#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
A2ML1	144568	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	9008181	9008181	+	Silent	SNP	G	G	A	rs201562692		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr12:9008181G>A	ENST00000299698.7	+	23	3021	c.2841G>A	c.(2839-2841)acG>acA	p.T947T	A2ML1_ENST00000539547.1_Silent_p.T456T	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.T947T(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CTTATGTTACGGTTCTGGGTA	0.512																																																	1	Substitution - coding silent(1)	kidney(1)						G		0,3912		0,0,1956	114.0	105.0	108.0		2841	-4.0	0.3	12		108	5,8267		0,5,4131	no	coding-synonymous	A2ML1	NM_144670.3		0,5,6087	AA,AG,GG		0.0604,0.0,0.041		947/1455	9008181	5,12179	1956	4136	6092	SO:0001819	synonymous_variant	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2841G>A	12.37:g.9008181G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																				0.512	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3		NM_144670	
ADAMTS18	170692	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	77353798	77353798	+	Missense_Mutation	SNP	C	C	T	rs149031657	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr16:77353798C>T	ENST00000282849.5	-	16	2898	c.2480G>A	c.(2479-2481)cGc>cAc	p.R827H		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	827	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R827H(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ACGTTCCGGGCGGTTGAAAGA	0.542																																																	1	Substitution - Missense(1)	kidney(1)											58.0	58.0	58.0					16																	77353798		2198	4300	6498	SO:0001583	missense	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2480G>A	16.37:g.77353798C>T	ENSP00000282849:p.Arg827His	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.058475	0.36277	.	.	ENSG00000140873	ENST00000282849	T	0.52057	0.68	5.54	-7.54	0.01332	ADAM-TS Spacer 1 (1);	0.503008	0.22144	N	0.064016	T	0.20333	0.0489	N	0.11313	0.125	0.25930	N	0.983009	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.05084	-1.0907	10	0.40728	T	0.16	.	9.665	0.39979	0.1016:0.2297:0.0:0.6687	.	827;827	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	H	827	ENSP00000282849:R827H	ENSP00000282849:R827H	R	-	2	0	ADAMTS18	75911299	0.001000	0.12720	0.137000	0.22149	0.730000	0.41778	-0.759000	0.04761	-1.307000	0.02321	-1.603000	0.00810	CGC		0.542	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			
AK7	122481	hgsc.bcm.edu	37	14	96949471	96949472	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr14:96949471_96949472insG	ENST00000267584.4	+	16	1933_1934	c.1889_1890insG	c.(1888-1893)ctggccfs	p.A631fs		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	631	Glu-rich.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GAGGAGCGGCTGGCCAGGGAGG	0.569																																																	0																																										SO:0001589	frameshift_variant	122481			AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1891dupG	14.37:g.96949473_96949473dupG	ENSP00000267584:p.Ala631fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYP6	Frame_Shift_Ins	INS	ENST00000267584.4	37	CCDS9945.1																																																																																				0.569	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			
ARMC4	55130	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	28229610	28229610	+	Missense_Mutation	SNP	G	G	A	rs375702916		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr10:28229610G>A	ENST00000305242.5	-	13	1960	c.1868C>T	c.(1867-1869)aCg>aTg	p.T623M	ARMC4_ENST00000545014.1_Missense_Mutation_p.T148M|ARMC4_ENST00000537576.1_Missense_Mutation_p.T315M	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	623					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.T623M(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						TTCTTTATTCGTATGACTCTT	0.532																																																	1	Substitution - Missense(1)	kidney(1)						A	MET/THR	0,4406		0,0,2203	115.0	105.0	108.0		1868	2.2	0.0	10		108	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARMC4	NM_018076.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	623/1045	28229610	1,13005	2203	4300	6503	SO:0001583	missense	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1868C>T	10.37:g.28229610G>A	ENSP00000306410:p.Thr623Met	Somatic		WXS	Illumina HiSeq	Phase_I	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	g	4.132	0.022685	0.08006	0.0	1.16E-4	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	T;T;T	0.65178	-0.14;-0.14;-0.14	5.24	2.16	0.27623	Armadillo-like helical (1);Armadillo-type fold (2);	1.286300	0.04796	N	0.432595	T	0.65048	0.2654	L	0.39245	1.2	0.09310	N	1	D;B	0.61697	0.99;0.006	P;B	0.56648	0.803;0.003	T	0.50268	-0.8848	10	0.62326	D	0.03	-0.1639	4.2904	0.10876	0.0803:0.3373:0.4059:0.1765	.	148;623	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	M	315;623;148	ENSP00000443208:T315M;ENSP00000306410:T623M;ENSP00000441076:T148M	ENSP00000306410:T623M	T	-	2	0	ARMC4	28269616	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	1.237000	0.32695	0.704000	0.31869	-0.119000	0.15052	ACG		0.532	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1		NM_018076	
BOC	91653	broad.mit.edu;ucsc.edu	37	3	112969550	112969550	+	Silent	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr3:112969550G>T	ENST00000495514.1	+	4	950	c.246G>T	c.(244-246)ctG>ctT	p.L82L	BOC_ENST00000485230.1_Silent_p.L82L|BOC_ENST00000355385.3_Silent_p.L82L|BOC_ENST00000273395.4_Silent_p.L82L|BOC_ENST00000484034.1_Silent_p.L82L			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	82	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.L82L(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			ATGATGCTCTGGGTGTCCTCA	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											134.0	129.0	131.0					3																	112969550		2203	4300	6503	SO:0001819	synonymous_variant	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.246G>T	3.37:g.112969550G>T		Somatic		WXS	Illumina GAIIx	Phase_I	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																				0.602	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3		NM_033254	
ASUN	55726	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	27081163	27081163	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr12:27081163T>C	ENST00000261191.7	-	5	1095	c.559A>G	c.(559-561)Aac>Gac	p.N187D	ASUN_ENST00000539625.1_Missense_Mutation_p.N86D	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	187					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.N187D(1)									GCAAGCTTGTTATGTTCATGA	0.299																																																	1	Substitution - Missense(1)	kidney(1)											100.0	93.0	95.0					12																	27081163		2203	4300	6503	SO:0001583	missense	0			AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"""spermatogenesis associated 30"""	615079	"""chromosome 12 open reading frame 11"", ""asunder, spermatogenesis regulator homolog (Drosphila)"""	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.559A>G	12.37:g.27081163T>C	ENSP00000261191:p.Asn187Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Missense_Mutation	SNP	ENST00000261191.7	37	CCDS8708.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454702	0.84209	.	.	ENSG00000064102	ENST00000261191;ENST00000539625;ENST00000538727;ENST00000544548	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.56	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.76838	2.35	0.80722	D	1	P	0.35468	0.503	B	0.37833	0.259	T	0.64782	-0.6326	10	0.87932	D	0	-18.6271	12.2716	0.54710	0.1272:0.0:0.0:0.8727	.	187	Q9NVM9	M89BB_HUMAN	D	187;86;86;187	ENSP00000261191:N187D;ENSP00000443724:N86D;ENSP00000448467:N86D;ENSP00000446183:N187D	ENSP00000261191:N187D	N	-	1	0	C12orf11	26972430	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.165000	0.77544	1.028000	0.39785	-0.336000	0.08194	AAC		0.299	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1		NM_018164	
KIAA1551	55196	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	32134198	32134198	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr12:32134198A>C	ENST00000312561.4	+	4	723	c.309A>C	c.(307-309)caA>caC	p.Q103H	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	103								p.Q103H(1)									GACCCAAACAACTAACTCACA	0.393																																																	1	Substitution - Missense(1)	kidney(1)											89.0	83.0	85.0					12																	32134198		2203	4300	6503	SO:0001583	missense	0			AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.309A>C	12.37:g.32134198A>C	ENSP00000310338:p.Gln103His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	17.60	3.431102	0.62844	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.09911	2.93;2.93	5.59	-5.03	0.02973	.	0.551000	0.16804	N	0.198842	T	0.05318	0.0141	L	0.34521	1.04	0.09310	N	1	P	0.48294	0.908	B	0.40677	0.337	T	0.17018	-1.0383	9	.	.	.	.	2.3701	0.04328	0.2506:0.2163:0.3844:0.1487	.	103	Q9HCM1	CL035_HUMAN	H	103	ENSP00000310338:Q103H;ENSP00000370442:Q103H	.	Q	+	3	2	C12orf35	32025465	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-0.242000	0.08928	-1.308000	0.02318	-0.280000	0.10049	CAA		0.393	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2		NM_018169	
CPED1	79974	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	120782148	120782148	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr7:120782148C>T	ENST00000310396.5	+	16	2475	c.2008C>T	c.(2008-2010)Cca>Tca	p.P670S	CPED1_ENST00000450913.2_Missense_Mutation_p.P670S|CPED1_ENST00000423795.1_Missense_Mutation_p.P450S	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	670						endoplasmic reticulum (GO:0005783)		p.P670S(1)									AGAAGACCGCCCAAGTCTGCC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											190.0	170.0	177.0					7																	120782148		2203	4299	6502	SO:0001583	missense	0				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2008C>T	7.37:g.120782148C>T	ENSP00000309772:p.Pro670Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802481	0.90538	.	.	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.25414	2.13;1.8;1.81	5.77	5.77	0.91146	.	0.056277	0.64402	D	0.000001	T	0.53142	0.1778	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.973	T	0.50189	-0.8857	10	0.72032	D	0.01	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	450;670;670	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	S	670;670;450	ENSP00000309772:P670S;ENSP00000406122:P670S;ENSP00000415573:P450S	ENSP00000309772:P670S	P	+	1	0	C7orf58	120569384	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.634000	0.67833	2.885000	0.99019	0.655000	0.94253	CCA		0.433	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1		NM_024913	
C9orf85	138241	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	74526670	74526670	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr9:74526670A>T	ENST00000377031.3	+	1	210	c.20A>T	c.(19-21)aAc>aTc	p.N7I	ABHD17B_ENST00000377041.2_5'Flank|C9orf85_ENST00000334731.2_Missense_Mutation_p.N7I|ABHD17B_ENST00000333421.6_5'Flank|C9orf85_ENST00000486911.2_Missense_Mutation_p.N7I			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	7								p.N7I(2)		kidney(2)|large_intestine(1)|lung(4)	7						CAGAAAGGCAACGTGGCTCGT	0.502																																																	2	Substitution - Missense(2)	kidney(2)											180.0	181.0	180.0					9																	74526670		2203	4300	6503	SO:0001583	missense	138241			BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.20A>T	9.37:g.74526670A>T	ENSP00000366230:p.Asn7Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Missense_Mutation	SNP	ENST00000377031.3	37		.	.	.	.	.	.	.	.	.	.	A	34	5.342519	0.95783	.	.	ENSG00000155621	ENST00000334731;ENST00000377031;ENST00000356065	T	0.35789	1.29	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.62853	0.2462	M	0.82323	2.585	0.53688	D	0.999978	D	0.89917	1.0	D	0.91635	0.999	T	0.68198	-0.5472	10	0.87932	D	0	-33.7882	12.9237	0.58247	1.0:0.0:0.0:0.0	.	7	Q96MD7-1	.	I	7	ENSP00000366230:N7I	ENSP00000334289:N7I	N	+	2	0	C9orf85	73716490	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.687000	0.61708	2.295000	0.77249	0.523000	0.50628	AAC		0.502	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2		NM_182505	
