#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
ABCC9	10060	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	21991035	21991035	+	Silent	SNP	T	T	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr12:21991035T>A	ENST00000261201.4	-	28	3542	c.3543A>T	c.(3541-3543)ggA>ggT	p.G1181G	ABCC9_ENST00000345162.2_Silent_p.G1145G|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Silent_p.G1181G	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1181	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)	p.G1181G(2)		NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGGTGGTGAGTCCTTCTGCTG	0.413																																																	2	Substitution - coding silent(2)	kidney(2)											122.0	119.0	120.0					12																	21991035		2203	4300	6503	SO:0001819	synonymous_variant	10060			AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.3543A>T	12.37:g.21991035T>A		Somatic		WXS	Illumina HiSeq	Phase_I	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																				0.413	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1		NM_005691	
ABHD2	11057	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	89731484	89731484	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr15:89731484C>G	ENST00000352732.5	+	8	1396	c.876C>G	c.(874-876)agC>agG	p.S292R	ABHD2_ENST00000355100.3_Missense_Mutation_p.S292R|ABHD2_ENST00000565973.1_Missense_Mutation_p.S292R	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	292					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.S292R(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					CGGACTTGAGCCGGCTCTACA	0.532																																					Colon(11;252 417 24570 33239 41878)												1	Substitution - Missense(1)	kidney(1)											118.0	102.0	108.0					15																	89731484		2200	4299	6499	SO:0001583	missense	11057			X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"""Abhydrolase domain containing"""	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.876C>G	15.37:g.89731484C>G	ENSP00000268129:p.Ser292Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406860	0.62399	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.62498	0.02;0.02	5.59	3.71	0.42584	Alpha/beta hydrolase fold-1 (1);	0.037406	0.85682	D	0.000000	T	0.53834	0.1821	L	0.51422	1.61	0.58432	D	0.999998	B	0.16802	0.019	B	0.16722	0.016	T	0.50898	-0.8773	10	0.30854	T	0.27	-3.6798	11.4168	0.49956	0.0:0.8556:0.0:0.1444	.	292	P08910	ABHD2_HUMAN	R	292	ENSP00000268129:S292R;ENSP00000347217:S292R	ENSP00000268129:S292R	S	+	3	2	ABHD2	87532488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.783000	0.55409	1.357000	0.45904	0.650000	0.86243	AGC		0.532	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			
IGHV6-1	28385	broad.mit.edu	37	14	106405448	106405448	+	RNA	DEL	C	C	-	rs375659082|rs77404616|rs373812673	byFrequency	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr14:106405448delC	ENST00000390593.2	-	0	415									immunoglobulin heavy variable 6-1																		aaaaaaaaaacaacaaCAGTT	0.408																																																	0																																												8755			X92224		14q32.33	2012-02-08			ENSG00000211933	ENSG00000211933		"""Immunoglobulins / IGH locus"""	5662	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152324		14.37:g.106405448delC		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000390593.2	37																																																																																					0.408	IGHV6-1-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325886.1		NG_001019	
AKAP6	9472	broad.mit.edu	37	14	33243070	33243070	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr14:33243070C>T	ENST00000280979.4	+	12	3729	c.3559C>T	c.(3559-3561)Cgt>Tgt	p.R1187C	AKAP6_ENST00000557272.1_Missense_Mutation_p.R1187C	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1187					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)	p.R1187C(1)		NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GTGGCAAACACGTCTACAAAA	0.413																																					Melanoma(49;821 1200 7288 13647 42351)												1	Substitution - Missense(1)	kidney(1)											71.0	68.0	69.0					14																	33243070		2203	4300	6503	SO:0001583	missense	9472			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3559C>T	14.37:g.33243070C>T	ENSP00000280979:p.Arg1187Cys	Somatic		WXS	Illumina GAIIx	Phase_I	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305101	0.60305	.	.	ENSG00000151320	ENST00000280979;ENST00000557272	T;T	0.37235	1.21;1.21	5.28	2.21	0.28008	.	0.069830	0.56097	D	0.000025	T	0.52725	0.1752	L	0.60455	1.87	0.45108	D	0.998127	D	0.89917	1.0	D	0.64410	0.925	T	0.59289	-0.7482	10	0.87932	D	0	-6.307	14.9331	0.70933	0.4586:0.5414:0.0:0.0	.	1187	Q13023	AKAP6_HUMAN	C	1187	ENSP00000280979:R1187C;ENSP00000451247:R1187C	ENSP00000280979:R1187C	R	+	1	0	AKAP6	32312821	0.126000	0.22350	0.995000	0.50966	0.974000	0.67602	0.484000	0.22308	0.691000	0.31592	0.591000	0.81541	CGT		0.413	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2		NM_004274	
ALKBH5	54890	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	18111566	18111566	+	Silent	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr17:18111566C>T	ENST00000399138.4	+	4	1046	c.1041C>T	c.(1039-1041)aaC>aaT	p.N347N	ALKBH5_ENST00000541285.1_Silent_p.N6N	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	347					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)	p.N347N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AGGAAGAGAACCGGCGCTCGG	0.602																																					Ovarian(166;154 1953 40235 46283 46309)												1	Substitution - coding silent(1)	kidney(1)											66.0	75.0	72.0					17																	18111566		1988	4159	6147	SO:0001819	synonymous_variant	54890			AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.1041C>T	17.37:g.18111566C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	37	CCDS42272.1																																																																																				0.602	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3		NM_017758	
APOB	338	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	21229236	21229236	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr2:21229236C>A	ENST00000233242.1	-	26	10631	c.10504G>T	c.(10504-10506)Ggt>Tgt	p.G3502C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3502	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.G3502C(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAACCGAACCCTTGACATCT	0.473																																																	1	Substitution - Missense(1)	kidney(1)											97.0	98.0	98.0					2																	21229236		2203	4300	6503	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10504G>T	2.37:g.21229236C>A	ENSP00000233242:p.Gly3502Cys	Somatic		WXS	Illumina HiSeq	Phase_I	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	12.37	1.916554	0.33815	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.80123	-1.34	5.67	4.78	0.61160	.	0.101421	0.43260	D	0.000585	D	0.88966	0.6581	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.90269	0.4306	10	0.87932	D	0	.	15.0593	0.71939	0.0:0.9309:0.0:0.0691	.	3502	P04114	APOB_HUMAN	C	3502	ENSP00000233242:G3502C	ENSP00000233242:G3502C	G	-	1	0	APOB	21082741	0.853000	0.29707	0.645000	0.29479	0.199000	0.23934	3.029000	0.49712	1.361000	0.45981	0.655000	0.94253	GGT		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			
ARID1A	8289	broad.mit.edu;hgsc.bcm.edu	37	1	27094308	27094308	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:27094308G>T	ENST00000324856.7	+	11	3387	c.3016G>T	c.(3016-3018)Gag>Tag	p.E1006*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.E623*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.E1006*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1006					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.E1006*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TACAACCAATGAGAAGATCAC	0.483			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Nonsense(1)	kidney(1)											113.0	98.0	103.0					1																	27094308		2203	4300	6503	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3016G>T	1.37:g.27094308G>T	ENSP00000320485:p.Glu1006*	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	40	8.248716	0.98724	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-14.304	18.8566	0.92255	0.0:0.0:1.0:0.0	.	.	.	.	X	1006;1006;623	.	ENSP00000320485:E1006X	E	+	1	0	ARID1A	26966895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.678000	0.91216	0.655000	0.94253	GAG		0.483	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2		NM_139135	
C12orf40	283461	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	40041619	40041619	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr12:40041619T>A	ENST00000324616.5	+	6	564	c.410T>A	c.(409-411)aTg>aAg	p.M137K	C12orf40_ENST00000398716.1_Missense_Mutation_p.M60K|C12orf40_ENST00000405531.3_Missense_Mutation_p.M137K	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	137								p.M137K(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						TCATATAGTATGCTTCACCCT	0.328																																																	1	Substitution - Missense(1)	kidney(1)											85.0	80.0	82.0					12																	40041619		1844	4092	5936	SO:0001583	missense	283461			AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.410T>A	12.37:g.40041619T>A	ENSP00000317671:p.Met137Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	1.634	-0.518301	0.04171	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.46819	0.86;0.87	3.98	1.51	0.23008	.	0.879697	0.09782	N	0.756539	T	0.30293	0.0760	N	0.19112	0.55	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.25187	-1.0139	10	0.62326	D	0.03	.	5.0315	0.14411	0.1617:0.0989:0.0:0.7395	.	137	Q86WS4	CL040_HUMAN	K	137;60;137	ENSP00000383897:M137K;ENSP00000317671:M137K	ENSP00000317671:M137K	M	+	2	0	C12orf40	38327886	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.360000	0.07622	0.012000	0.14892	-1.481000	0.00988	ATG		0.328	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2		NM_173599	
