NM_006885	
ZNF407	55628	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	72346773	72346773	+	Silent	SNP	T	T	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr18:72346773T>C	ENST00000299687.5	+	1	3798	c.3798T>C	c.(3796-3798)gtT>gtC	p.V1266V	ZNF407_ENST00000309902.6_Silent_p.V1266V|ZNF407_ENST00000582337.1_Silent_p.V1266V|ZNF407_ENST00000577538.1_Silent_p.V1266V	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.V1266V(2)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTGTGCTCGTTGTGACAAGAA	0.562																																																	2	Substitution - coding silent(2)	kidney(2)											34.0	38.0	37.0					18																	72346773		1940	4141	6081	SO:0001819	synonymous_variant	55628			AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3798T>C	18.37:g.72346773T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																				0.562	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1		NM_017757	
ZNF763	284390	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	12089265	12089265	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr19:12089265G>A	ENST00000358987.3	+	4	653	c.526G>A	c.(526-528)Gaa>Aaa	p.E176K	ZNF763_ENST00000343949.5_Missense_Mutation_p.E179K|ZNF763_ENST00000538752.1_Missense_Mutation_p.E196K|ZNF763_ENST00000545530.1_Missense_Mutation_p.E54K|ZNF763_ENST00000590798.1_Missense_Mutation_p.E196K			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	176					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E178K(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGCTTGTAAAGAATGTGGAAA	0.418																																																	1	Substitution - Missense(1)	kidney(1)											107.0	112.0	111.0					19																	12089265		2201	4300	6501	SO:0001583	missense	284390			AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.526G>A	19.37:g.12089265G>A	ENSP00000402017:p.Glu176Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRU3|B4DRE7	Missense_Mutation	SNP	ENST00000358987.3	37		.	.	.	.	.	.	.	.	.	.	g	9.276	1.046958	0.19748	.	.	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	T;T;T;T	0.16597	2.33;2.33;2.33;2.33	1.16	-2.32	0.06745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10337	0.0253	L	0.28504	0.86	0.09310	N	1	B;B;B	0.33583	0.418;0.006;0.004	B;B;B	0.33890	0.172;0.007;0.011	T	0.27872	-1.0061	9	0.52906	T	0.07	.	4.0701	0.09879	0.208:0.2387:0.5533:0.0	.	196;176;179	F5H0A9;Q0D2J5;Q0D2J5-2	.;ZN763_HUMAN;.	K	196;179;54;176	ENSP00000438117:E196K;ENSP00000369774:E179K;ENSP00000446166:E54K;ENSP00000402017:E176K	ENSP00000369774:E179K	E	+	1	0	ZNF763	11950265	0.000000	0.05858	0.014000	0.15608	0.110000	0.19582	-0.034000	0.12225	-0.340000	0.08388	0.195000	0.17529	GAA		0.418	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1		NM_001012753	
ZNF814	730051	broad.mit.edu;hgsc.bcm.edu	37	19	58386268	58386268	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78b7e188-9252-48b6-9e10-04eb8690b879	bfa15fdf-d1f5-4e0c-986f-c888e0cf77da	g.chr19:58386268G>T	ENST00000435989.2	-	3	724	c.490C>A	c.(490-492)Cat>Aat	p.H164N	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	164					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H164N(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CCTGACACATGCAACTTACAC	0.507																																																	1	Substitution - Missense(1)	kidney(1)											134.0	99.0	109.0					19																	58386268		692	1590	2282	SO:0001583	missense	730051				CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.490C>A	19.37:g.58386268G>T	ENSP00000410545:p.His164Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.158	0.788865	0.16258	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.07800	3.16	2.27	-0.901	0.10540	.	.	.	.	.	T	0.11580	0.0282	M	0.87328	2.875	0.09310	N	1	P	0.36647	0.563	B	0.28305	0.088	T	0.10636	-1.0621	9	0.72032	D	0.01	.	7.5253	0.27652	0.2018:0.0:0.7982:0.0	.	164	B7Z6K7	ZN814_HUMAN	N	164	ENSP00000410545:H164N	ENSP00000365378:H164N	H	-	1	0	ZNF814	63078080	0.826000	0.29277	0.000000	0.03702	0.070000	0.16714	1.395000	0.34520	-0.150000	0.11195	0.195000	0.17529	CAT		0.507	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1		XM_001725708	