CARS2	79587	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	111340142	111340142	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr13:111340142G>T	ENST00000257347.4	-	5	560	c.497C>A	c.(496-498)aCc>aAc	p.T166N	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	166					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)	p.T166N(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AATATTTTCGGTTACCCTCAG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											150.0	156.0	154.0					13																	111340142		2203	4300	6503	SO:0001583	missense	79587			BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.497C>A	13.37:g.111340142G>T	ENSP00000257347:p.Thr166Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.999273	0.54147	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.39997	1.05	4.71	4.71	0.59529	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79003	0.4373	H	0.98918	4.37	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.88362	0.2988	10	0.87932	D	0	-18.1091	16.8035	0.85620	0.0:0.0:1.0:0.0	.	166	Q9HA77	SYCM_HUMAN	N	166;157	ENSP00000257347:T166N	ENSP00000257347:T166N	T	-	2	0	CARS2	110138143	1.000000	0.71417	0.591000	0.28745	0.016000	0.09150	7.467000	0.80930	2.303000	0.77524	0.557000	0.71058	ACC		0.463	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3		NM_024537	
CCDC160	347475	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	133379666	133379666	+	Missense_Mutation	SNP	G	G	A	rs200917250		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:133379666G>A	ENST00000517294.1	+	3	1219	c.836G>A	c.(835-837)aGt>aAt	p.S279N	CCDC160_ENST00000370809.4_Missense_Mutation_p.S279N			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	279								p.S279I(1)|p.S279N(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GGAGAGCTCAGTGTCATCAAG	0.383																																																	2	Substitution - Missense(2)	kidney(2)						G	ASN/SER	0,3103		0,0,0,1266,571	42.0	38.0	39.0		836	-1.7	0.0	X		39	1,6368		0,0,1,2296,1776	yes	missense	CCDC160	NM_001101357.1	46	0,0,1,3562,2347	AA,AG,A,GG,G		0.0157,0.0,0.0106	benign	279/326	133379666	1,9471	1837	4073	5910	SO:0001583	missense	347475			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.836G>A	X.37:g.133379666G>A	ENSP00000427951:p.Ser279Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	G	0.053	-1.244894	0.01481	0.0	1.57E-4	ENSG00000203952	ENST00000517294;ENST00000370809	D;D	0.90444	-2.67;-2.67	5.29	-1.73	0.08081	.	1.068870	0.07308	N	0.875388	T	0.74207	0.3686	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.59820	-0.7382	10	0.18710	T	0.47	-0.7691	4.9933	0.14226	0.4906:0.266:0.2434:0.0	.	279	A6NGH7	CC160_HUMAN	N	279	ENSP00000427951:S279N;ENSP00000359845:S279N	ENSP00000359845:S279N	S	+	2	0	CCDC160	133207332	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.618000	0.24373	-0.644000	0.05465	-1.427000	0.01099	AGT		0.383	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1		NM_001101357	
CDH4	1002	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	60511821	60511821	+	Silent	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr20:60511821C>T	ENST00000360469.5	+	16	2659	c.2571C>T	c.(2569-2571)ccC>ccT	p.P857P	CDH4_ENST00000543233.1_Silent_p.P783P	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	857					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P857P(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ACAACGACCCCACGGCACCCC	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											46.0	46.0	46.0					20																	60511821		2203	4300	6503	SO:0001819	synonymous_variant	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2571C>T	20.37:g.60511821C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																				0.647	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2		NM_001794	
CDV3	55573	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	133302937	133302937	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr3:133302937T>C	ENST00000264993.3	+	3	724	c.409T>C	c.(409-411)Tct>Cct	p.S137P	CDV3_ENST00000515421.1_Missense_Mutation_p.S35P|CDV3_ENST00000420115.2_Missense_Mutation_p.S35P|CDV3_ENST00000508481.1_Missense_Mutation_p.S35P|CDV3_ENST00000511392.1_Missense_Mutation_p.S35P|CDV3_ENST00000431519.2_Missense_Mutation_p.S137P	NM_001134422.1|NM_001282763.1|NM_017548.4	NP_001127894.1|NP_001269692.1|NP_060018.1	Q9UKY7	CDV3_HUMAN	CDV3 homolog (mouse)	137					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)		p.S137P(2)		kidney(3)|lung(1)|prostate(1)	5						TATGGAAAAATCTTCAGGTCC	0.403																																																	2	Substitution - Missense(2)	kidney(2)											139.0	129.0	132.0					3																	133302937		2203	4300	6503	SO:0001583	missense	55573			AK096865	CCDS3079.1, CCDS46917.1, CCDS46918.1, CCDS75013.1, CCDS75014.1, CCDS75015.1	3q22.1	2008-02-05			ENSG00000091527	ENSG00000091527			26928	protein-coding gene	gene with protein product						10497265	Standard	NM_017548		Approved	H41	uc003epq.3	Q9UKY7	OTTHUMG00000159764	ENST00000264993.3:c.409T>C	3.37:g.133302937T>C	ENSP00000264993:p.Ser137Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B3KUC2|Q96IP9	Missense_Mutation	SNP	ENST00000264993.3	37	CCDS3079.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912131	0.72983	.	.	ENSG00000091527	ENST00000264993;ENST00000431519;ENST00000508481;ENST00000420115;ENST00000504867;ENST00000507408;ENST00000511392;ENST00000515421	.	.	.	5.7	4.48	0.54585	.	0.239935	0.44483	D	0.000450	T	0.76414	0.3984	M	0.73598	2.24	0.38060	D	0.936043	P;D;D	0.76494	0.718;0.999;0.999	P;D;D	0.71656	0.528;0.974;0.929	T	0.80848	-0.1199	9	0.59425	D	0.04	.	12.5311	0.56115	0.0:0.0:0.1389:0.8611	.	35;137;137	Q9UKY7-3;Q9UKY7;Q9UKY7-2	.;CDV3_HUMAN;.	P	137;137;35;35;35;34;35;35	.	ENSP00000264993:S137P	S	+	1	0	CDV3	134785627	0.999000	0.42202	0.925000	0.36789	0.979000	0.70002	2.389000	0.44407	2.188000	0.69820	0.528000	0.53228	TCT		0.403	CDV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357203.1		NM_017548	
CLCN4	1183	hgsc.bcm.edu;ucsc.edu	37	X	10180545	10180545	+	Silent	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:10180545C>T	ENST00000380833.4	+	10	1819	c.1428C>T	c.(1426-1428)ggC>ggT	p.G476G	CLCN4_ENST00000380829.1_Silent_p.G445G|CLCN4_ENST00000421085.2_Silent_p.G382G	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	476					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TGGCTGTGGGCGCGATAGCGG	0.582																																					Melanoma(74;1050 1296 1576 30544 38374)												0													80.0	71.0	74.0					X																	10180545		2203	4300	6503	SO:0001819	synonymous_variant	1183			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1428C>T	X.37:g.10180545C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																				0.582	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			
CRIPAK	285464	hgsc.bcm.edu	37	4	1388500	1388500	+	Silent	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr4:1388500C>T	ENST00000324803.4	+	1	3161	c.201C>T	c.(199-201)caC>caT	p.H67H		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	67					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGCCTGCTCACACACGTGTCC	0.632																																																	0													279.0	245.0	256.0					4																	1388500		2203	4300	6503	SO:0001819	synonymous_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.201C>T	4.37:g.1388500C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																				0.632	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2		NM_175918	
CUL7	9820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	43019452	43019452	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr6:43019452C>G	ENST00000265348.3	-	3	715	c.630G>C	c.(628-630)gaG>gaC	p.E210D	CUL7_ENST00000535468.1_Missense_Mutation_p.E294D			Q14999	CUL7_HUMAN	cullin 7	210					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.E210D(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCAGGTGTTTCTCAATGGCTT	0.532																																																	1	Substitution - Missense(1)	kidney(1)											162.0	146.0	151.0					6																	43019452		2203	4300	6503	SO:0001583	missense	9820			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.630G>C	6.37:g.43019452C>G	ENSP00000265348:p.Glu210Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.567924	0.65651	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;D	0.89050	0.88;-2.46	5.53	3.7	0.42460	.	0.000000	0.85682	D	0.000000	D	0.91178	0.7221	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	D	0.91605	0.5298	10	0.87932	D	0	-14.5593	8.5116	0.33220	0.0:0.6969:0.0:0.3031	.	294;210	F5H0L1;Q14999	.;CUL7_HUMAN	D	210;294	ENSP00000265348:E210D;ENSP00000438788:E294D	ENSP00000265348:E210D	E	-	3	2	CUL7	43127430	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.368000	0.34216	1.295000	0.44724	0.555000	0.69702	GAG		0.532	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1		NM_014780	
CUX1	1523	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	101926034	101926034	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr7:101926034A>T	ENST00000437600.4	+	22	2279	c.1927A>T	c.(1927-1929)Atg>Ttg	p.M643L	CUX1_ENST00000292538.4_Missense_Mutation_p.M645L|CUX1_ENST00000547394.2_Missense_Mutation_p.M629L|SH2B2_ENST00000536178.1_5'Flank|CUX1_ENST00000393824.3_Missense_Mutation_p.M606L|CUX1_ENST00000425244.2_Missense_Mutation_p.M599L|CUX1_ENST00000560541.1_3'UTR	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	0					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.M645L(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GAGCGAGAGCATGGAGAGGGA	0.682																																																	1	Substitution - Missense(1)	kidney(1)											64.0	57.0	59.0					7																	101926034		2203	4300	6503	SO:0001583	missense	1523			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1927A>T	7.37:g.101926034A>T	ENSP00000414091:p.Met643Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.365385	0.24684	.	.	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	3.67	-7.24	0.01475	CASP, C-terminal (1);	.	.	.	.	T	0.12220	0.0297	N	0.04508	-0.205	0.22112	N	0.999355	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.002;0.0;0.0;0.0	T	0.37776	-0.9691	9	0.21014	T	0.42	.	12.8467	0.57833	0.1937:0.0:0.8063:0.0	.	606;599;629;643;645	B4DZZ2;B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;.;CASP_HUMAN	L	645;629;599;643	ENSP00000292538:M645L;ENSP00000449371:M629L;ENSP00000409745:M599L;ENSP00000414091:M643L	ENSP00000292538:M645L	M	+	1	0	CUX1	101712754	0.007000	0.16637	0.248000	0.24265	0.726000	0.41606	0.128000	0.15810	-1.776000	0.01285	-1.261000	0.01458	ATG		0.682	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3		NM_001913	
DNAH6	1768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	84912547	84912547	+	Silent	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr2:84912547T>C	ENST00000237449.6	+	42	7022	c.7014T>C	c.(7012-7014)atT>atC	p.I2338I	DNAH6_ENST00000398278.2_Intron|DNAH6_ENST00000389394.3_Silent_p.I2338I|DNAH6_ENST00000602588.1_Intron			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2338					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I2338I(1)		NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATCGCTTGATTAATAATGAAG	0.338																																																	1	Substitution - coding silent(1)	kidney(1)											95.0	84.0	88.0					2																	84912547		692	1589	2281	SO:0001819	synonymous_variant	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7014T>C	2.37:g.84912547T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																				0.338	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2		NM_001370	
FAM47C	442444	broad.mit.edu;hgsc.bcm.edu	37	X	37028223	37028223	+	Silent	SNP	C	C	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:37028223C>A	ENST00000358047.3	+	1	1792	c.1740C>A	c.(1738-1740)tcC>tcA	p.S580S		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	580								p.S580S(2)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						CTGGAGTGTCCCATCTCTGCC	0.657																																																	2	Substitution - coding silent(2)	kidney(2)											47.0	53.0	51.0					X																	37028223		2202	4300	6502	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1740C>A	X.37:g.37028223C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				0.657	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1		NM_001013736	