CACNA1H	8912	broad.mit.edu;hgsc.bcm.edu	37	16	1260841	1260841	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr16:1260841A>T	ENST00000348261.5	+	21	4341	c.4093A>T	c.(4093-4095)Aac>Tac	p.N1365Y	CACNA1H_ENST00000358590.4_Missense_Mutation_p.N1365Y|CACNA1H_ENST00000565831.1_Missense_Mutation_p.N1365Y	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1365					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)	p.N1365Y(2)		breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GAGCAGCTGGAACCTGCTGGA	0.677																																																	2	Substitution - Missense(2)	kidney(2)											63.0	72.0	69.0					16																	1260841		2190	4282	6472	SO:0001583	missense	8912			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4093A>T	16.37:g.1260841A>T	ENSP00000334198:p.Asn1365Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680450	0.88542	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.99259	-5.64;-5.64	4.24	4.24	0.50183	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99585	0.9850	H	0.96576	3.845	0.58432	D	0.99999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.97110	1.0;1.0;0.995;0.999;0.999	D	0.97812	1.0251	10	0.87932	D	0	.	12.9429	0.58357	1.0:0.0:0.0:0.0	.	106;106;106;1365;1365	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	Y	1365	ENSP00000334198:N1365Y;ENSP00000351401:N1365Y	ENSP00000334198:N1365Y	N	+	1	0	CACNA1H	1200842	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.080000	0.76837	1.913000	0.55393	0.478000	0.44815	AAC		0.677	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1		NM_001005407	
CNTN1	1272	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	41422971	41422971	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr12:41422971G>A	ENST00000551295.2	+	23	3047	c.2930G>A	c.(2929-2931)cGc>cAc	p.R977H	CNTN1_ENST00000348761.2_Missense_Mutation_p.R966H|CNTN1_ENST00000347616.1_Missense_Mutation_p.R977H	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	977	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R977H(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GTGGAGGTTCGCGCGCACAGT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											229.0	213.0	218.0					12																	41422971		2203	4300	6503	SO:0001583	missense	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.2930G>A	12.37:g.41422971G>A	ENSP00000447006:p.Arg977His	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990461	0.74589	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.46063	0.88;0.88;0.88	5.18	5.18	0.71444	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.67599	0.2910	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.71027	-0.4711	10	0.66056	D	0.02	.	19.0769	0.93167	0.0:0.0:1.0:0.0	.	966;977	Q12860-2;Q12860	.;CNTN1_HUMAN	H	977;977;966	ENSP00000447006:R977H;ENSP00000325660:R977H;ENSP00000261160:R966H	ENSP00000325660:R977H	R	+	2	0	CNTN1	39709238	1.000000	0.71417	0.996000	0.52242	0.298000	0.27526	8.779000	0.91792	2.588000	0.87417	0.591000	0.81541	CGC		0.448	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2		NM_001843	
CPSF3L	54973	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	1250912	1250912	+	Silent	SNP	A	A	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:1250912A>C	ENST00000435064.1	-	5	598	c.516T>G	c.(514-516)tcT>tcG	p.S172S	CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000545578.1_Silent_p.S143S|RP5-890O3.9_ENST00000444968.1_RNA|CPSF3L_ENST00000419704.1_Silent_p.S71S|CPSF3L_ENST00000421495.2_5'UTR|CPSF3L_ENST00000450926.2_Silent_p.S150S|CPSF3L_ENST00000411962.1_Silent_p.S74S|CPSF3L_ENST00000540437.1_Silent_p.S178S	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	172					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)	p.S172S(1)		endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		TGTAGACCACAGACTCTGAGC	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											126.0	104.0	112.0					1																	1250912		2203	4300	6503	SO:0001819	synonymous_variant	54973			AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.516T>G	1.37:g.1250912A>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Silent	SNP	ENST00000435064.1	37	CCDS21.1																																																																																				0.582	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2		NM_017871	
CUL9	23113	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	43173114	43173114	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr6:43173114G>A	ENST00000252050.4	+	24	4830	c.4746G>A	c.(4744-4746)atG>atA	p.M1582I	CUL9_ENST00000354495.3_Missense_Mutation_p.M1472I|CUL9_ENST00000372647.2_Missense_Mutation_p.M1582I	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1582					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.M1582I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						AACCCATTATGGTCCTTTCTG	0.552																																																	1	Substitution - Missense(1)	kidney(1)											160.0	165.0	164.0					6																	43173114		2203	4300	6503	SO:0001583	missense	23113			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.4746G>A	6.37:g.43173114G>A	ENSP00000252050:p.Met1582Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911852	0.52439	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.73789	-0.78;-0.78;-0.78	5.74	4.87	0.63330	Cullin, N-terminal (1);Cullin homology (2);	0.119793	0.53938	D	0.000041	T	0.46795	0.1411	L	0.36672	1.1	0.34139	D	0.666189	B;B;B	0.18310	0.027;0.01;0.01	B;B;B	0.23275	0.037;0.027;0.045	T	0.51733	-0.8668	10	0.87932	D	0	-29.0205	5.6449	0.17584	0.077:0.1706:0.631:0.1215	.	1472;1582;1582	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	I	1582;1472;1582	ENSP00000252050:M1582I;ENSP00000346490:M1472I;ENSP00000361730:M1582I	ENSP00000252050:M1582I	M	+	3	0	CUL9	43281092	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.024000	0.30077	1.430000	0.47334	0.561000	0.74099	ATG		0.552	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2		NM_015089	
CYSLTR1	10800	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	77528390	77528390	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chrX:77528390G>T	ENST00000373304.3	-	3	1146	c.854C>A	c.(853-855)gCa>gAa	p.A285E		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	285					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)	p.A285E(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	ACAATTGGATGCAGCCAGAGA	0.418																																																	1	Substitution - Missense(1)	kidney(1)											67.0	65.0	66.0					X																	77528390		2203	4299	6502	SO:0001583	missense	10800			AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"""GPCR / Class A : Leukotriene receptors"""	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.854C>A	X.37:g.77528390G>T	ENSP00000362401:p.Ala285Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B2R954|D3DTE4|Q5JS94|Q8IV19	Missense_Mutation	SNP	ENST00000373304.3	37	CCDS14439.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852922	0.71719	.	.	ENSG00000173198	ENST00000373304	T	0.31769	1.48	4.07	4.07	0.47477	GPCR, rhodopsin-like superfamily (1);	0.054577	0.64402	D	0.000001	T	0.53158	0.1779	M	0.76170	2.325	0.53005	D	0.999964	D	0.89917	1.0	D	0.91635	0.999	T	0.54655	-0.8261	10	0.42905	T	0.14	.	12.7439	0.57268	0.0:0.0:1.0:0.0	.	285	Q9Y271	CLTR1_HUMAN	E	285	ENSP00000362401:A285E	ENSP00000362401:A285E	A	-	2	0	CYSLTR1	77415046	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.342000	0.97044	1.855000	0.53841	0.468000	0.43344	GCA		0.418	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1			
ECE2	9718	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	184001749	184001749	+	Silent	SNP	T	T	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr3:184001749T>A	ENST00000402825.3	+	8	1347	c.1347T>A	c.(1345-1347)atT>atA	p.I449I	ECE2_ENST00000359140.4_Silent_p.I302I|ECE2_ENST00000357474.5_Silent_p.I377I|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Silent_p.I331I	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	449	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.I377I(1)|p.I449I(1)|p.I302I(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGATGAGCATTTCGGAGCTGC	0.617																																																	3	Substitution - coding silent(3)	kidney(3)											63.0	54.0	57.0					3																	184001749		2203	4300	6503	SO:0001819	synonymous_variant	9718			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1347T>A	3.37:g.184001749T>A		Somatic		WXS	Illumina HiSeq	Phase_I	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																				0.617	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3		NM_014693	
EPPK1	83481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	144943012	144943012	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr8:144943012C>T	ENST00000525985.1	-	2	4481	c.4410G>A	c.(4408-4410)tgG>tgA	p.W1470*				P58107	EPIPL_HUMAN	epiplakin 1	1470						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.W1470*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCAGCAGGTCCCAGAGTGACA	0.652																																																	1	Substitution - Nonsense(1)	kidney(1)											35.0	39.0	38.0					8																	144943012		2191	4281	6472	SO:0001587	stop_gained	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4410G>A	8.37:g.144943012C>T	ENSP00000436337:p.Trp1470*	Somatic		WXS	Illumina HiSeq	Phase_I	Q76E58|Q9NSU9	Nonsense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	42	9.659326	0.99231	.	.	ENSG00000227184	ENST00000525985	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	14.5162	0.67821	0.0:1.0:0.0:0.0	.	.	.	.	X	1470	.	ENSP00000436337:W1470X	W	-	3	0	EPPK1	145015000	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	5.802000	0.69122	2.278000	0.76064	0.591000	0.81541	TGG		0.652	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1		NM_031308	
FAM13A	10144	hgsc.bcm.edu	37	4	89772247	89772248	+	Frame_Shift_Ins	INS	-	-	T	rs371646460		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr4:89772247_89772248insT	ENST00000264344.5	-	7	1137_1138	c.930_931insA	c.(928-933)ttgcggfs	p.R311fs	FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_Intron	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	311					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R311W(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TAACTTAGCCGCAAGCTGAGCT	0.45																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001589	frameshift_variant	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.930_931insA	4.37:g.89772247_89772248insT	ENSP00000264344:p.Arg311fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Frame_Shift_Ins	INS	ENST00000264344.5	37	CCDS34029.1																																																																																				0.450	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			
FAM96A	84191	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	64380992	64380992	+	Silent	SNP	C	C	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr15:64380992C>A	ENST00000300030.3	-	2	432	c.183G>T	c.(181-183)gtG>gtT	p.V61V	FAM96A_ENST00000380290.3_Silent_p.V61V|FAM96A_ENST00000557835.1_Silent_p.V61V|FAM96A_ENST00000559950.1_Silent_p.V61V	NM_032231.4	NP_115607.1	Q9H5X1	FA96A_HUMAN	family with sequence similarity 96, member A	61					chromosome segregation (GO:0007059)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.V61V(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						TTTCCGAGACCACTTCCAGTT	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											83.0	76.0	79.0					15																	64380992		2203	4300	6503	SO:0001819	synonymous_variant	84191				CCDS10189.1, CCDS45278.1	15q22.31	2014-01-16			ENSG00000166797	ENSG00000166797			26235	protein-coding gene	gene with protein product						23891004	Standard	NM_032231		Approved	FLJ22875	uc002amt.1	Q9H5X1	OTTHUMG00000132961	ENST00000300030.3:c.183G>T	15.37:g.64380992C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NKS1|B2R5F8|B7Z8Z5	Silent	SNP	ENST00000300030.3	37	CCDS10189.1																																																																																				0.388	FAM96A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256520.1		NM_032231	
FGD4	121512	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	32786521	32786521	+	Silent	SNP	T	T	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr12:32786521T>G	ENST00000427716.2	+	15	2224	c.1800T>G	c.(1798-1800)ctT>ctG	p.L600L	FGD4_ENST00000525053.1_Silent_p.L712L|FGD4_ENST00000266482.3_Silent_p.L352L|FGD4_ENST00000546442.1_Silent_p.L507L|FGD4_ENST00000534526.2_Silent_p.L737L|FGD4_ENST00000531134.1_Silent_p.L685L	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	600					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.L600L(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAGCTCAACTTGAATATGATG	0.303																																																	1	Substitution - coding silent(1)	kidney(1)											89.0	89.0	89.0					12																	32786521		2203	4300	6503	SO:0001819	synonymous_variant	121512			AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.1800T>G	12.37:g.32786521T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																				0.303	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1		NM_139241	
FRG2C	100288801	hgsc.bcm.edu	37	3	75714806	75714806	+	Frame_Shift_Del	DEL	G	G	-	rs144577984|rs201191365		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr3:75714806delG	ENST00000308062.3	+	4	513	c.463delG	c.(463-465)gggfs	p.G155fs	FRG2C_ENST00000464571.1_Frame_Shift_Del_p.G154fs	NM_001124759.1	NP_001118231.1	A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	155						nucleus (GO:0005634)				breast(2)|ovary(1)	3						GGCTTGCACTGGGCGCAGCAA	0.527																																																	0																																										SO:0001589	frameshift_variant	100288801				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969			33626	protein-coding gene	gene with protein product							Standard	NM_001124759		Approved			A6NGY1	OTTHUMG00000158963	ENST00000308062.3:c.463delG	3.37:g.75714806delG	ENSP00000312299:p.Gly155fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000308062.3	37	CCDS43108.1																																																																																				0.527	FRG2C-001	KNOWN	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352694.1		NM_001124759.1	
GGT3P	2679	broad.mit.edu	37	22	18778601	18778601	+	RNA	SNP	C	C	T	rs200601572		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr22:18778601C>T	ENST00000412448.1	-	0	804							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										GCTTGGCATCCGCGGCCACGG	0.627																																																	0																																												2679					22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18778601C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000412448.1	37																																																																																					0.627	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341281.1		NR_003267	
HMGN2	3151	hgsc.bcm.edu;ucsc.edu	37	1	26799998	26799998	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:26799998delA	ENST00000361427.5	+	2	134	c.40delA	c.(40-42)aaafs	p.K14fs	HMGN2_ENST00000493418.1_3'UTR	NM_005517.3	NP_005508.1	P05204	HMGN2_HUMAN	high mobility group nucleosomal binding domain 2	14						chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|lung(2)	3		all_cancers(24;1.9e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.38e-49)|OV - Ovarian serous cystadenocarcinoma(117;5.38e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.026)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TAAGGGAGATAAAGCAAAGGT	0.428																																																	0													96.0	98.0	97.0					1																	26799998		2203	4300	6503	SO:0001589	frameshift_variant	3151			BC081567	CCDS283.1	1p36.1	2011-07-01	2011-04-05	2002-08-16	ENSG00000198830	ENSG00000198830		"""High-mobility group / Canonical"""	4986	protein-coding gene	gene with protein product		163910	"""high-mobility group (nonhistone chromosomal) protein 17"", ""high-mobility group nucleosomal binding domain 2"""	HMG17		2037294	Standard	NM_005517		Approved		uc001bmp.4	P05204	OTTHUMG00000003555	ENST00000361427.5:c.40delA	1.37:g.26799998delA	ENSP00000355228:p.Lys14fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q0VGD5|Q6FGI5|Q96C64	Frame_Shift_Del	DEL	ENST00000361427.5	37	CCDS283.1																																																																																				0.428	HMGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009901.1		NM_005517	
HTR1A	3350	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	63256620	63256620	+	Missense_Mutation	SNP	G	G	T	rs140681943		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr5:63256620G>T	ENST00000323865.3	-	1	1160	c.927C>A	c.(925-927)agC>agA	p.S309R	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	309					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.S309R(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GACCAGCCTCGCTGGGCAGAG	0.647																																																	1	Substitution - Missense(1)	kidney(1)											37.0	37.0	37.0					5																	63256620		2202	4300	6502	SO:0001583	missense	3350			AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5286	protein-coding gene	gene with protein product		109760	"""5-hydroxytryptamine (serotonin) receptor 1A"""	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.927C>A	5.37:g.63256620G>T	ENSP00000316244:p.Ser309Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q6LAE7	Missense_Mutation	SNP	ENST00000323865.3	37	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	G	8.475	0.858361	0.17178	.	.	ENSG00000178394	ENST00000323865	T	0.63417	-0.04	5.17	1.89	0.25635	GPCR, rhodopsin-like superfamily (1);	0.170192	0.53938	D	0.000054	T	0.44871	0.1314	L	0.31752	0.955	0.37315	D	0.909311	B	0.09022	0.002	B	0.09377	0.004	T	0.35674	-0.9779	10	0.19147	T	0.46	.	10.6001	0.45362	0.2592:0.0:0.7408:0.0	.	309	P08908	5HT1A_HUMAN	R	309	ENSP00000316244:S309R	ENSP00000316244:S309R	S	-	3	2	HTR1A	63292376	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.599000	0.54045	0.640000	0.30582	0.655000	0.94253	AGC		0.647	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1		NM_000524	
IGSF3	3321	broad.mit.edu;hgsc.bcm.edu	37	1	117156509	117156509	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:117156509T>C	ENST00000369486.3	-	4	1475	c.710A>G	c.(709-711)cAg>cGg	p.Q237R	IGSF3_ENST00000318837.6_Missense_Mutation_p.Q237R|IGSF3_ENST00000369483.1_Missense_Mutation_p.Q237R	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	237	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.Q237R(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GTCAGAAGGCTGCAGGTGGAA	0.627																																																	2	Substitution - Missense(2)	kidney(2)											40.0	37.0	38.0					1																	117156509		2203	4300	6503	SO:0001583	missense	3321			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.710A>G	1.37:g.117156509T>C	ENSP00000358498:p.Gln237Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096756	0.76870	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.64438	-0.1;-0.1;-0.1	4.77	3.64	0.41730	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.131799	0.53938	N	0.000060	T	0.52853	0.1760	L	0.52206	1.635	0.41757	D	0.989691	P;P	0.46578	0.88;0.866	P;P	0.54544	0.755;0.689	T	0.53041	-0.8494	10	0.36615	T	0.2	-30.2954	8.624	0.33877	0.0:0.0923:0.0:0.9077	.	237;237	O75054;A6NJZ6	IGSF3_HUMAN;.	R	237	ENSP00000358498:Q237R;ENSP00000358495:Q237R;ENSP00000321184:Q237R	ENSP00000321184:Q237R	Q	-	2	0	IGSF3	116958032	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.820000	0.69250	0.840000	0.34995	0.455000	0.32223	CAG		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1		NM_001542	