FCGRT	2217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50017370	50017370	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:50017370T>A	ENST00000221466.5	+	3	791	c.305T>A	c.(304-306)tTc>tAc	p.F102Y	FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000426395.3_Missense_Mutation_p.F102Y|FCGRT_ENST00000596975.1_Missense_Mutation_p.F102Y	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	102	Alpha-1.			Missing (in Ref. 3; AAG31421). {ECO:0000305}.	antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)	p.F102Y(1)		endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		CTGGAAGCTTTCAAAGCTTTG	0.587																																																	1	Substitution - Missense(1)	kidney(1)											28.0	33.0	32.0					19																	50017370		2203	4299	6502	SO:0001583	missense	2217			U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"""Immunoglobulin superfamily / C1-set domain containing"""	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.305T>A	19.37:g.50017370T>A	ENSP00000221466:p.Phe102Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5HYM5|Q9HBV7|Q9NZ19	Missense_Mutation	SNP	ENST00000221466.5	37	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860629	0.71834	.	.	ENSG00000104870	ENST00000221466;ENST00000426395;ENST00000415900;ENST00000452439	T;T	0.00724	5.78;5.78	4.6	4.6	0.57074	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.930568	0.08708	N	0.905439	T	0.01189	0.0039	L	0.46157	1.445	0.09310	N	1	P	0.38440	0.631	B	0.35182	0.197	T	0.52472	-0.8571	10	0.66056	D	0.02	.	10.2953	0.43620	0.0:0.0:0.0:1.0	.	102	P55899	FCGRN_HUMAN	Y	102	ENSP00000221466:F102Y;ENSP00000410798:F102Y	ENSP00000221466:F102Y	F	+	2	0	FCGRT	54709182	0.003000	0.15002	0.004000	0.12327	0.807000	0.45602	1.301000	0.33447	1.936000	0.56123	0.459000	0.35465	TTC		0.587	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			
FCRL5	83416	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	157497598	157497598	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:157497598G>A	ENST00000361835.3	-	9	1926	c.1769C>T	c.(1768-1770)cCg>cTg	p.P590L	FCRL5_ENST00000356953.4_Missense_Mutation_p.P590L|FCRL5_ENST00000368191.3_Missense_Mutation_p.P505L|FCRL5_ENST00000368190.3_Missense_Mutation_p.P590L	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	590	Ig-like C2-type 6.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)		p.P590L(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				AGAGCCTCTCGGGGCCTCACA	0.592																																																	1	Substitution - Missense(1)	kidney(1)											50.0	54.0	52.0					1																	157497598		2203	4300	6503	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.1769C>T	1.37:g.157497598G>A	ENSP00000354691:p.Pro590Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	G	0.534	-0.856532	0.02630	.	.	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191	T;T;T;T	0.03301	3.98;3.98;3.98;3.98	3.53	-7.06	0.01568	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.291230	0.02368	N	0.077557	T	0.00356	0.0011	N	0.01742	-0.745	0.09310	N	1	B;B;B;B	0.14438	0.001;0.0;0.01;0.01	B;B;B;B	0.12837	0.003;0.002;0.008;0.003	T	0.47302	-0.9128	10	0.20046	T	0.44	.	0.9691	0.01412	0.2751:0.1071:0.3055:0.3123	.	505;590;590;590	F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9	.;.;.;FCRL5_HUMAN	L	590;590;590;505	ENSP00000354691:P590L;ENSP00000349434:P590L;ENSP00000357173:P590L;ENSP00000357174:P505L	ENSP00000349434:P590L	P	-	2	0	FCRL5	155764222	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.865000	0.04250	-1.601000	0.01601	-1.153000	0.01818	CCG		0.592	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1		NM_031281	
GALNT10	55568	broad.mit.edu;ucsc.edu	37	5	153709212	153709212	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr5:153709212T>C	ENST00000297107.6	+	4	619	c.482T>C	c.(481-483)cTc>cCc	p.L161P	GALNT10_ENST00000425427.2_Missense_Mutation_p.L161P|GALNT10_ENST00000377661.2_Missense_Mutation_p.L161P|SAP30L-AS1_ENST00000519727.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	161	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.L161P(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TGGTCCTCCCTCCTCCGCACC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											181.0	131.0	148.0					5																	153709212		2203	4300	6503	SO:0001583	missense	55568			AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.482T>C	5.37:g.153709212T>C	ENSP00000297107:p.Leu161Pro	Somatic		WXS	Illumina GAIIx	Phase_I	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694335	0.88830	.	.	ENSG00000164574	ENST00000425427;ENST00000297107;ENST00000377661	T;T;T	0.73681	-0.77;-0.77;-0.77	5.07	5.07	0.68467	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	D	0.92795	0.7709	H	0.99859	4.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95938	0.8944	10	0.87932	D	0	.	14.8309	0.70149	0.0:0.0:0.0:1.0	.	161;161;161	Q86SR1-2;Q86SR1;Q86SR1-3	.;GLT10_HUMAN;.	P	161	ENSP00000415210:L161P;ENSP00000297107:L161P;ENSP00000366889:L161P	ENSP00000297107:L161P	L	+	2	0	GALNT10	153689405	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.726000	0.84824	1.908000	0.55244	0.533000	0.62120	CTC		0.582	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1		NM_198321	
GDF15	9518	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	18497194	18497194	+	Silent	SNP	C	C	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:18497194C>A	ENST00000252809.3	+	1	227	c.195C>A	c.(193-195)acC>acA	p.T65T	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	65					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)	p.T65T(1)		kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						ACCTGCTAACCAGGCTGCGGG	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											39.0	38.0	39.0					19																	18497194		2203	4300	6503	SO:0001819	synonymous_variant	9518			BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"""prostate differentiation factor"""	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.195C>A	19.37:g.18497194C>A		Somatic		WXS	Illumina HiSeq	Phase_I	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																				0.602	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2		NM_004864	
HIST2H2AB	317772	hgsc.bcm.edu;ucsc.edu	37	1	149859184	149859185	+	Frame_Shift_Ins	INS	-	-	CA			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:149859184_149859185insCA	ENST00000331128.3	-	1	281_282	c.282_283insTG	c.(280-285)ctcaacfs	p.N95fs	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_175065.2	NP_778235.1	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	95						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			AGTAACTTGTTGAGCTCTTCGT	0.579																																																	0																																										SO:0001589	frameshift_variant	317772			AY131972	CCDS938.1	1q21.2	2011-01-27	2006-10-11		ENSG00000184270	ENSG00000184270		"""Histones / Replication-dependent"""	20508	protein-coding gene	gene with protein product		615014	"""histone 2, H2ab"""			12408966	Standard	NM_175065		Approved		uc001ete.3	Q8IUE6	OTTHUMG00000012085	ENST00000331128.3:c.282_283insTG	1.37:g.149859184_149859185insCA	ENSP00000332790:p.Asn95fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	INS	ENST00000331128.3	37	CCDS938.1																																																																																				0.579	HIST2H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033440.1		NM_175065	
IPO7	10527	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	9459375	9459375	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr11:9459375G>A	ENST00000379719.3	+	21	2485	c.2343G>A	c.(2341-2343)atG>atA	p.M781I		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	781					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)	p.M781I(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTCGAACTATGTGTCTGCAAG	0.373																																																	1	Substitution - Missense(1)	kidney(1)											88.0	80.0	83.0					11																	9459375		2201	4294	6495	SO:0001583	missense	10527			AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2343G>A	11.37:g.9459375G>A	ENSP00000369042:p.Met781Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849356	0.91277	.	.	ENSG00000205339	ENST00000379719	T	0.65732	-0.17	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	M	0.88512	2.96	0.80722	D	1	P	0.47545	0.897	P	0.50537	0.643	T	0.76102	-0.3082	10	0.19590	T	0.45	.	18.1413	0.89641	0.0:0.0:1.0:0.0	.	781	O95373	IPO7_HUMAN	I	781	ENSP00000369042:M781I	ENSP00000369042:M781I	M	+	3	0	IPO7	9415951	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.864000	0.99589	2.270000	0.75569	0.460000	0.39030	ATG		0.373	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1		NM_006391	
KIR3DL1	3811	broad.mit.edu;hgsc.bcm.edu	37	19	55351066	55351066	+	Intron	SNP	C	C	T	rs1130503		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:55351066C>T	ENST00000402254.2	+	6	1033				KIR2DS4_ENST00000339924.8_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.T185M(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CTGCCACCCACGGAGGGACCT	0.587																																																	1	Substitution - Missense(1)	kidney(1)											187.0	174.0	179.0					19																	55351066		2170	4156	6326	SO:0001627	intron_variant	3809			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000402254.2:c.1000+14533C>T	19.37:g.55351066C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000402254.2	37																																																																																					0.587	KIR3DL1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_013289	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197614	39197614	+	Silent	SNP	G	G	A	rs141856614	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr17:39197614G>A	ENST00000306271.4	-	1	99	c.36C>T	c.(34-36)ccC>ccT	p.P12P		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	12			PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGAGCAGCTGGGAAATCCAC	0.587													g|||	501	0.10004	0.1846	0.1138	5008	,	,		15385	0.1419		0.0169	False		,,,				2504	0.0184																0													48.0	56.0	53.0					17																	39197614		1952	4163	6115	SO:0001819	synonymous_variant	81851			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.36C>T	17.37:g.39197614G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																				0.587	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1		NM_030967	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197638	39197638	+	Silent	SNP	A	A	G	rs112542604	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr17:39197638A>G	ENST00000306271.4	-	1	75	c.12T>C	c.(10-12)tgT>tgC	p.C4C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	4						keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCTGGTCTGACAGCAGGCCA	0.562													a|||	527	0.105232	0.1899	0.1153	5008	,	,		16504	0.1597		0.0169	False		,,,				2504	0.0184																0								A		553,3361		37,479,1441	49.0	54.0	53.0		12	-3.9	0.0	17	dbSNP_132	53	124,8182		5,114,4034	no	coding-synonymous	KRTAP1-1	NM_030967.2		42,593,5475	GG,GA,AA		1.4929,14.1288,5.5401		4/178	39197638	677,11543	1957	4153	6110	SO:0001819	synonymous_variant	81851			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.12T>C	17.37:g.39197638A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																				0.562	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1		NM_030967	
KLHL10	317719	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	40004451	40004451	+	Silent	SNP	A	A	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr17:40004451A>C	ENST00000293303.4	+	5	1872	c.1719A>C	c.(1717-1719)ccA>ccC	p.P573P	RP11-156E6.1_ENST00000560400.1_RNA	NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	573					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)		p.P573P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				GTGTAGTACCAGGGCTGGCCA	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											122.0	121.0	122.0					17																	40004451		2003	4176	6179	SO:0001819	synonymous_variant	317719			AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"""Kelch-like"", ""BTB/POZ domain containing"""	18829	protein-coding gene	gene with protein product		608778	"""kelch-like 10 (Drosophila)"""				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.1719A>C	17.37:g.40004451A>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q6NW28|Q96MC0	Silent	SNP	ENST00000293303.4	37	CCDS42340.1																																																																																				0.463	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1		NM_152467	
LAMA3	3909	hgsc.bcm.edu	37	18	21353525	21353525	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr18:21353525C>G	ENST00000313654.9	+	9	1488	c.1247C>G	c.(1246-1248)cCa>cGa	p.P416R	LAMA3_ENST00000399516.3_Missense_Mutation_p.P416R	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	416	Domain V.|Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TATGGGGTTCCAGTGGATGCC	0.463																																																	0													68.0	71.0	70.0					18																	21353525		1908	4109	6017	SO:0001583	missense	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1247C>G	18.37:g.21353525C>G	ENSP00000324532:p.Pro416Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559992	0.65538	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669;ENST00000538801	T;T	0.20463	2.09;2.07	5.77	5.77	0.91146	EGF-like, laminin (3);	.	.	.	.	T	0.48502	0.1503	M	0.70108	2.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.992;1.0;0.999	T	0.27502	-1.0072	9	0.48119	T	0.1	.	19.1176	0.93348	0.0:1.0:0.0:0.0	.	416;416;416	F5H8G3;Q6VU67;Q16787	.;.;LAMA3_HUMAN	R	416;416;414;416	ENSP00000324532:P416R;ENSP00000382432:P416R	ENSP00000324532:P416R	P	+	2	0	LAMA3	19607523	0.999000	0.42202	0.948000	0.38648	0.403000	0.30841	4.563000	0.60823	2.884000	0.98904	0.655000	0.94253	CCA		0.463	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3		NM_000227, NM_198129	
LAMA3	3909	hgsc.bcm.edu;ucsc.edu	37	18	21353526	21353527	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr18:21353526_21353527insT	ENST00000313654.9	+	9	1489_1490	c.1248_1249insT	c.(1249-1251)gtgfs	p.V417fs	LAMA3_ENST00000399516.3_Frame_Shift_Ins_p.V417fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	417	Domain V.|Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					ATGGGGTTCCAGTGGATGCCCC	0.46																																																	0																																										SO:0001589	frameshift_variant	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	Exception_encountered	18.37:g.21353526_21353527insT	ENSP00000324532:p.Val417fs	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Ins	INS	ENST00000313654.9	37	CCDS42419.1																																																																																				0.460	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3		NM_000227, NM_198129	
LIG1	3978	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	48634399	48634399	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:48634399C>A	ENST00000263274.7	-	19	2174	c.1755G>T	c.(1753-1755)aaG>aaT	p.K585N	LIG1_ENST00000536218.1_Missense_Mutation_p.K517N|LIG1_ENST00000427526.2_Missense_Mutation_p.K554N	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	585					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)	p.K585N(1)		breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	TGCTGAAGATCTTCACCTCCC	0.582								Nucleotide excision repair (NER)																																									1	Substitution - Missense(1)	kidney(1)											207.0	136.0	160.0					19																	48634399		2203	4300	6503	SO:0001583	missense	3978				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1755G>T	19.37:g.48634399C>A	ENSP00000263274:p.Lys585Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874149	0.33069	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218	D;D;D	0.82255	-1.59;-1.59;-1.59	5.49	2.23	0.28157	DNA ligase, ATP-dependent, central (1);	0.281296	0.33916	N	0.004432	T	0.73497	0.3594	L	0.54323	1.7	0.80722	D	1	B;B;B	0.33299	0.247;0.192;0.407	B;B;B	0.33799	0.17;0.045;0.17	T	0.64305	-0.6439	10	0.27082	T	0.32	-34.601	3.8993	0.09154	0.1686:0.5705:0.0:0.2609	.	554;517;585	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	N	585;616;554;517	ENSP00000263274:K585N;ENSP00000442841:K554N;ENSP00000441531:K517N	ENSP00000263274:K585N	K	-	3	2	LIG1	53326211	0.986000	0.35501	1.000000	0.80357	0.998000	0.95712	0.149000	0.16243	0.812000	0.34326	0.650000	0.86243	AAG		0.582	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1		NM_000234	
LMO7	4008	hgsc.bcm.edu;ucsc.edu	37	13	76381790	76381791	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr13:76381790_76381791insT	ENST00000321797.8	+	8	1393_1394	c.672_673insT	c.(673-675)ttafs	p.L225fs	LMO7_ENST00000526202.1_Intron|LMO7_ENST00000465261.2_Frame_Shift_Ins_p.L225fs|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Frame_Shift_Ins_p.L510fs|LMO7_ENST00000377534.3_Frame_Shift_Ins_p.L510fs|LMO7_ENST00000341547.4_Intron			Q8WWI1	LMO7_HUMAN	LIM domain 7	510					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TGGATCCTGACTTAGAGAATGA	0.46																																																	0																																										SO:0001589	frameshift_variant	4008			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.674dupT	13.37:g.76381792_76381792dupT	ENSP00000317802:p.Leu225fs	Somatic		WXS	Illumina HiSeq	Phase_I	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Frame_Shift_Ins	INS	ENST00000321797.8	37																																																																																					0.460	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3		NM_005358	
LPAR4	2846	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	78011222	78011222	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:78011222G>T	ENST00000435339.3	+	2	1242	c.856G>T	c.(856-858)Gaa>Taa	p.E286*		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	286					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.E286*(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						TTGCTTTTTGGAAAGATTTGC	0.418																																																	1	Substitution - Nonsense(1)	kidney(1)											172.0	135.0	148.0					X																	78011222		2203	4300	6503	SO:0001587	stop_gained	2846			U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	4478	protein-coding gene	gene with protein product		300086	"""G protein-coupled receptor 23"""	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.856G>T	X.37:g.78011222G>T	ENSP00000408205:p.Glu286*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAC7|O15132|Q502U9|Q6NSP5	Nonsense_Mutation	SNP	ENST00000435339.3	37	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	G	38	7.184785	0.98121	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	.	.	.	3.99	3.99	0.46301	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	13.9688	0.64225	0.0:0.0:1.0:0.0	.	.	.	.	X	286	.	ENSP00000362398:E286X	E	+	1	0	LPAR4	77897878	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.112000	0.94314	1.832000	0.53329	0.422000	0.28245	GAA		0.418	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2		NM_005296	
LRRCC1	85444	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	86037088	86037088	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr8:86037088A>C	ENST00000360375.3	+	8	1335	c.1186A>C	c.(1186-1188)Aac>Cac	p.N396H	LRRCC1_ENST00000414626.2_Missense_Mutation_p.N376H	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	396					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.N396H(1)|p.N376H(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ATCTTTAGCAAACTGTCCTAT	0.308																																																	2	Substitution - Missense(2)	kidney(2)											89.0	89.0	89.0					8																	86037088		1811	4065	5876	SO:0001583	missense	85444			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1186A>C	8.37:g.86037088A>C	ENSP00000353538:p.Asn396His	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065946	0.55539	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.32988	1.48;1.43	4.63	4.63	0.57726	.	0.312303	0.23332	N	0.049332	T	0.46889	0.1416	L	0.50333	1.59	0.09310	N	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.993	D;D;D;P	0.85130	0.997;0.964;0.997;0.659	T	0.26292	-1.0107	10	0.54805	T	0.06	-6.563	10.7403	0.46149	1.0:0.0:0.0:0.0	.	303;376;303;396	B4DV06;Q9C099-2;E9PE41;Q9C099	.;.;.;LRCC1_HUMAN	H	396;376	ENSP00000353538:N396H;ENSP00000394695:N376H	ENSP00000353538:N396H	N	+	1	0	LRRCC1	86224340	0.091000	0.21658	0.006000	0.13384	0.070000	0.16714	2.549000	0.45803	2.311000	0.77944	0.533000	0.62120	AAC		0.308	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1		NM_033402	
LRRTM2	26045	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	138209538	138209538	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr5:138209538A>C	ENST00000274711.6	-	2	1090	c.712T>G	c.(712-714)Tgg>Ggg	p.W238G	LRRTM2_ENST00000521094.2_Intron|LRRTM2_ENST00000523537.1_5'Flank|CTNNA1_ENST00000520400.1_Intron|CTNNA1_ENST00000540387.1_5'Flank|CTNNA1_ENST00000302763.7_Intron|LRRTM2_ENST00000518785.1_3'UTR|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000518825.1_Intron	NM_015564.2	NP_056379.1	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2	238					long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|synapse organization (GO:0050808)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.W238G(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|urinary_tract(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATTTTGTTCCATTGTAAGAAG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											303.0	294.0	297.0					5																	138209538		1943	4142	6085	SO:0001583	missense	26045			AB007876	CCDS47272.1	5q31	2008-02-05				ENSG00000146006			19409	protein-coding gene	gene with protein product		610868				12676565	Standard	NM_015564		Approved	KIAA0416	uc011cyz.1	O43300		ENST00000274711.6:c.712T>G	5.37:g.138209538A>C	ENSP00000274711:p.Trp238Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVL3|A8K4U9|B7ZLN8|Q7L770	Missense_Mutation	SNP	ENST00000274711.6	37	CCDS47272.1	.	.	.	.	.	.	.	.	.	.	A	2.359	-0.347035	0.05208	.	.	ENSG00000146006	ENST00000274711	T	0.03689	3.84	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.04998	0.0134	M	0.62723	1.935	0.58432	D	0.999991	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34625	-0.9821	10	0.25106	T	0.35	.	7.4579	0.27276	0.713:0.1464:0.0:0.1406	.	104;238	B7Z4G4;O43300	.;LRRT2_HUMAN	G	238	ENSP00000274711:W238G	ENSP00000274711:W238G	W	-	1	0	LRRTM2	138237437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.932000	0.56537	2.307000	0.77673	0.528000	0.53228	TGG		0.443	LRRTM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374043.2			