ITGA10	8515	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	145530386	145530386	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:145530386C>T	ENST00000369304.3	+	6	776	c.601C>T	c.(601-603)Cag>Tag	p.Q201*	ITGA10_ENST00000538811.1_Nonsense_Mutation_p.Q70*|ITGA10_ENST00000539363.1_Nonsense_Mutation_p.Q58*	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	201	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.Q201*(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGACCCAGAACAGATACAGGT	0.502																																																	1	Substitution - Nonsense(1)	kidney(1)											97.0	88.0	91.0					1																	145530386		2203	4300	6503	SO:0001587	stop_gained	8515			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.601C>T	1.37:g.145530386C>T	ENSP00000358310:p.Gln201*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Nonsense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	C	36	5.965173	0.97151	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	.	.	.	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	16.1947	0.82018	0.0:1.0:0.0:0.0	.	.	.	.	X	201;167;58;70	.	ENSP00000358310:Q201X	Q	+	1	0	ITGA10	144241743	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.223000	0.78033	2.424000	0.82194	0.650000	0.86243	CAG		0.502	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2		NM_003637	
KCNK17	89822	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	39267378	39267378	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr6:39267378G>A	ENST00000373231.4	-	5	1056	c.824C>T	c.(823-825)tCc>tTc	p.S275F	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	275					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.S275F(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						GTGGCAGCAGGAACATACCCT	0.562																																																	1	Substitution - Missense(1)	kidney(1)											100.0	92.0	95.0					6																	39267378		2203	4300	6503	SO:0001583	missense	89822			AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.824C>T	6.37:g.39267378G>A	ENSP00000362328:p.Ser275Phe	Somatic		WXS	Illumina HiSeq	Phase_I	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.075717	0.36662	.	.	ENSG00000124780	ENST00000373231	T	0.26223	1.75	4.64	2.82	0.32997	.	.	.	.	.	T	0.04998	0.0134	L	0.27053	0.805	0.09310	N	0.999992	P	0.45283	0.855	B	0.34652	0.187	T	0.22208	-1.0223	9	0.52906	T	0.07	.	4.6564	0.12620	0.1901:0.0:0.6381:0.1718	.	275	Q96T54	KCNKH_HUMAN	F	275	ENSP00000362328:S275F	ENSP00000362328:S275F	S	-	2	0	KCNK17	39375356	.	.	0.409000	0.26459	0.137000	0.21094	.	.	0.369000	0.24510	0.655000	0.94253	TCC		0.562	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2		NM_031460	
KIAA0319L	79932	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	35909816	35909816	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:35909816G>A	ENST00000325722.3	-	17	2836	c.2602C>T	c.(2602-2604)Cgg>Tgg	p.R868W	KIAA0319L_ENST00000373266.4_Missense_Mutation_p.R305W|KIAA0319L_ENST00000485551.1_5'UTR	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	868						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R868W(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTTTGCTTCCGCAGCTCACTC	0.478																																																	2	Substitution - Missense(2)	kidney(2)											89.0	86.0	87.0					1																	35909816		2203	4300	6503	SO:0001583	missense	79932			AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.2602C>T	1.37:g.35909816G>A	ENSP00000318406:p.Arg868Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.224726	0.58668	.	.	ENSG00000142687	ENST00000325722;ENST00000373266;ENST00000426982	T;T;T	0.10860	3.08;2.83;3.07	5.68	2.34	0.29019	.	0.314319	0.39210	N	0.001434	T	0.15219	0.0367	L	0.28115	0.83	0.80722	D	1	D;D;D	0.76494	0.999;0.978;0.994	P;B;P	0.55667	0.781;0.328;0.502	T	0.02868	-1.1100	10	0.33940	T	0.23	-1.8241	16.2829	0.82707	0.0:0.0:0.5654:0.4346	.	868;868;310	Q8IZA0-2;Q8IZA0;Q8IZA0-3	.;K319L_HUMAN;.	W	868;305;868	ENSP00000318406:R868W;ENSP00000362363:R305W;ENSP00000395883:R868W	ENSP00000318406:R868W	R	-	1	2	KIAA0319L	35682403	1.000000	0.71417	0.992000	0.48379	0.943000	0.58893	3.103000	0.50298	0.678000	0.31325	-0.314000	0.08810	CGG		0.478	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2		NM_024874	
KLHL34	257240	broad.mit.edu;hgsc.bcm.edu	37	X	21674907	21674907	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chrX:21674907G>T	ENST00000379499.2	-	1	1541	c.1000C>A	c.(1000-1002)Cag>Aag	p.Q334K		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	334						extracellular space (GO:0005615)		p.Q334K(1)		cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						ACCACGTTCTGGGTGAGCTCC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											44.0	19.0	27.0					X																	21674907		2191	4290	6481	SO:0001583	missense	257240			AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"""Kelch-like"", ""BTB/POZ domain containing"""	26634	protein-coding gene	gene with protein product			"""kelch-like 34 (Drosophila)"""				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.1000C>A	X.37:g.21674907G>T	ENSP00000368813:p.Gln334Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	G	7.035	0.561448	0.13498	.	.	ENSG00000185915	ENST00000379499	T	0.66099	-0.19	4.93	4.93	0.64822	Kelch-type beta propeller (1);	0.169717	0.28001	N	0.016989	T	0.31765	0.0807	N	0.04090	-0.28	0.35440	D	0.79476	B	0.26744	0.158	B	0.17433	0.018	T	0.40757	-0.9546	10	0.05833	T	0.94	.	9.7085	0.40231	0.0:0.0:0.7769:0.223	.	334	Q8N239	KLH34_HUMAN	K	334	ENSP00000368813:Q334K	ENSP00000368813:Q334K	Q	-	1	0	KLHL34	21584828	0.996000	0.38824	0.994000	0.49952	0.941000	0.58515	3.869000	0.56062	2.276000	0.75962	0.422000	0.28245	CAG		0.647	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1		NM_153270	
KRTAP1-3	81850	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	39191063	39191063	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr17:39191063C>G	ENST00000344363.5	-	1	44	c.11G>C	c.(10-12)tGc>tCc	p.C4S		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	4						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.C4S(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCTGGTCTGGCAGCAGGTCAT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											57.0	65.0	63.0					17																	39191063		1969	4162	6131	SO:0001583	missense	81850			AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"""Keratin associated proteins"""	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.11G>C	17.37:g.39191063C>G	ENSP00000344420:p.Cys4Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.433002	0.25813	.	.	ENSG00000221880	ENST00000344363	T	0.48522	0.81	4.44	2.33	0.28932	.	.	.	.	.	T	0.54143	0.1840	.	.	.	0.31425	N	0.673811	D	0.54207	0.965	P	0.52823	0.71	T	0.60974	-0.7156	8	0.87932	D	0	.	9.3212	0.37966	0.4305:0.5695:0.0:0.0	.	4	Q8IUG1	KRA13_HUMAN	S	4	ENSP00000344420:C4S	ENSP00000344420:C4S	C	-	2	0	KRTAP1-3	36444589	0.782000	0.28689	0.976000	0.42696	0.295000	0.27426	1.208000	0.32345	0.711000	0.32018	0.655000	0.94253	TGC		0.572	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			
LIPE	3991	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	42907058	42907058	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr19:42907058C>T	ENST00000244289.4	-	9	2944	c.2668G>A	c.(2668-2670)Gac>Aac	p.D890N	LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	890					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)	p.D890N(1)		breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				TCGGGGGTGTCCGACGACGTC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											88.0	71.0	77.0					19																	42907058		2203	4300	6503	SO:0001583	missense	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2668G>A	19.37:g.42907058C>T	ENSP00000244289:p.Asp890Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	C	10.11	1.261603	0.23051	.	.	ENSG00000079435	ENST00000244289	T	0.03330	3.97	4.85	1.5	0.22942	.	1.521020	0.04023	N	0.300158	T	0.05914	0.0154	L	0.54323	1.7	0.09310	N	1	P	0.39665	0.682	B	0.39706	0.307	T	0.36163	-0.9759	10	0.52906	T	0.07	-12.0486	4.3896	0.11334	0.0:0.6097:0.189:0.2013	.	890	Q05469	LIPS_HUMAN	N	890	ENSP00000244289:D890N	ENSP00000244289:D890N	D	-	1	0	LIPE	47598898	0.000000	0.05858	0.001000	0.08648	0.187000	0.23431	0.217000	0.17603	0.727000	0.32360	0.591000	0.81541	GAC		0.607	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1		NM_005357	
FAR2P1	440905	broad.mit.edu	37	2	130786055	130786055	+	RNA	SNP	A	A	T	rs1139712		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr2:130786055A>T	ENST00000325390.3	-	0	2812					NR_026758.1																						AGACCTGGAAACCTGGGGGAA	0.428																																																	0																																												440905																															2.37:g.130786055A>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000325390.3	37																																																																																					0.428	AC018865.8-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331630.3			
BMS1P20	96610	broad.mit.edu	37	22	22664721	22664721	+	RNA	SNP	T	T	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr22:22664721T>C	ENST00000426066.1	+	0	902					NR_027293.1				BMS1 pseudogene 20																		AACTCAGGCTTGCCCATGGTG	0.512																																																	0																																												96610					22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664721T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000426066.1	37																																																																																					0.512	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			