LTBP1	4052	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	33534615	33534615	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr2:33534615C>G	ENST00000404816.2	+	23	3949	c.3596C>G	c.(3595-3597)aCa>aGa	p.T1199R	LTBP1_ENST00000272273.5_Missense_Mutation_p.T139R|LTBP1_ENST00000354476.3_Missense_Mutation_p.T1200R|LTBP1_ENST00000404525.1_Missense_Mutation_p.T820R|LTBP1_ENST00000390003.4_Missense_Mutation_p.T874R|LTBP1_ENST00000407925.1_Missense_Mutation_p.T873R|LTBP1_ENST00000418533.2_Missense_Mutation_p.T873R|LTBP1_ENST00000402934.1_Missense_Mutation_p.T820R			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1199	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.T1200R(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GACAATAAAACATGTCAAGGT	0.408																																																	1	Substitution - Missense(1)	kidney(1)											179.0	165.0	170.0					2																	33534615		2203	4300	6503	SO:0001583	missense	4052				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3596C>G	2.37:g.33534615C>G	ENSP00000386043:p.Thr1199Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.069|0.069	-1.206592|-1.206592	0.01568|0.01568	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	.|D;D;D;D;D;D;D;D;D	.|0.87103	.|-2.21;-2.21;-2.21;-2.21;-2.21;-2.21;-2.21;-2.21;-2.21	5.93|5.93	-0.821|-0.821	0.10822|0.10822	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	T|T	0.77691|0.77691	0.4168|0.4168	L|L	0.41824|0.41824	1.3|1.3	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B	.|0.06405	.|0.001;0.002;0.0;0.002;0.001;0.001;0.001	T|T	0.58607|0.58607	-0.7607|-0.7607	5|9	.|0.16420	.|T	.|0.52	.|.	7.4792|7.4792	0.27395|0.27395	0.2781:0.2143:0.5077:0.0|0.2781:0.2143:0.5077:0.0	.|.	.|139;1199;873;820;873;874;1200	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	D|R	161|1199;1200;874;873;820;820;873;139;77	.|ENSP00000386043:T1199R;ENSP00000346467:T1200R;ENSP00000374653:T874R;ENSP00000393057:T873R;ENSP00000384373:T820R;ENSP00000385359:T820R;ENSP00000384091:T873R;ENSP00000272273:T139R;ENSP00000395211:T77R	.|ENSP00000272273:T139R	H|T	+|+	1|2	0|0	LTBP1|LTBP1	33388119|33388119	0.899000|0.899000	0.30636|0.30636	0.008000|0.008000	0.14137|0.14137	0.016000|0.016000	0.09150|0.09150	0.857000|0.857000	0.27831|0.27831	-0.081000|-0.081000	0.12662|0.12662	-0.165000|-0.165000	0.13383|0.13383	CAT|ACA		0.408	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2		NM_206943	
MKKS	8195	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	10393381	10393381	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr20:10393381A>G	ENST00000347364.3	-	3	1544	c.782T>C	c.(781-783)gTg>gCg	p.V261A	MKKS_ENST00000399054.2_Missense_Mutation_p.V261A	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	261	Substrate-binding apical domain.				artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)	p.V261A(1)		kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						ATAACTGACCACCACAGTTCC	0.458																																					Melanoma(79;1979 2212 6640)												1	Substitution - Missense(1)	kidney(1)											111.0	106.0	107.0					20																	10393381		2203	4300	6503	SO:0001583	missense	8195			AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"""Heat Shock Proteins / Chaperonins"""	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.782T>C	20.37:g.10393381A>G	ENSP00000246062:p.Val261Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	37	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	A	0.073	-1.198109	0.01594	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	T;T	0.78364	-1.17;-1.17	5.72	3.46	0.39613	.	0.602004	0.18715	N	0.133165	T	0.66577	0.2803	L	0.57536	1.79	0.24644	N	0.993558	B	0.11235	0.004	B	0.12156	0.007	T	0.49762	-0.8905	10	0.09084	T	0.74	-29.4074	4.5363	0.12032	0.6319:0.0:0.2359:0.1322	.	261	Q9NPJ1	MKKS_HUMAN	A	261	ENSP00000246062:V261A;ENSP00000382008:V261A	ENSP00000246062:V261A	V	-	2	0	MKKS	10341381	0.131000	0.22433	0.748000	0.31131	0.389000	0.30415	1.173000	0.31920	0.523000	0.28482	0.528000	0.53228	GTG		0.458	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			
MLLT4	4301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	168344647	168344647	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr6:168344647G>T	ENST00000447894.2	+	25	3245	c.3245G>T	c.(3244-3246)aGc>aTc	p.S1082I	MLLT4_ENST00000344191.4_Missense_Mutation_p.S1082I|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000392108.3_Missense_Mutation_p.S1082I|MLLT4_ENST00000366806.2_Missense_Mutation_p.S1082I|MLLT4_ENST00000392112.1_Missense_Mutation_p.S1065I|MLLT4_ENST00000351017.4_Missense_Mutation_p.S1089I|MLLT4_ENST00000400822.3_Missense_Mutation_p.S1081I			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1082	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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.S1082I(1)|p.S1066I(1)		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)		ACAAGAACAAGCTCTGTGGTG	0.493			T	MLL	AL																																			Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	2	Substitution - Missense(2)	kidney(2)											122.0	105.0	111.0					6																	168344647		2203	4300	6503	SO:0001583	missense	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.3245G>T	6.37:g.168344647G>T	ENSP00000404595:p.Ser1082Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	G	25.8	4.679706	0.88542	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0	4.92	4.92	0.64577	PDZ/DHR/GLGF (4);	0.058057	0.64402	D	0.000002	T	0.49167	0.1541	M	0.67569	2.06	0.47183	D	0.999346	P;P;P;P	0.46706	0.708;0.883;0.828;0.654	P;P;B;P	0.53313	0.723;0.533;0.431;0.533	T	0.55860	-0.8074	10	0.87932	D	0	-0.865	18.1404	0.89637	0.0:0.0:1.0:0.0	.	1082;1081;1082;1066	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	I	1082;1089;1082;1082;1065;1082;1081;1082	ENSP00000341118:S1082I;ENSP00000252692:S1089I;ENSP00000375956:S1082I;ENSP00000355771:S1082I;ENSP00000375960:S1065I;ENSP00000383623:S1081I;ENSP00000404595:S1082I	ENSP00000345834:S1082I	S	+	2	0	MLLT4	168087496	1.000000	0.71417	0.919000	0.36401	0.991000	0.79684	7.434000	0.80377	2.257000	0.74773	0.650000	0.86243	AGC		0.493	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1		NM_005936	
MMP2	4313	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	55519518	55519518	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr16:55519518G>A	ENST00000219070.4	+	5	1170	c.661G>A	c.(661-663)Gtc>Atc	p.V221I	MMP2_ENST00000543485.1_Missense_Mutation_p.V145I|MMP2_ENST00000437642.2_Missense_Mutation_p.V171I|MMP2_ENST00000570308.1_Missense_Mutation_p.V145I	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	221	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.V221I(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CTCTTTAGTGGTCCGTGTGAA	0.542																																																	1	Substitution - Missense(1)	kidney(1)											116.0	97.0	104.0					16																	55519518		2198	4300	6498	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.661G>A	16.37:g.55519518G>A	ENSP00000219070:p.Val221Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949674	0.53186	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.09350	2.99;2.99;2.99	4.39	4.39	0.52855	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (1);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.000000	0.85682	D	0.000000	T	0.12220	0.0297	N	0.22421	0.69	0.80722	D	1	B;P	0.44195	0.303;0.828	P;P	0.47015	0.534;0.449	T	0.17018	-1.0383	10	0.32370	T	0.25	.	17.0342	0.86470	0.0:0.0:1.0:0.0	.	171;221	E9PE45;P08253	.;MMP2_HUMAN	I	221;145;171	ENSP00000219070:V221I;ENSP00000444143:V145I;ENSP00000394237:V171I	ENSP00000219070:V221I	V	+	1	0	MMP2	54077019	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	8.050000	0.89445	2.011000	0.59026	0.436000	0.28706	GTC		0.542	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			
MTOR	2475	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	11177077	11177077	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:11177077A>C	ENST00000361445.4	-	50	7076	c.7000T>G	c.(7000-7002)Tta>Gta	p.L2334V	MTOR_ENST00000376838.1_Missense_Mutation_p.L539V	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2334	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.L2334V(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCCAGGCCTAAAATATACCCA	0.378																																																	1	Substitution - Missense(1)	kidney(1)											150.0	145.0	147.0					1																	11177077		2203	4300	6503	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7000T>G	1.37:g.11177077A>C	ENSP00000354558:p.Leu2334Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497136	0.64186	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	D;D	0.82433	-1.61;-1.61	5.69	4.57	0.56435	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.90045	0.6891	M	0.83012	2.62	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.89615	0.3844	10	0.87932	D	0	-18.532	7.9897	0.30233	0.7743:0.0:0.2257:0.0	.	2334	P42345	MTOR_HUMAN	V	2334;539	ENSP00000354558:L2334V;ENSP00000366034:L539V	ENSP00000354558:L2334V	L	-	1	2	MTOR	11099664	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.824000	0.39072	1.000000	0.39049	0.379000	0.24179	TTA		0.378	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1		NM_004958	
ICE2	79664	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	60740179	60740179	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr15:60740179T>A	ENST00000261520.4	-	11	2519	c.2285A>T	c.(2284-2286)aAa>aTa	p.K762I	NARG2_ENST00000439632.1_Missense_Mutation_p.K625I	NM_024611.4	NP_078887.2												p.K762I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TCTTCTGATTTTCTTCCGTTT	0.343																																																	1	Substitution - Missense(1)	kidney(1)											160.0	149.0	153.0					15																	60740179		2203	4300	6503	SO:0001583	missense	79664																														ENST00000261520.4:c.2285A>T	15.37:g.60740179T>A	ENSP00000261520:p.Lys762Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000261520.4	37	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181173	0.78677	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.9	4.78	0.61160	NMDA receptor-regulated gene protein 2 (1);	0.203908	0.51477	D	0.000100	T	0.63745	0.2537	L	0.36672	1.1	0.41313	D	0.987124	D	0.69078	0.997	D	0.66847	0.947	T	0.66044	-0.6021	9	0.87932	D	0	-24.8787	9.8545	0.41077	0.0:0.0771:0.0:0.9229	.	762	Q659A1	NARG2_HUMAN	I	762;625	.	ENSP00000261520:K762I	K	-	2	0	NARG2	58527471	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.454000	0.44979	1.054000	0.40438	0.477000	0.44152	AAA		0.343	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			
NDUFA1	4694	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	119005937	119005937	+	Silent	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:119005937G>A	ENST00000371437.4	+	1	488	c.63G>A	c.(61-63)ctG>ctA	p.L21L	RNF113A_ENST00000371442.2_5'Flank	NM_004541.3	NP_004532.1	O15239	NDUA1_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5kDa	21					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)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.L21L(1)		endometrium(1)|kidney(1)|large_intestine(2)|stomach(1)	5						TTCCAGGACTGGCTACTGCGT	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											162.0	133.0	143.0					X																	119005937		2203	4300	6503	SO:0001819	synonymous_variant	4694				CCDS14590.1	Xq24	2011-07-04	2002-08-29		ENSG00000125356	ENSG00000125356		"""Mitochondrial respiratory chain complex / Complex I"""	7683	protein-coding gene	gene with protein product	"""NADH:ubiquinone oxidoreductase (complex 1)"", ""type I dehydrogenase"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 (7.5kD, MWFE)"", ""complex I MWFE subunit"""	300078	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 (7.5kD, MWFE)"""			8938439	Standard	NM_004541		Approved	MWFE, CI-MWFE	uc004esc.4	O15239	OTTHUMG00000022287	ENST00000371437.4:c.63G>A	X.37:g.119005937G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000371437.4	37	CCDS14590.1																																																																																				0.602	NDUFA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058080.1		NM_004541	
NFATC4	4776	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	24845299	24845299	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr14:24845299T>G	ENST00000250373.4	+	8	2189	c.2048T>G	c.(2047-2049)tTt>tGt	p.F683C	NFATC4_ENST00000554050.1_Missense_Mutation_p.F683C|NFATC4_ENST00000554473.1_Missense_Mutation_p.F218C|NFATC4_ENST00000554591.1_Missense_Mutation_p.F746C|NFATC4_ENST00000413692.2_Missense_Mutation_p.F746C|NFATC4_ENST00000556759.1_Missense_Mutation_p.F218C|NFATC4_ENST00000555453.1_Missense_Mutation_p.F671C|NFATC4_ENST00000422617.3_Missense_Mutation_p.F671C|NFATC4_ENST00000555167.1_Missense_Mutation_p.F218C|NFATC4_ENST00000539237.2_Missense_Mutation_p.F715C|NFATC4_ENST00000424781.2_Missense_Mutation_p.F696C|NFATC4_ENST00000557451.1_Missense_Mutation_p.F613C|NFATC4_ENST00000553879.1_Missense_Mutation_p.F613C|NFATC4_ENST00000556279.1_Missense_Mutation_p.F715C|NFATC4_ENST00000553469.1_Missense_Mutation_p.F715C|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000554661.1_Missense_Mutation_p.F613C|NFATC4_ENST00000554966.1_Missense_Mutation_p.F696C|NFATC4_ENST00000554344.1_Missense_Mutation_p.F613C|NFATC4_ENST00000553708.1_Missense_Mutation_p.F683C|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000556169.1_Missense_Mutation_p.F671C|NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000555590.1_Missense_Mutation_p.F696C	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	683	IPT/TIG.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)	p.F746C(1)|p.F683C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		AGTTTCAGGTTTCTGCCTGGT	0.577																																																	2	Substitution - Missense(2)	kidney(2)											95.0	103.0	100.0					14																	24845299		2203	4300	6503	SO:0001583	missense	4776			BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2048T>G	14.37:g.24845299T>G	ENSP00000250373:p.Phe683Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451119	0.63290	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.36878	2.98;3.0;2.98;3.02;3.0;3.0;2.97;3.01;3.02;2.99;3.01;2.66;2.66;2.7;2.69;2.68;2.68;2.65;1.28;1.24;1.23	5.36	5.36	0.76844	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.113377	0.64402	D	0.000014	T	0.49253	0.1546	L	0.46157	1.445	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.998;1.0;0.998;0.999;1.0;1.0;1.0;1.0;0.999;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D	0.74674	0.947;0.964;0.951;0.964;0.951;0.973;0.964;0.98;0.98;0.964;0.973;0.973;0.984	T	0.51204	-0.8735	10	0.87932	D	0	-6.7618	8.6427	0.33987	0.17:0.0:0.0:0.83	.	671;671;715;715;696;696;696;746;746;671;715;746;683	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	C	746;746;696;696;696;715;715;715;683;683;683;613;613;613;671;613;671;671;218;218;218	ENSP00000388910:F746C;ENSP00000452039:F746C;ENSP00000451224:F696C;ENSP00000450644:F696C;ENSP00000388668:F696C;ENSP00000439350:F715C;ENSP00000452270:F715C;ENSP00000451502:F715C;ENSP00000451151:F683C;ENSP00000250373:F683C;ENSP00000450590:F683C;ENSP00000452349:F613C;ENSP00000450469:F613C;ENSP00000450733:F613C;ENSP00000451454:F671C;ENSP00000451284:F613C;ENSP00000396788:F671C;ENSP00000450686:F671C;ENSP00000450810:F218C;ENSP00000451183:F218C;ENSP00000451395:F218C	ENSP00000250373:F683C	F	+	2	0	NFATC4	23915139	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.901000	0.48695	2.246000	0.74042	0.533000	0.62120	TTT		0.577	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6		NM_004554	
NFIA	4774	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	61743222	61743222	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:61743222C>T	ENST00000403491.3	+	3	1074	c.590C>T	c.(589-591)cCa>cTa	p.P197L	NFIA_ENST00000371189.4_Missense_Mutation_p.P242L|NFIA_ENST00000371185.2_Intron|NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000485903.2_Missense_Mutation_p.P197L|NFIA_ENST00000371187.3_Missense_Mutation_p.P197L|NFIA_ENST00000371184.2_Intron|NFIA_ENST00000371191.1_Missense_Mutation_p.P220L|NFIA_ENST00000407417.3_Missense_Mutation_p.P189L	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	197					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P197L(1)|p.P242L(1)	NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						CCCAGCCAGCCAAGTGACGCT	0.473																																																	2	Substitution - Missense(2)	kidney(2)											87.0	83.0	84.0					1																	61743222		2203	4300	6503	SO:0001583	missense	4774			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.590C>T	1.37:g.61743222C>T	ENSP00000384523:p.Pro197Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Missense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049202	0.55110	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371187	T;T;T;T;T;T	0.42900	0.97;0.98;0.96;0.97;0.98;0.97	6.02	6.02	0.97574	.	0.103329	0.64402	D	0.000002	T	0.49304	0.1549	N	0.14661	0.345	0.80722	D	1	B;P;P;P	0.51449	0.137;0.909;0.909;0.945	B;P;D;P	0.64595	0.133;0.713;0.927;0.851	T	0.44667	-0.9313	10	0.35671	T	0.21	-16.1695	20.5373	0.99239	0.0:1.0:0.0:0.0	.	242;220;197;197	F8W8W3;B1AKN8;Q12857;Q12857-2	.;.;NFIA_HUMAN;.	L	220;189;242;197;197;197	ENSP00000360233:P220L;ENSP00000384680:P189L;ENSP00000360231:P242L;ENSP00000384523:P197L;ENSP00000419785:P197L;ENSP00000360229:P197L	ENSP00000360229:P197L	P	+	2	0	NFIA	61515810	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.212000	0.72188	2.857000	0.98124	0.650000	0.86243	CCA		0.473	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3		NM_005595	
OPN4	94233	broad.mit.edu;hgsc.bcm.edu	37	10	88422065	88422065	+	Missense_Mutation	SNP	G	G	A	rs142050572		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr10:88422065G>A	ENST00000241891.5	+	8	1297	c.1130G>A	c.(1129-1131)cGg>cAg	p.R377Q	OPN4_ENST00000372071.2_Missense_Mutation_p.R388Q	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	377					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)	p.R388Q(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GTATCACGCCGGCACAGTCGC	0.677													G|||	1	0.000199681	0.0	0.0	5008	,	,		16865	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	36.0	28.0	31.0		1163,1130	1.4	0.3	10	dbSNP_134	31	1,8597		0,1,4298	yes	missense,missense	OPN4	NM_001030015.2,NM_033282.3	43,43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	388/490,377/479	88422065	1,13003	2203	4299	6502	SO:0001583	missense	94233			AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.1130G>A	10.37:g.88422065G>A	ENSP00000241891:p.Arg377Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	3.037	-0.198384	0.06219	0.0	1.16E-4	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.38401	1.14;1.14;1.14	5.39	1.37	0.22104	.	0.528842	0.18832	N	0.129956	T	0.08492	0.0211	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.18166	0.026;0.005;0.015	B;B;B	0.06405	0.001;0.001;0.002	T	0.35574	-0.9783	10	0.12103	T	0.63	.	6.3953	0.21609	0.6399:0.134:0.2261:0.0	.	388;377;388	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	Q	388;377;388	ENSP00000361141:R388Q;ENSP00000241891:R377Q;ENSP00000393132:R388Q	ENSP00000241891:R377Q	R	+	2	0	OPN4	88412045	0.321000	0.24625	0.274000	0.24659	0.910000	0.53928	1.674000	0.37544	0.343000	0.23821	-0.302000	0.09304	CGG		0.677	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2		NM_033282	
OR10G4	390264	broad.mit.edu;hgsc.bcm.edu	37	11	123887117	123887117	+	Missense_Mutation	SNP	C	C	T	rs201358968	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr11:123887117C>T	ENST00000320891.4	+	1	836	c.836C>T	c.(835-837)aCg>aTg	p.T279M		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T279M(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		ACTGTGCTGACGCCCCTTCTC	0.473													-|||	2	0.000399361	0.0	0.0029	5008	,	,		19664	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	large_intestine(1)|kidney(1)						C	MET/THR	0,4402		0,0,2201	108.0	93.0	98.0		836	2.6	0.5	11		98	3,8595		0,3,4296	yes	missense	OR10G4	NM_001004462.1	81	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	279/312	123887117	3,12997	2201	4299	6500	SO:0001583	missense	390264			AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.836C>T	11.37:g.123887117C>T	ENSP00000325076:p.Thr279Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	.	.	.	.	.	.	.	.	.	.	N	11.01	1.513019	0.27123	0.0	3.49E-4	ENSG00000254737	ENST00000320891	T	0.38401	1.14	3.48	2.56	0.30785	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40640	N	0.001050	T	0.62429	0.2427	M	0.90309	3.105	0.22996	N	0.998452	D	0.76494	0.999	D	0.72338	0.977	T	0.56275	-0.8006	10	0.87932	D	0	.	10.2744	0.43501	0.0:0.8997:0.0:0.1003	.	279	Q8NGN3	O10G4_HUMAN	M	279	ENSP00000325076:T279M	ENSP00000325076:T279M	T	+	2	0	OR10G4	123392327	0.000000	0.05858	0.491000	0.27477	0.069000	0.16628	0.831000	0.27476	0.809000	0.34255	0.580000	0.79431	ACG		0.473	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1		NM_001004462	
OR2J2	26707	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	29141782	29141782	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr6:29141782T>C	ENST00000377167.2	+	1	472	c.370T>C	c.(370-372)Tat>Cat	p.Y124H		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y124H(1)		endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						ATATGATCGTTATGTAGCTGT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											336.0	313.0	321.0					6																	29141782		2086	4198	6284	SO:0001583	missense	26707				CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.370T>C	6.37:g.29141782T>C	ENSP00000366372:p.Tyr124His	Somatic		WXS	Illumina HiSeq	Phase_I	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.033593	0.35893	.	.	ENSG00000204700	ENST00000377167	T	0.02103	4.45	2.3	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08626	0.0214	M	0.92923	3.36	0.36927	D	0.891677	D	0.89917	1.0	D	0.91635	0.999	T	0.01472	-1.1346	9	0.87932	D	0	.	9.0762	0.36522	0.0:0.0:0.0:1.0	.	124	O76002	OR2J2_HUMAN	H	124	ENSP00000366372:Y124H	ENSP00000366372:Y124H	Y	+	1	0	OR2J2	29249761	0.761000	0.28439	0.999000	0.59377	0.226000	0.24999	4.130000	0.57964	1.039000	0.40074	0.172000	0.16884	TAT		0.448	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			
OR5K3	403277	hgsc.bcm.edu	37	3	98110406	98110407	+	Frame_Shift_Ins	INS	-	-	A	rs144759043|rs145803525|rs79045298	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr3:98110406_98110407insA	ENST00000383695.1	+	1	897_898	c.897_898insA	c.(898-900)aaafs	p.K300fs	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						TAAATATTATGAAAAAAATTAT	0.262													AAAAAAA|AAAAAAA|AAAAAAAA|insertion	1648	0.329073	0.208	0.3689	5008	,	,		12958	0.127		0.5964	False		,,,				2504	0.3978																0																																										SO:0001589	frameshift_variant	403277				CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.904dupA	3.37:g.98110413_98110413dupA	ENSP00000373194:p.Lys300fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000383695.1	37	CCDS33803.1																																																																																				0.262	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			
PER1	5187	broad.mit.edu;ucsc.edu	37	17	8052099	8052099	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr17:8052099C>A	ENST00000317276.4	-	8	1148	c.911G>T	c.(910-912)gGt>gTt	p.G304V	PER1_ENST00000578089.1_5'Flank|PER1_ENST00000581082.1_Missense_Mutation_p.G284V|PER1_ENST00000354903.5_Missense_Mutation_p.G288V	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	304					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.G304V(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CCGGTCAGGACCTCCTCTAGC	0.587			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes																																Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	1	Substitution - Missense(1)	kidney(1)											48.0	47.0	48.0					17																	8052099		2203	4300	6503	SO:0001583	missense	5187			AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.911G>T	17.37:g.8052099C>A	ENSP00000314420:p.Gly304Val	Somatic		WXS	Illumina GAIIx	Phase_I	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603006	0.87157	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.41065	2.38;1.01	5.28	5.28	0.74379	.	0.051936	0.85682	D	0.000000	T	0.60130	0.2245	M	0.77616	2.38	0.80722	D	1	P;D	0.65815	0.768;0.995	B;P	0.55112	0.282;0.769	T	0.66304	-0.5957	10	0.87932	D	0	-12.0585	16.405	0.83656	0.0:1.0:0.0:0.0	.	288;304	B4DI49;O15534	.;PER1_HUMAN	V	304;288	ENSP00000314420:G304V;ENSP00000346979:G288V	ENSP00000314420:G304V	G	-	2	0	PER1	7992824	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.016000	0.64041	2.483000	0.83821	0.563000	0.77884	GGT		0.587	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			