LTA	4049	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	31541279	31541279	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr6:31541279C>G	ENST00000454783.1	+	4	685	c.427C>G	c.(427-429)Ccc>Gcc	p.P143A	TNF_ENST00000449264.2_5'Flank|LTA_ENST00000418386.2_Missense_Mutation_p.P143A	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	143					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)	p.P143A(1)		endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	CTCCCAGTACCCCTTCCATGT	0.607																																																	1	Substitution - Missense(1)	kidney(1)											185.0	171.0	176.0					6																	31541279		2203	4300	6503	SO:0001583	missense	4049			X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.427C>G	6.37:g.31541279C>G	ENSP00000403495:p.Pro143Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N4C3|Q9UKS8	Missense_Mutation	SNP	ENST00000454783.1	37	CCDS4701.1	.	.	.	.	.	.	.	.	.	.	C	0.122	-1.124487	0.01770	.	.	ENSG00000226979	ENST00000454783;ENST00000418386	T;T	0.65364	-0.15;-0.15	5.16	2.33	0.28932	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.531595	0.20687	N	0.087534	T	0.29945	0.0749	L	0.45470	1.425	0.30523	N	0.768247	B	0.17038	0.02	B	0.16289	0.015	T	0.10683	-1.0619	10	0.38643	T	0.18	-30.4887	6.3498	0.21369	0.0:0.6799:0.0:0.3201	.	143	P01374	TNFB_HUMAN	A	143	ENSP00000403495:P143A;ENSP00000413450:P143A	ENSP00000413450:P143A	P	+	1	0	LTA	31649258	0.028000	0.19301	0.968000	0.41197	0.599000	0.36880	0.933000	0.28897	0.299000	0.22661	-0.140000	0.14226	CCC		0.607	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1			
MAGI2	9863	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	77885771	77885771	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr7:77885771C>A	ENST00000354212.4	-	10	1789	c.1536G>T	c.(1534-1536)ttG>ttT	p.L512F	MAGI2_ENST00000419488.1_Missense_Mutation_p.L512F|MAGI2_ENST00000535697.1_Missense_Mutation_p.L349F|MAGI2_ENST00000536571.1_Missense_Mutation_p.L344F|MAGI2_ENST00000522391.1_Missense_Mutation_p.L512F	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	512					cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.L512F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GATCAAAGGGCAAAGGGTAGC	0.483																																																	1	Substitution - Missense(1)	kidney(1)											75.0	63.0	67.0					7																	77885771		2203	4300	6503	SO:0001583	missense	9863			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1536G>T	7.37:g.77885771C>A	ENSP00000346151:p.Leu512Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.463207	0.63513	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	5.93	5.05	0.67936	PDZ/DHR/GLGF (1);	0.000000	0.30630	U	0.009211	T	0.64427	0.2597	M	0.82193	2.58	0.80722	D	1	D;P;D;D;D;P	0.89917	1.0;0.888;0.996;0.996;1.0;0.788	D;D;D;D;D;P	0.91635	0.999;0.99;0.997;0.997;0.999;0.73	T	0.68644	-0.5354	10	0.87932	D	0	.	9.1866	0.37174	0.1467:0.7811:0.0:0.0721	.	349;344;512;512;512;512	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	F	512;512;512;512;344;349	ENSP00000405766:L512F;ENSP00000346151:L512F;ENSP00000428389:L512F;ENSP00000441584:L344F;ENSP00000441603:L349F	ENSP00000346151:L512F	L	-	3	2	MAGI2	77723707	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.181000	0.42547	1.507000	0.48752	0.555000	0.69702	TTG		0.483	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3		NM_012301	
MATN1	4146	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	31188992	31188992	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:31188992C>T	ENST00000373765.4	-	5	1006	c.971G>A	c.(970-972)cGc>cAc	p.R324H	MATN1-AS1_ENST00000454613.1_RNA|MATN1-AS1_ENST00000414532.2_RNA|MATN1_ENST00000477320.1_5'UTR|MATN1-AS1_ENST00000414763.1_RNA	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	324	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.R324H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		GAACTCCTGGCGCACAGAGCT	0.567																																																	1	Substitution - Missense(1)	kidney(1)											81.0	88.0	85.0					1																	31188992		2203	4300	6503	SO:0001583	missense	4146			M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.971G>A	1.37:g.31188992C>T	ENSP00000362870:p.Arg324His	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7E3|Q5TBB9	Missense_Mutation	SNP	ENST00000373765.4	37	CCDS336.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.544286	0.45280	.	.	ENSG00000162510	ENST00000373765	D	0.83591	-1.74	5.34	4.42	0.53409	von Willebrand factor, type A (3);	.	.	.	.	D	0.89040	0.6602	L	0.60455	1.87	0.43435	D	0.995602	D;P	0.89917	1.0;0.909	D;B	0.70716	0.97;0.397	D	0.90191	0.4250	9	0.87932	D	0	-25.4758	16.0215	0.80499	0.0:0.8652:0.1347:0.0	.	308;324	A3KMG0;P21941	.;MATN1_HUMAN	H	324	ENSP00000362870:R324H	ENSP00000362870:R324H	R	-	2	0	MATN1	30961579	1.000000	0.71417	0.870000	0.34147	0.147000	0.21601	3.097000	0.50251	1.232000	0.43678	-0.182000	0.12963	CGC		0.567	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1		NM_002379	
MLLT4	4301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	168344080	168344080	+	Splice_Site	SNP	A	A	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr6:168344080A>G	ENST00000447894.2	+	24	3144		c.e24-1		MLLT4_ENST00000366806.2_Splice_Site|MLLT4_ENST00000392112.1_Splice_Site|MLLT4_ENST00000351017.4_Splice_Site|MLLT4_ENST00000400822.3_Splice_Site|MLLT4_ENST00000392108.3_Splice_Site|MLLT4_ENST00000344191.4_Splice_Site|MLLT4_ENST00000507679.1_Splice_Site			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4						adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.?(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GGATTTGCCTAGGATGGACGT	0.458			T	MLL	AL																																			Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	2	Unknown(2)	kidney(2)											221.0	199.0	207.0					6																	168344080		2203	4300	6503	SO:0001630	splice_region_variant	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3145-1A>G	6.37:g.168344080A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Splice_Site	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	A	21.5	4.151670	0.78001	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0548	0.71904	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MLLT4	168086929	1.000000	0.71417	0.952000	0.39060	0.849000	0.48306	8.654000	0.91092	1.954000	0.56735	0.528000	0.53228	.		0.458	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1		NM_005936	Intron
MS4A6A	64231	broad.mit.edu;hgsc.bcm.edu	37	11	59949129	59949129	+	Silent	SNP	T	T	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr11:59949129T>C	ENST00000530839.1	-	3	564	c.72A>G	c.(70-72)gcA>gcG	p.A24A	MS4A6A_ENST00000533023.1_Silent_p.A24A|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000528851.1_Silent_p.A24A|MS4A6A_ENST00000426738.2_Silent_p.A24A|MS4A6A_ENST00000529054.1_Silent_p.A52A|MS4A6A_ENST00000532169.1_Silent_p.A24A|MS4A6A_ENST00000420732.2_Silent_p.A24A|MS4A6A_ENST00000412309.2_Silent_p.A52A|MS4A6A_ENST00000323961.3_Silent_p.A24A	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	24						integral component of membrane (GO:0016021)		p.A24A(1)|p.A52A(1)		endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CGGGTTTCTCTGCTTGGGAGA	0.438																																																	2	Substitution - coding silent(2)	kidney(2)											215.0	192.0	200.0					11																	59949129		2201	4295	6496	SO:0001819	synonymous_variant	64231			AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.72A>G	11.37:g.59949129T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	T	6.364	0.435293	0.12045	.	.	ENSG00000110077	ENST00000533989	.	.	.	4.72	3.57	0.40892	.	.	.	.	.	T	0.27313	0.0670	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	T	0.13415	-1.0510	4	.	.	.	.	5.5935	0.17313	0.0:0.1267:0.0:0.8733	.	.	.	.	R	4	.	.	Q	-	2	0	MS4A6A	59705705	0.008000	0.16893	0.009000	0.14445	0.005000	0.04900	0.335000	0.19806	1.973000	0.57446	0.533000	0.62120	CAG		0.438	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			
MTTP	4547	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	100515934	100515934	+	Missense_Mutation	SNP	T	T	C	rs146513720		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr4:100515934T>C	ENST00000265517.5	+	7	1006	c.803T>C	c.(802-804)aTg>aCg	p.M268T	MTTP_ENST00000457717.1_Missense_Mutation_p.M268T|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000511045.1_Missense_Mutation_p.M295T			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	268	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)	p.M268T(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	CCAAGATTGATGTCTGGAAAG	0.438																																																	1	Substitution - Missense(1)	kidney(1)						T	THR/MET	0,4406		0,0,2203	109.0	100.0	103.0		803	-3.6	0.0	4	dbSNP_134	103	1,8599	1.2+/-3.3	0,1,4299	no	missense	MTTP	NM_000253.2	81	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	268/895	100515934	1,13005	2203	4300	6503	SO:0001583	missense	4547				CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.803T>C	4.37:g.100515934T>C	ENSP00000265517:p.Met268Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	T	1.605	-0.525626	0.04141	0.0	1.16E-4	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.38560	1.13;1.13;1.13	4.96	-3.62	0.04543	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.980957	0.08410	N	0.950035	T	0.20820	0.0501	N	0.22421	0.69	0.09310	N	1	B;B	0.14438	0.001;0.01	B;B	0.16722	0.006;0.016	T	0.24693	-1.0153	10	0.17369	T	0.5	-15.731	2.131	0.03750	0.3261:0.066:0.235:0.3728	.	295;268	E9PBP6;P55157	.;MTP_HUMAN	T	295;268;268;268	ENSP00000427679:M295T;ENSP00000400821:M268T;ENSP00000265517:M268T	ENSP00000265517:M268T	M	+	2	0	MTTP	100734957	0.019000	0.18553	0.003000	0.11579	0.029000	0.11900	0.096000	0.15147	-0.746000	0.04766	-0.461000	0.05368	ATG		0.438	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			
NAPB	63908	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	23377799	23377799	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr20:23377799C>G	ENST00000377026.4	-	3	290	c.205G>C	c.(205-207)Gcc>Ccc	p.A69P	NAPB_ENST00000398425.3_5'UTR|NAPB_ENST00000432543.2_Intron|NAPB_ENST00000472855.1_Intron	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	69					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)		p.A69P(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					TGGAGCTTGGCTGCCTGACAA	0.502																																																	1	Substitution - Missense(1)	kidney(1)											95.0	76.0	83.0					20																	23377799		2203	4300	6503	SO:0001583	missense	63908			AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.205G>C	20.37:g.23377799C>G	ENSP00000366225:p.Ala69Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	37	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	C	35	5.456176	0.96223	.	.	ENSG00000125814	ENST00000377026;ENST00000431864	T	0.56776	0.44	5.5	5.5	0.81552	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.83589	0.5287	H	0.97829	4.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.89728	0.3924	10	0.87932	D	0	-19.6617	18.3684	0.90399	0.0:1.0:0.0:0.0	.	69;69	B4DIV0;Q9H115	.;SNAB_HUMAN	P	69;26	ENSP00000366225:A69P	ENSP00000366225:A69P	A	-	1	0	NAPB	23325799	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.640000	0.83355	2.582000	0.87167	0.563000	0.77884	GCC		0.502	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2		NM_022080	
NDUFB6	4712	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	32571039	32571039	+	Silent	SNP	T	T	C	rs146518353	byFrequency	TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr9:32571039T>C	ENST00000379847.3	-	2	293	c.192A>G	c.(190-192)gtA>gtG	p.V64V	NDUFB6_ENST00000350021.2_Silent_p.V64V	NM_002493.4	NP_002484.1	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa	64					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.V64V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|urinary_tract(1)	8			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)		TCTTTTTGTATACCCCATGGA	0.338													T|||	2	0.000399361	0.0	0.0	5008	,	,		17089	0.002		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											45.0	44.0	45.0					9																	32571039		2203	4294	6497	SO:0001819	synonymous_variant	4712			AF035840	CCDS6528.1, CCDS6529.1, CCDS75826.1	9p13.2	2011-07-04	2002-08-29		ENSG00000165264	ENSG00000165264		"""Mitochondrial respiratory chain complex / Complex I"""	7701	protein-coding gene	gene with protein product	"""NADH-ubiquinone oxidoreductase beta subunit, 6"", ""NADH-ubiquinone oxidoreductase B17 subunit"", ""complex I, mitochondrial respiratory chain, B17 subunit"""	603322	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (17kD, B17)"""			9763677, 9760212	Standard	NM_002493		Approved	B17, CI	uc003zre.2	O95139	OTTHUMG00000019741	ENST00000379847.3:c.192A>G	9.37:g.32571039T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K0Y7|Q5VYT2|Q6IB84	Silent	SNP	ENST00000379847.3	37	CCDS6528.1																																																																																				0.338	NDUFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052001.1		NM_002493	
TENM2	57451	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	167645829	167645829	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr5:167645829A>T	ENST00000518659.1	+	23	4972	c.4933A>T	c.(4933-4935)Atg>Ttg	p.M1645L	TENM2_ENST00000520394.1_Missense_Mutation_p.M1406L|TENM2_ENST00000545108.1_Missense_Mutation_p.M1644L|TENM2_ENST00000519204.1_Missense_Mutation_p.M1524L|TENM2_ENST00000403607.2_Missense_Mutation_p.M1469L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1645					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.M1524L(1)|p.M1478L(1)|p.M1645L(1)									CAGCAGTGGCATGCCCCGTCA	0.502																																																	3	Substitution - Missense(3)	kidney(3)											146.0	147.0	147.0					5																	167645829		2087	4223	6310	SO:0001583	missense	0			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4933A>T	5.37:g.167645829A>T	ENSP00000429430:p.Met1645Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	A	10.21	1.287641	0.23478	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.55588	1.6;0.51;1.6;1.6;1.6	5.85	-1.92	0.07618	.	0.395773	0.33419	N	0.004937	T	0.21022	0.0506	N	0.10972	0.075	0.26948	N	0.966098	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.04811	-1.0925	10	0.19147	T	0.46	.	0.9659	0.01405	0.4234:0.2282:0.1276:0.2208	.	1644;1645;1406	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	L	1645;1644;1524;1406;1469	ENSP00000429430:M1645L;ENSP00000438635:M1644L;ENSP00000428964:M1524L;ENSP00000427874:M1406L;ENSP00000384905:M1469L	ENSP00000384905:M1469L	M	+	1	0	ODZ2	167578407	0.991000	0.36638	0.954000	0.39281	0.997000	0.91878	1.347000	0.33975	0.089000	0.17243	0.533000	0.62120	ATG		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1		NM_001122679	
OR1L1	26737	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	125424692	125424692	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr9:125424692G>C	ENST00000373686.1	+	1	848	c.848G>C	c.(847-849)gGa>gCa	p.G283A	OR1L1_ENST00000309623.1_Missense_Mutation_p.G233A			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G283A(1)		breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						TCAGCTGCTGGAAAGCGTAAA	0.428																																																	1	Substitution - Missense(1)	kidney(1)											172.0	172.0	172.0					9																	125424692		2203	4300	6503	SO:0001583	missense	26737				CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"""GPCR / Class A : Olfactory receptors"""	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.848G>C	9.37:g.125424692G>C	ENSP00000362790:p.Gly283Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		.	.	.	.	.	.	.	.	.	.	G	13.32	2.203172	0.38905	.	.	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00285	8.3;8.3	3.26	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00637	0.0021	M	0.82517	2.595	0.09310	N	1	D	0.71674	0.998	D	0.75484	0.986	T	0.46992	-0.9151	9	0.87932	D	0	.	9.9154	0.41430	0.1151:0.0:0.8849:0.0	.	283	Q8NH94	OR1L1_HUMAN	A	283;233	ENSP00000362790:G283A;ENSP00000310773:G233A	ENSP00000310773:G233A	G	+	2	0	OR1L1	124464513	0.837000	0.29446	0.407000	0.26434	0.076000	0.17211	2.878000	0.48515	1.801000	0.52704	0.313000	0.20887	GGA		0.428	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				
PHC2	1912	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	33820614	33820614	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:33820614G>T	ENST00000257118.5	-	7	1270	c.1217C>A	c.(1216-1218)cCa>cAa	p.P406Q	PHC2_ENST00000419414.2_Missense_Mutation_p.P406Q|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000373422.3_Missense_Mutation_p.P11Q|PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Missense_Mutation_p.P377Q	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	406					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.P406Q(1)		autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ACACTGGAGTGGCAGGGCGGG	0.662																																																	1	Substitution - Missense(1)	kidney(1)											46.0	49.0	48.0					1																	33820614		2203	4300	6503	SO:0001583	missense	1912			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1217C>A	1.37:g.33820614G>T	ENSP00000257118:p.Pro406Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021213	0.54576	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000419414	T;T;T;T	0.62364	1.79;1.29;0.03;1.68	5.7	5.7	0.88788	.	0.066680	0.64402	D	0.000009	T	0.78181	0.4243	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.997	T	0.79460	-0.1794	10	0.66056	D	0.02	-11.6843	15.3328	0.74226	0.0:0.0:1.0:0.0	.	406;377;406	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	Q	377;406;11;406	ENSP00000389436:P377Q;ENSP00000257118:P406Q;ENSP00000362521:P11Q;ENSP00000391440:P406Q	ENSP00000257118:P406Q	P	-	2	0	PHC2	33593201	1.000000	0.71417	0.996000	0.52242	0.227000	0.25037	4.888000	0.63164	2.686000	0.91538	0.591000	0.81541	CCA		0.662	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1		NM_198040	
TMEM199	147007	hgsc.bcm.edu	37	17	26684392	26684392	+	5'Flank	SNP	T	T	C	rs55887815		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr17:26684392T>C	ENST00000292114.3	+	0	0				TMEM199_ENST00000395404.3_5'Flank|POLDIP2_ENST00000540200.1_Splice_Site_p.K27R|TMEM199_ENST00000509083.1_5'Flank|POLDIP2_ENST00000003607.4_5'UTR|CTB-96E2.3_ENST00000591482.1_RNA	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		ACAGAGCGGCTTTGCCACCGG	0.761																																																	0													4.0	4.0	4.0					17																	26684392		1481	3473	4954	SO:0001631	upstream_gene_variant	26073			AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26684392T>C	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000292114.3	37	CCDS11228.1																																																																																				0.761	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2		NM_152464	