POMT1	10585	broad.mit.edu;ucsc.edu	37	9	134379711	134379711	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr9:134379711T>C	ENST00000372228.3	+	2	285	c.106T>C	c.(106-108)Tac>Cac	p.Y36H	POMT1_ENST00000541219.1_Intron|POMT1_ENST00000354713.4_Missense_Mutation_p.Y36H|POMT1_ENST00000341012.7_Intron|POMT1_ENST00000402686.3_Missense_Mutation_p.Y36H|POMT1_ENST00000419118.2_Intron|POMT1_ENST00000423007.1_Missense_Mutation_p.Y36H|POMT1_ENST00000404875.2_Intron	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	36					carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)	p.Y36H(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GCGACTCACCTACCCGCGGGC	0.537											OREG0019563	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											121.0	103.0	109.0					9																	134379711		2203	4300	6503	SO:0001583	missense	10585			AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.106T>C	9.37:g.134379711T>C	ENSP00000361302:p.Tyr36His	Somatic	1610	WXS	Illumina GAIIx	Phase_I	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Missense_Mutation	SNP	ENST00000372228.3	37	CCDS6943.1	.	.	.	.	.	.	.	.	.	.	T	8.975	0.974019	0.18736	.	.	ENSG00000130714	ENST00000423007;ENST00000372228;ENST00000402686;ENST00000354713;ENST00000418774	D;D;D;D;D	0.86030	-2.01;-2.01;-2.01;-2.06;-2.01	5.02	3.88	0.44766	Glycosyl transferase, family 39 (1);	0.213252	0.41500	D	0.000871	D	0.86243	0.5886	L	0.39898	1.24	0.80722	D	1	B;D;D;B	0.89917	0.206;1.0;1.0;0.016	B;D;D;B	0.76575	0.043;0.987;0.988;0.049	T	0.81154	-0.1062	10	0.15499	T	0.54	-27.9908	9.8283	0.40925	0.0:0.0809:0.0:0.9191	.	36;36;36;36	B4DTW4;B4DWD8;Q9Y6A1;Q9Y6A1-2	.;.;POMT1_HUMAN;.	H	36	ENSP00000404119:Y36H;ENSP00000361302:Y36H;ENSP00000385797:Y36H;ENSP00000346748:Y36H;ENSP00000390737:Y36H	ENSP00000346748:Y36H	Y	+	1	0	POMT1	133369532	1.000000	0.71417	0.947000	0.38551	0.177000	0.22998	5.015000	0.64035	0.762000	0.33152	-0.250000	0.11733	TAC		0.537	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1		NM_007171	
PRB4	5545	broad.mit.edu;hgsc.bcm.edu	37	12	11461568	11461568	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr12:11461568G>T	ENST00000535904.1	-	3	382	c.349C>A	c.(349-351)Cca>Aca	p.P117T	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.P117T			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	138	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).			extracellular region (GO:0005576)		p.P117T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGCTTTCCTGGAGGAGGTGGG	0.597										HNSCC(22;0.051)																																							1	Substitution - Missense(1)	kidney(1)											145.0	161.0	155.0					12																	11461568		2203	4300	6503	SO:0001583	missense	5545				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.349C>A	12.37:g.11461568G>T	ENSP00000442834:p.Pro117Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A1L439|O00600|P02813|P10161|P10162|P81489	Missense_Mutation	SNP	ENST00000535904.1	37	CCDS8641.1	.	.	.	.	.	.	.	.	.	.	.	3.507	-0.100609	0.06967	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.06068	3.35;3.35	0.796	-0.246	0.13022	.	.	.	.	.	T	0.10121	0.0248	M	0.75777	2.31	0.09310	N	1	D	0.61080	0.989	P	0.47744	0.556	T	0.17623	-1.0363	9	0.46703	T	0.11	.	3.3145	0.07029	0.3284:0.0:0.6716:0.0	.	117	E9PAL0	.	T	117	ENSP00000279575:P117T;ENSP00000442834:P117T	ENSP00000279575:P117T	P	-	1	0	PRB4	11352835	0.000000	0.05858	0.004000	0.12327	0.033000	0.12548	-0.380000	0.07427	-0.128000	0.11641	0.197000	0.17608	CCA		0.597	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1		NM_002723	
PRRG2	5639	hgsc.bcm.edu	37	19	50093217	50093218	+	In_Frame_Ins	INS	-	-	CCACCC			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:50093217_50093218insCCACCC	ENST00000246794.5	+	6	667_668	c.498_499insCCACCC	c.(499-501)cca>CCACCCcca	p.167_167P>PPP	PRRG2_ENST00000596700.1_3'UTR|PRR12_ENST00000418929.2_5'Flank	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	167	Poly-Pro.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		cgcccctgcctccacccccacc	0.658																																																	0																																										SO:0001652	inframe_insertion	5639				CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.511_516dupCCACCC	19.37:g.50093218_50093223dupCCACCC	ENSP00000246794:p.ProPro173dup	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IBF8	In_Frame_Ins	INS	ENST00000246794.5	37	CCDS12773.1																																																																																				0.658	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1		NM_000951	
RBM8A	9939	broad.mit.edu;hgsc.bcm.edu	37	1	145509177	145509177	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:145509177G>T	ENST00000330165.8	+	6	560	c.491G>T	c.(490-492)aGa>aTa	p.R164I	RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RBM8A_ENST00000369307.3_Missense_Mutation_p.R163I|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	164					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R164I(1)		kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGTGGCCGAAGACGCAGCAGA	0.498																																																	1	Substitution - Missense(1)	kidney(1)											78.0	76.0	77.0					1																	145509177		2203	4300	6503	SO:0001583	missense	9939			AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"""RNA binding motif (RRM) containing"""	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.491G>T	1.37:g.145509177G>T	ENSP00000333001:p.Arg164Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	Missense_Mutation	SNP	ENST00000330165.8	37	CCDS916.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793381	0.70452	.	.	ENSG00000131795	ENST00000330165;ENST00000369307	T;T	0.75704	-0.96;-0.96	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.74405	0.3712	L	0.36672	1.1	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.78314	0.991;0.979	T	0.75453	-0.3312	10	0.44086	T	0.13	-8.353	14.5313	0.67929	0.0:0.0:1.0:0.0	.	163;164	Q9Y5S9-2;Q9Y5S9	.;RBM8A_HUMAN	I	164;163	ENSP00000333001:R164I;ENSP00000358313:R163I	ENSP00000333001:R164I	R	+	2	0	RBM8A	144220534	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.658000	0.74407	2.279000	0.76181	0.561000	0.74099	AGA		0.498	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2		NM_005105	
RBM34	23029	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	235295228	235295228	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:235295228T>G	ENST00000408888.3	-	11	1323	c.1093A>C	c.(1093-1095)Aaa>Caa	p.K365Q	RBM34_ENST00000495224.1_5'UTR|TOMM20_ENST00000366607.4_5'Flank|RBM34_ENST00000366606.3_Missense_Mutation_p.K360Q			P42696	RBM34_HUMAN	RNA binding motif protein 34	365						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K365Q(1)		central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			AATTTTTCTTTATTAACAGAA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											83.0	76.0	78.0					1																	235295228		1812	4070	5882	SO:0001583	missense	23029				CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"""RNA binding motif (RRM) containing"""	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.1093A>C	1.37:g.235295228T>G	ENSP00000386226:p.Lys365Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	37	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294604	0.40594	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000447801	T;T;T	0.76186	-1.0;-1.0;-1.0	5.64	4.47	0.54385	Nucleotide-binding, alpha-beta plait (1);	0.306169	0.38959	N	0.001505	T	0.69504	0.3118	M	0.77820	2.39	0.50467	D	0.999871	P	0.37061	0.58	B	0.34489	0.184	T	0.70132	-0.4956	10	0.38643	T	0.18	-23.5119	6.9825	0.24711	0.0:0.0758:0.15:0.7743	.	365	P42696	RBM34_HUMAN	Q	365;360;343	ENSP00000386226:K365Q;ENSP00000355565:K360Q;ENSP00000400000:K343Q	ENSP00000355565:K360Q	K	-	1	0	RBM34	233361851	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	2.819000	0.48049	2.149000	0.67028	0.460000	0.39030	AAA		0.338	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1		NM_015014	
ROCK2	9475	broad.mit.edu;hgsc.bcm.edu;ucsc.edu|broad.mit.edu;ucsc.edu	37	2	11348011	11348012	+	Missense_Mutation	DNP	TC	TC	AT			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr2:11348011_11348012TC>AT	ENST00000315872.6	-	20	2837_2838	c.2389_2390GA>AT	c.(2389-2391)GAg>ATg	p.E797M	ROCK2_ENST00000401753.1_Missense_Mutation_p.E554M	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	797					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.E797K(2)|p.E797V(2)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		AGTTTCTTGCTCTATTTTTAAT	0.307																																																	4	Substitution - Missense(4)	kidney(4)																																								SO:0001583	missense	9475			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.2389_2390delinsAT	2.37:g.11348011_11348012delinsAT	ENSP00000317985:p.Glu797Met	Somatic		WXS	Illumina HiSeq|Illumina GAIIx	Phase_I	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1																																																																																				0.307	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			
SERPINB1	1992	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	2836102	2836102	+	Silent	SNP	C	C	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr6:2836102C>T	ENST00000380739.5	-	6	925	c.723G>A	c.(721-723)acG>acA	p.T241T	SERPINB1_ENST00000537185.1_Silent_p.T90T|SERPINB1_ENST00000476896.1_5'Flank	NM_030666.3	NP_109591.1	P30740	ILEU_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 1	241					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.T241T(1)		breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|ovary(2)	13	Ovarian(93;0.0412)			OV - Ovarian serous cystadenocarcinoma(45;0.0717)		TCTTCAGGCCCGTGGACTCGT	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											92.0	77.0	82.0					6																	2836102		2203	4300	6503	SO:0001819	synonymous_variant	1992			M93056	CCDS4477.1	6p25.2	2014-02-18	2005-08-18		ENSG00000021355	ENSG00000021355		"""Serine (or cysteine) peptidase inhibitors"""	3311	protein-coding gene	gene with protein product		130135	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1"""	ELANH2		1376927, 24172014	Standard	NM_030666		Approved	EI, PI2, anti-elastase	uc003mub.4	P30740	OTTHUMG00000014124	ENST00000380739.5:c.723G>A	6.37:g.2836102C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K5L2|B4DNT0|Q53FB9|Q5W0E1|Q9UDF8	Silent	SNP	ENST00000380739.5	37	CCDS4477.1																																																																																				0.542	SERPINB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039637.1			
SETX	23064	hgsc.bcm.edu;ucsc.edu	37	9	135202188	135202190	+	In_Frame_Del	DEL	AAA	AAA	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	AAA	AAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr9:135202188_135202190delAAA	ENST00000224140.5	-	10	4977_4979	c.4795_4797delTTT	c.(4795-4797)tttdel	p.F1599del	SETX_ENST00000393220.1_In_Frame_Del_p.F1599del|SETX_ENST00000372169.2_In_Frame_Del_p.F1599del	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1599					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TCTTTGAGCTAAAAATCTTAGTG	0.404																																																	0																																										SO:0001651	inframe_deletion	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.4795_4797delTTT	9.37:g.135202188_135202190delAAA	ENSP00000224140:p.Phe1599del	Somatic		WXS	Illumina HiSeq	Phase_I	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	In_Frame_Del	DEL	ENST00000224140.5	37	CCDS6947.1																																																																																				0.404	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3		NM_015046	
SMARCE1	6605	hgsc.bcm.edu;ucsc.edu	37	17	38793756	38793758	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr17:38793756_38793758delCCT	ENST00000348513.6	-	5	1003_1005	c.223_225delAGG	c.(223-225)aggdel	p.R75del	SMARCE1_ENST00000580419.1_In_Frame_Del_p.R40del|SMARCE1_ENST00000431889.2_In_Frame_Del_p.R57del|SMARCE1_ENST00000544009.1_In_Frame_Del_p.R5del|SMARCE1_ENST00000578044.1_In_Frame_Del_p.R5del|SMARCE1_ENST00000377808.4_In_Frame_Del_p.R40del|SMARCE1_ENST00000400122.3_In_Frame_Del_p.R5del|KRT222_ENST00000476049.1_Intron	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	75					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)			large_intestine(1)	1		Breast(137;0.000812)				TTCTGCTGTACCTCATGTAGGGC	0.458																																																	0																																										SO:0001651	inframe_deletion	6605			AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.223_225delAGG	17.37:g.38793756_38793758delCCT	ENSP00000323967:p.Arg75del	Somatic		WXS	Illumina HiSeq	Phase_I	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	In_Frame_Del	DEL	ENST00000348513.6	37	CCDS11370.1																																																																																				0.458	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1		NM_003079	