PSMA6	5687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	35761756	35761756	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr14:35761756T>C	ENST00000261479.4	+	1	194	c.74T>C	c.(73-75)gTa>gCa	p.V25A	KIAA0391_ENST00000557565.1_Intron|PSMA6_ENST00000553809.1_Missense_Mutation_p.V25A|AL121594.1_ENST00000578587.1_RNA|PSMA6_ENST00000555764.1_5'UTR|PSMA6_ENST00000556506.1_Missense_Mutation_p.V25A|PSMA6_ENST00000540871.1_Intron	NM_002791.1	NP_002782.1	P60900	PSA6_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 6	25					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of inflammatory response (GO:0050727)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myofibril (GO:0030016)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)|sarcomere (GO:0030017)	endopeptidase activity (GO:0004175)|NF-kappaB binding (GO:0051059)|purine ribonucleoside triphosphate binding (GO:0035639)|RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)	p.V25A(1)		kidney(2)|large_intestine(1)|lung(5)|prostate(1)|urinary_tract(1)	10	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)		CTCTACCAAGTAGGTGAGTGA	0.567																																																	1	Substitution - Missense(1)	kidney(1)											94.0	90.0	91.0					14																	35761756		2203	4300	6503	SO:0001583	missense	5687			X59417	CCDS9655.1, CCDS61437.1, CCDS61438.1	14q13	2003-03-12			ENSG00000100902	ENSG00000100902		"""Proteasome (prosome, macropain) subunits"""	9535	protein-coding gene	gene with protein product		602855				1888762, 8811196	Standard	NM_002791		Approved	IOTA, PROS27, p27K, MGC22756, MGC2333, MGC23846	uc001wtd.3	P60900	OTTHUMG00000140221	ENST00000261479.4:c.74T>C	14.37:g.35761756T>C	ENSP00000261479:p.Val25Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7J9|B4DQR4|B4DXJ9|P34062|Q6IB60	Missense_Mutation	SNP	ENST00000261479.4	37	CCDS9655.1	.	.	.	.	.	.	.	.	.	.	T	34	5.377067	0.95945	.	.	ENSG00000100902	ENST00000261479;ENST00000553809;ENST00000556506	T;T;T	0.58652	0.32;0.32;0.32	5.87	5.87	0.94306	Proteasome, alpha-subunit, conserved site (3);	0.000000	0.85682	D	0.000000	D	0.85093	0.5618	H	0.98612	4.28	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90634	0.4569	10	0.87932	D	0	-4.7662	14.4865	0.67622	0.0:0.0:0.0:1.0	.	25	P60900	PSA6_HUMAN	A	25	ENSP00000261479:V25A;ENSP00000452603:V25A;ENSP00000450528:V25A	ENSP00000261479:V25A	V	+	2	0	PSMA6	34831507	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.280000	0.72626	2.242000	0.73789	0.482000	0.46254	GTA		0.567	PSMA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276684.1			
QSER1	79832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	32953804	32953804	+	Silent	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr11:32953804C>T	ENST00000399302.2	+	4	948	c.613C>T	c.(613-615)Ctg>Ttg	p.L205L	QSER1_ENST00000527788.1_Silent_p.L205L	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	205	Ser-rich.							p.L205L(1)		breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TCAGGCACAACTGACTGGTTC	0.408																																																	1	Substitution - coding silent(1)	kidney(1)											75.0	69.0	71.0					11																	32953804		1896	4110	6006	SO:0001819	synonymous_variant	79832			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.613C>T	11.37:g.32953804C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	CCDS41631.1																																																																																				0.408	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1		NM_024774	
PVRL1	5818	broad.mit.edu	37	11	119510667	119510667	+	Silent	SNP	G	G	T	rs368086348		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr11:119510667G>T	ENST00000341398.2	-	6	1058	c.1059C>A	c.(1057-1059)acC>acA	p.T353T	RP11-196E1.3_ENST00000601999.1_RNA|RP11-196E1.3_ENST00000532153.1_RNA	NM_203285.1	NP_976030.1	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	9					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.T353T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		ACACGGCCACGGTGCCCGCCA	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											33.0	36.0	35.0					11																	119510667		2199	4295	6494	SO:0001819	synonymous_variant	5818			X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000341398.2:c.1059C>A	11.37:g.119510667G>T		Somatic		WXS	Illumina GAIIx	Phase_I	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Silent	SNP	ENST00000341398.2	37	CCDS8425.1																																																																																				0.597	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1			
RXRB	6257	broad.mit.edu;hgsc.bcm.edu	37	6	33163381	33163381	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr6:33163381C>T	ENST00000374680.3	-	7	1433	c.1222G>A	c.(1222-1224)Gcc>Acc	p.A408T	RXRB_ENST00000374685.4_Missense_Mutation_p.A408T|RXRB_ENST00000544186.1_Missense_Mutation_p.A218T	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	408	Ligand-binding. {ECO:0000250}.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|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 transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.A408T(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCTGAATGGGCTGAGTTGCGG	0.567																																																	1	Substitution - Missense(1)	kidney(1)											93.0	88.0	90.0					6																	33163381		1510	2708	4218	SO:0001583	missense	6257			M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.1222G>A	6.37:g.33163381C>T	ENSP00000363812:p.Ala408Thr	Somatic		WXS	Illumina HiSeq	Phase_I	P28703|Q59G65|Q5JP92|Q5STQ1	Missense_Mutation	SNP	ENST00000374680.3	37	CCDS4768.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731639	0.89390	.	.	ENSG00000204231	ENST00000374685;ENST00000374680;ENST00000544186	D;D;D	0.96802	-4.13;-4.13;-4.13	5.35	5.35	0.76521	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.96577	0.8883	M	0.81112	2.525	0.80722	D	1	P;D;D;D	0.55605	0.799;0.972;0.972;0.972	P;P;P;P	0.50162	0.633;0.59;0.59;0.59	D	0.96799	0.9588	10	0.72032	D	0.01	.	16.5991	0.84804	0.0:1.0:0.0:0.0	.	218;408;448;408	E9PK95;Q5STP9;Q59G65;P28702	.;.;.;RXRB_HUMAN	T	408;408;218	ENSP00000363817:A408T;ENSP00000363812:A408T;ENSP00000439222:A218T	ENSP00000363812:A408T	A	-	1	0	RXRB	33271359	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	7.644000	0.83416	2.784000	0.95788	0.549000	0.68633	GCC		0.567	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2		NM_021976	
SLC4A1AP	22950	broad.mit.edu;hgsc.bcm.edu	37	2	27908052	27908052	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr2:27908052delG	ENST00000326019.6	+	10	2306	c.2024delG	c.(2023-2025)agtfs	p.S675fs		NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	675	Glu-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					GGAAGCCTCAGTAGGCCACAG	0.463																																																	0													93.0	97.0	96.0					2																	27908052		2203	4300	6503	SO:0001589	frameshift_variant	22950				CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.2024delG	2.37:g.27908052delG	ENSP00000323837:p.Ser675fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Frame_Shift_Del	DEL	ENST00000326019.6	37	CCDS33166.1																																																																																				0.463	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1		NM_018158	
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27908054	27908054	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr2:27908054A>T	ENST00000326019.6	+	10	2308	c.2026A>T	c.(2026-2028)Agg>Tgg	p.R676W		NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	676	Glu-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					AAGCCTCAGTAGGCCACAGCC	0.463																																																	0													96.0	99.0	98.0					2																	27908054		2203	4300	6503	SO:0001583	missense	22950				CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.2026A>T	2.37:g.27908054A>T	ENSP00000323837:p.Arg676Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	37	CCDS33166.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.987638	0.74589	.	.	ENSG00000163798	ENST00000326019	T	0.30448	1.53	4.82	-3.93	0.04143	.	2.094550	0.01644	N	0.024203	T	0.26882	0.0658	L	0.56769	1.78	0.09310	N	1	P	0.52692	0.955	B	0.40101	0.319	T	0.44528	-0.9322	10	0.37606	T	0.19	2.17	5.4227	0.16409	0.4553:0.2561:0.2885:0.0	.	676	Q9BWU0	NADAP_HUMAN	W	676	ENSP00000323837:R676W	ENSP00000323837:R676W	R	+	1	2	SLC4A1AP	27761558	0.000000	0.05858	0.000000	0.03702	0.970000	0.65996	0.017000	0.13399	-0.441000	0.07201	0.379000	0.24179	AGG		0.463	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1		NM_018158	
SMAP2	64744	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	40872508	40872508	+	5'UTR	SNP	T	T	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr1:40872508T>A	ENST00000539317.1	+	0	157					NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2						regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.V68V(1)		central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			TAAAGTCAGTTAACCTCGACC	0.473																																																	1	Substitution - coding silent(1)	kidney(1)											107.0	101.0	103.0					1																	40872508		2203	4300	6503	SO:0001623	5_prime_UTR_variant	64744			AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"""ADP-ribosylation factor GTPase activating proteins"""	25082	protein-coding gene	gene with protein product			"""stromal membrane-associated protein 1-like"", ""stromal membrane-associated GTPase-activating protein 2"""	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.-37T>A	1.37:g.40872508T>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Silent	SNP	ENST00000539317.1	37	CCDS55593.1																																																																																				0.473	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding			NM_022733	
TBCCD1	55171	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	186276258	186276258	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr3:186276258C>A	ENST00000424280.1	-	3	919	c.440G>T	c.(439-441)aGa>aTa	p.R147I	TBCCD1_ENST00000446782.1_Missense_Mutation_p.R51I|TBCCD1_ENST00000338733.5_Missense_Mutation_p.R147I	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	147					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)		p.R147I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AGATTTGTTTCTGGGACTGGG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											140.0	139.0	139.0					3																	186276258		2203	4300	6503	SO:0001583	missense	55171			BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.440G>T	3.37:g.186276258C>A	ENSP00000411253:p.Arg147Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	37	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.597726	0.66332	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782;ENST00000413695;ENST00000430560	T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;0.49	5.24	4.37	0.52481	.	0.093129	0.64402	D	0.000008	T	0.77343	0.4116	L	0.57536	1.79	0.80722	D	1	D;D	0.57571	0.967;0.98	P;P	0.59221	0.805;0.854	T	0.78033	-0.2362	10	0.51188	T	0.08	-14.4751	12.1604	0.54101	0.0:0.9158:0.0:0.0842	.	51;147	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	I	147;147;51;147;131	ENSP00000411253:R147I;ENSP00000341652:R147I;ENSP00000397091:R51I;ENSP00000391109:R147I;ENSP00000407506:R131I	ENSP00000341652:R147I	R	-	2	0	TBCCD1	187758952	1.000000	0.71417	0.988000	0.46212	0.353000	0.29299	3.369000	0.52365	1.348000	0.45733	-0.137000	0.14449	AGA		0.408	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1		NM_018138	
TKTL1	8277	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	153524232	153524232	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chrX:153524232G>C	ENST00000369915.3	+	1	209	c.20G>C	c.(19-21)aGg>aCg	p.R7T	TEX28_ENST00000369926.1_5'Flank|TKTL1_ENST00000217905.7_5'UTR	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	7					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.R7T(1)		NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTGAGGCGAGGGCTGAGTTC	0.612																																																	1	Substitution - Missense(1)	kidney(1)											90.0	80.0	84.0					X																	153524232		2203	4300	6503	SO:0001583	missense	8277			X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.20G>C	X.37:g.153524232G>C	ENSP00000358931:p.Arg7Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Missense_Mutation	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	G	9.862	1.196463	0.22037	.	.	ENSG00000007350	ENST00000369915	T	0.28895	1.59	4.1	0.121	0.14695	.	1.850980	0.03044	N	0.153646	T	0.12860	0.0312	N	0.08118	0	0.09310	N	0.999999	B;B	0.14012	0.009;0.009	B;B	0.08055	0.003;0.003	T	0.16837	-1.0389	10	0.02654	T	1	.	3.3015	0.06984	0.3438:0.0:0.4709:0.1853	.	7;7	B7Z7I0;P51854	.;TKTL1_HUMAN	T	7	ENSP00000358931:R7T	ENSP00000358931:R7T	R	+	2	0	TKTL1	153177426	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.110000	0.10824	-0.257000	0.09459	0.529000	0.55759	AGG		0.612	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1		NM_012253	
TRPC4	7223	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	38357212	38357212	+	Missense_Mutation	SNP	C	C	T	rs140628205		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr13:38357212C>T	ENST00000379705.3	-	2	1116	c.259G>A	c.(259-261)Gaa>Aaa	p.E87K	TRPC4_ENST00000379673.2_Missense_Mutation_p.E87K|TRPC4_ENST00000355779.2_Missense_Mutation_p.E87K|TRPC4_ENST00000426868.2_Missense_Mutation_p.E87K|TRPC4_ENST00000447043.1_Missense_Mutation_p.E87K|TRPC4_ENST00000358477.2_Missense_Mutation_p.E87K|TRPC4_ENST00000379681.3_Missense_Mutation_p.E87K|TRPC4_ENST00000379679.1_Missense_Mutation_p.E87K|TRPC4_ENST00000338947.5_Missense_Mutation_p.E87K			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	87	Multimerization domain. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.E87K(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AAGAGTAGTTCgatgagctcc	0.363																																																	2	Substitution - Missense(2)	kidney(2)						C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	72.0	72.0	72.0		259,259,259,259,259,259	6.0	1.0	13	dbSNP_134	72	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	56,56,56,56,56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign	87/894,87/829,87/837,87/805,87/983,87/978	38357212	1,13005	2203	4300	6503	SO:0001583	missense	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.259G>A	13.37:g.38357212C>T	ENSP00000369027:p.Glu87Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	C	35	5.427679	0.96131	2.27E-4	0.0	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000426868;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07;0.07;0.07;0.07	6.01	6.01	0.97437	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.64757	0.2627	N	0.13272	0.32	0.80722	D	1	P;D;D;D;D;D	0.76494	0.939;0.994;0.999;0.999;0.978;0.992	P;P;D;D;P;P	0.76575	0.491;0.769;0.988;0.988;0.629;0.852	T	0.69647	-0.5089	10	0.87932	D	0	-27.6247	20.5211	0.99222	0.0:1.0:0.0:0.0	.	87;87;87;87;87;87	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	K	87	ENSP00000369027:E87K;ENSP00000369003:E87K;ENSP00000342580:E87K;ENSP00000369001:E87K;ENSP00000410133:E87K;ENSP00000348025:E87K;ENSP00000351264:E87K;ENSP00000368995:E87K;ENSP00000414316:E87K	ENSP00000342580:E87K	E	-	1	0	TRPC4	37255212	1.000000	0.71417	0.972000	0.41901	0.933000	0.57130	7.818000	0.86416	2.861000	0.98227	0.650000	0.86243	GAA		0.363	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2		NM_003306	
TUSC5	286753	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	1198811	1198811	+	Silent	SNP	C	C	T	rs529434651		TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr17:1198811C>T	ENST00000333813.3	+	2	753	c.414C>T	c.(412-414)aaC>aaT	p.N138N		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	138					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)		p.N138N(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AACAGGGCAACGTGGACGGCG	0.632													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18642	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											103.0	120.0	114.0					17																	1198811		2087	4221	6308	SO:0001819	synonymous_variant	286753			AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"""located at seventeen p thirteen point three 1"", ""interferon induced transmembrane protein domain containing 3"""	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.414C>T	17.37:g.1198811C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NMK4	Silent	SNP	ENST00000333813.3	37	CCDS42225.1																																																																																				0.632	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1		NM_172367	
TYR	7299	hgsc.bcm.edu;ucsc.edu	37	11	89017963	89017964	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr11:89017963_89017964insG	ENST00000263321.5	+	4	1709_1710	c.1207_1208insG	c.(1207-1209)aggfs	p.R403fs		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	403			R -> S (in OCA1A and OCA1B). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:1642278}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GTGGCTCCGAAGGCACCGTCCT	0.371																																																	0			GRCh37	CD056206	TYR	D																																				SO:0001589	frameshift_variant	7299			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1209dupG	11.37:g.89017965_89017965dupG	ENSP00000263321:p.Arg403fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Frame_Shift_Ins	INS	ENST00000263321.5	37	CCDS8284.1																																																																																				0.371	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2		NM_000372	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu|broad.mit.edu;ucsc.edu	37	3	10188308	10188309	+	Missense_Mutation	DNP	AT	AT	TA			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A|T	A|T	A|.	T|.	A|.	A|.	Unknown	Valid|Untested	Somatic	Phase_I	WXS	PGM|none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr3:10188308_10188309AT>TA	ENST00000256474.2	+	2	1291_1292	c.451_452AT>TA	c.(451-453)ATc>TAc	p.I151Y	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	151	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.I151T(7)|p.I151S(6)|p.I151N(3)|p.I151F(2)|p.?(1)|p.N150fs*7(1)|p.N150fs*23(1)|p.I151_T152del(1)|p.I151>?(1)|p.I151fs*8(1)|p.N150_I151insY(1)|p.G144fs*19(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)		TTTTGCCAATATCACACTGCCA	0.401		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"""	26	Substitution - Missense(18)|Deletion - Frameshift(3)|Deletion - In frame(1)|Insertion - Frameshift(1)|Insertion - In frame(1)|Complex(1)|Unknown(1)	kidney(26)	GRCh37	CI941928|CM994244	VHL	I|M	rs5030624																																			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	Exception_encountered	3.37:g.10188308_10188309delinsTA	ENSP00000256474:p.Ile151Tyr	Somatic		WXS	Illumina HiSeq|Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.401	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZNF528	84436	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	52918551	52918551	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-6032-01A-11D-1669-08	TCGA-CJ-6032-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c9823f0-69af-474d-adb7-5ec8ef4e5af7	d060b91c-6151-496a-bd87-d88c1fae20ea	g.chr19:52918551A>G	ENST00000360465.3	+	7	872	c.446A>G	c.(445-447)gAa>gGa	p.E149G	ZNF528_ENST00000391788.2_3'UTR	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E149G(1)		breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		TCACCGCTTGAAAAAATTTCT	0.358																																																	1	Substitution - Missense(1)	kidney(1)											37.0	40.0	39.0					19																	52918551		2200	4299	6499	SO:0001583	missense	84436			AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"""Zinc fingers, C2H2-type"", ""-"""	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.446A>G	19.37:g.52918551A>G	ENSP00000353652:p.Glu149Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	10.29	1.308139	0.23821	.	.	ENSG00000167555	ENST00000360465	T	0.05447	3.44	2.15	2.15	0.27550	.	.	.	.	.	T	0.04815	0.0130	N	0.20986	0.625	0.09310	N	1	B	0.13145	0.007	B	0.12837	0.008	T	0.35051	-0.9804	9	0.72032	D	0.01	.	6.1476	0.20294	1.0:0.0:0.0:0.0	.	149	Q3MIS6	ZN528_HUMAN	G	149	ENSP00000353652:E149G	ENSP00000353652:E149G	E	+	2	0	ZNF528	57610363	0.018000	0.18449	0.002000	0.10522	0.023000	0.10783	1.809000	0.38922	0.986000	0.38683	0.477000	0.44152	GAA		0.358	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1		NM_032423	