SUN5	140732	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	31571646	31571646	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr20:31571646G>A	ENST00000356173.3	-	13	1186	c.1094C>T	c.(1093-1095)cCg>cTg	p.P365L	SUN5_ENST00000375523.3_Missense_Mutation_p.P340L	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5	365					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.P365L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						CTCTCTGGGCGGGGCCACAGA	0.557																																																	1	Substitution - Missense(1)	kidney(1)											75.0	85.0	82.0					20																	31571646		2203	4300	6503	SO:0001583	missense	140732			AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"""testis and spermatogenesis related gene 4"""	613942	"""sperm associated antigen 4-like"""	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.1094C>T	20.37:g.31571646G>A	ENSP00000348496:p.Pro365Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJ82|Q5T9R0	Missense_Mutation	SNP	ENST00000356173.3	37	CCDS13209.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.662797	0.29515	.	.	ENSG00000167098	ENST00000356173;ENST00000375523	T;T	0.12465	2.68;2.7	5.16	-4.18	0.03846	.	0.822034	0.11188	N	0.590237	T	0.09905	0.0243	M	0.65498	2.005	0.09310	N	1	B	0.26041	0.14	B	0.12156	0.007	T	0.36212	-0.9757	10	0.37606	T	0.19	-5.0289	0.4493	0.00499	0.339:0.1192:0.2235:0.3184	.	365	Q8TC36	SUN5_HUMAN	L	365;340	ENSP00000348496:P365L;ENSP00000364673:P340L	ENSP00000348496:P365L	P	-	2	0	SUN5	31035307	0.140000	0.22579	0.001000	0.08648	0.005000	0.04900	0.206000	0.17375	-0.274000	0.09232	-0.181000	0.13052	CCG		0.557	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1		NM_080675	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191499	10191499	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr3:10191499delG	ENST00000256474.2	+	3	1332	c.492delG	c.(490-492)cagfs	p.Q164fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Frame_Shift_Del_p.Q123fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	164	Interaction with Elongin BC complex.		Q -> H (in VHLD).|Q -> R (in VHLD; type II). {ECO:0000269|PubMed:8825918, ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.Q164H(3)|p.Q164fs*9(2)|p.V165fs*5(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)		GATGCCTCCAGGTTGTCCGGA	0.507		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	6	Substitution - Missense(3)|Deletion - Frameshift(3)	kidney(4)|adrenal_gland(2)	GRCh37	CM031757|CM074631	VHL	M							92.0	83.0	86.0					3																	10191499		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.492delG	3.37:g.10191499delG	ENSP00000256474:p.Gln164fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.507	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WDR78	79819	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	67358977	67358977	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:67358977T>G	ENST00000371026.3	-	3	520	c.465A>C	c.(463-465)gaA>gaC	p.E155D	WDR78_ENST00000371023.3_Missense_Mutation_p.E155D|WDR78_ENST00000371022.3_Missense_Mutation_p.E155D|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	155					hematopoietic progenitor cell differentiation (GO:0002244)			p.E155D(1)		NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						AAGATATAAATTCTGATCCAA	0.363																																																	1	Substitution - Missense(1)	kidney(1)											174.0	175.0	175.0					1																	67358977		2203	4300	6503	SO:0001583	missense	79819			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.465A>C	1.37:g.67358977T>G	ENSP00000360065:p.Glu155Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.881373	0.00532	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	T;T;T	0.55413	0.52;2.31;1.57	5.29	-10.6	0.00265	.	0.887861	0.10069	N	0.719964	T	0.02571	0.0078	N	0.00197	-1.87	0.26653	N	0.972064	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.11329	0.006;0.0;0.0	T	0.37126	-0.9719	10	0.02654	T	1	-4.8838	11.2791	0.49184	0.2668:0.0:0.5962:0.1369	.	155;155;155	Q5TAD8;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	D	155	ENSP00000360065:E155D;ENSP00000360062:E155D;ENSP00000360061:E155D	ENSP00000360061:E155D	E	-	3	2	WDR78	67131565	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-3.937000	0.00330	-2.116000	0.00830	-1.537000	0.00914	GAA		0.363	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1		NM_024763	
XRN2	22803	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	21321460	21321460	+	Silent	SNP	A	A	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr20:21321460A>T	ENST00000377191.3	+	15	1475	c.1380A>T	c.(1378-1380)gcA>gcT	p.A460A	XRN2_ENST00000430571.2_Silent_p.A384A|XRN2_ENST00000539513.1_Silent_p.A406A	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	460					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A460A(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						CGAGACAAGCAGCCTATGAAA	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											123.0	125.0	125.0					20																	21321460		2203	4300	6503	SO:0001819	synonymous_variant	22803			AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.1380A>T	20.37:g.21321460A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Silent	SNP	ENST00000377191.3	37	CCDS13144.1																																																																																				0.428	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2		NM_012255	
ZHX3	23051	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	39832047	39832047	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr20:39832047C>A	ENST00000309060.3	-	4	1925	c.1510G>T	c.(1510-1512)Gaa>Taa	p.E504*	ZHX3_ENST00000544979.2_Nonsense_Mutation_p.E504*|ZHX3_ENST00000540170.1_Nonsense_Mutation_p.E504*|ZHX3_ENST00000432768.2_Nonsense_Mutation_p.E504*|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000559234.1_Nonsense_Mutation_p.E504*|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000560361.1_Nonsense_Mutation_p.E504*			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	504	Required for nuclear localization.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.E504*(1)		endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				GACAGCTGTTCATGAGATTTC	0.527																																																	1	Substitution - Nonsense(1)	kidney(1)											58.0	59.0	58.0					20																	39832047		2203	4300	6503	SO:0001587	stop_gained	23051			AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.1510G>T	20.37:g.39832047C>A	ENSP00000312222:p.Glu504*	Somatic		WXS	Illumina HiSeq	Phase_I	E1P5W5|F5H820|O43145|Q6NUJ7	Nonsense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.429290|8.429290	0.98808|0.98808	.|.	.|.	ENSG00000174306|ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262|ENST00000421422	.|.	.|.	.|.	5.93|5.93	3.92|3.92	0.45320|0.45320	.|.	0.206543|.	0.49305|.	D|.	0.000147|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.66056|.	D|.	0.02|.	-14.0299|-14.0299	11.4112|11.4112	0.49927|0.49927	0.1333:0.6098:0.2569:0.0|0.1333:0.6098:0.2569:0.0	.|.	.|.	.|.	.|.	X|L	504;504;504;504;282|212	.|.	ENSP00000312222:E504X|.	E|X	-|-	1|2	0|2	ZHX3|ZHX3	39265461|39265461	1.000000|1.000000	0.71417|0.71417	0.571000|0.571000	0.28486|0.28486	0.968000|0.968000	0.65278|0.65278	4.880000|4.880000	0.63107|0.63107	0.777000|0.777000	0.33496|0.33496	0.561000|0.561000	0.74099|0.74099	GAA|TGA		0.527	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3		NM_015035	
ZSCAN18	65982	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	58597544	58597544	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:58597544G>T	ENST00000240727.6	-	6	1234	c.835C>A	c.(835-837)Cca>Aca	p.P279T	ZSCAN18_ENST00000600404.1_Missense_Mutation_p.P335T|ZSCAN18_ENST00000601144.1_Missense_Mutation_p.P279T|ZSCAN18_ENST00000421612.2_Missense_Mutation_p.P144T	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	279					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P335T(1)|p.P279T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		ACCTCACCTGGGAGGCTGCTT	0.597																																																	2	Substitution - Missense(2)	kidney(2)											88.0	67.0	74.0					19																	58597544		2203	4300	6503	SO:0001583	missense	65982			AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"""-"", ""Zinc fingers, C2H2-type"""	21037	protein-coding gene	gene with protein product			"""zinc finger protein 447"""	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.835C>A	19.37:g.58597544G>T	ENSP00000240727:p.Pro279Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	37	CCDS12971.1	.	.	.	.	.	.	.	.	.	.	G	9.690	1.151653	0.21371	.	.	ENSG00000121413	ENST00000433686;ENST00000240727;ENST00000421612	T;T	0.03663	4.38;3.85	3.3	-1.54	0.08584	.	0.971866	0.08370	N	0.956326	T	0.02012	0.0063	N	0.19112	0.55	0.09310	N	1	P;P;P;P	0.39809	0.51;0.689;0.642;0.51	B;B;B;B	0.31547	0.045;0.132;0.098;0.045	T	0.48468	-0.9033	10	0.14656	T	0.56	.	7.1276	0.25482	0.6912:0.0:0.3088:0.0	.	335;144;279;279	B4DG23;E9PBI0;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	T	335;279;144	ENSP00000240727:P279T;ENSP00000392653:P144T	ENSP00000240727:P279T	P	-	1	0	ZSCAN18	63289356	0.022000	0.18835	0.087000	0.20705	0.186000	0.23388	-0.175000	0.09825	-0.353000	0.08224	0.561000	0.74099	CCA		0.597	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1		NM_023926	
ALMS1	7840	broad.mit.edu	37	2	73613032	73613037	+	In_Frame_Del	DEL	GGAGGA	GGAGGA	-	rs61156725|rs70965731|rs72319667|rs3074417	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	GGAGGA	GGAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr2:73613032_73613037delGGAGGA	ENST00000264448.6	+	1	147_152	c.36_41delGGAGGA	c.(34-42)ctggaggag>ctg	p.EE27del	ALMS1_ENST00000377715.1_In_Frame_Del_p.EE27del|ALMS1_ENST00000409009.1_In_Frame_Del_p.EE27del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	27	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)|p.E28_A29insE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGGGCGAGCTggaggaggaggaggag	0.694														3836	0.765974	0.9183	0.7176	5008	,	,		6363	0.7024		0.6819	False		,,,				2504	0.7464																2	Insertion - In frame(1)|Deletion - In frame(1)	ovary(1)|breast(1)																																								SO:0001651	inframe_deletion	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.36_41delGGAGGA	2.37:g.73613038_73613043delGGAGGA	ENSP00000264448:p.Glu27_Glu28del	Somatic		WXS	Illumina GAIIx	Phase_I	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																				0.694	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1		NM_015120	
ATP5EP2	432369	broad.mit.edu	37	13	28519646	28519646	+	3'UTR	DEL	A	A	-	rs555129296		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr13:28519646delA	ENST00000381026.3	+	0	304							Q5VTU8	AT5EL_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2						ATP synthesis coupled proton transport (GO:0015986)	mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			ovary(1)	1						ATTTCATGGGAAAAAAAAATC	0.333																																																	0																																										SO:0001624	3_prime_UTR_variant	432369			EC567419		13q12	2008-10-21			ENSG00000180389	ENSG00000180389			34026	pseudogene	pseudogene							Standard	NR_002162		Approved		uc001uru.3	Q5VTU8	OTTHUMG00000016642	ENST00000381026.3:c.*94A>-	13.37:g.28519646delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000381026.3	37																																																																																					0.333	ATP5EP2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000044314.1		NR_002162	
BRCC3	79184	broad.mit.edu	37	X	154344345	154344345	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chrX:154344345G>A	ENST00000369462.1	+	9	662	c.637G>A	c.(637-639)Gaa>Aaa	p.E213K	BRCC3_ENST00000369459.2_Intron|BRCC3_ENST00000330045.7_Missense_Mutation_p.E188K|BRCC3_ENST00000340647.4_Missense_Mutation_p.E189K|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000399042.1_Missense_Mutation_p.E213K	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	213					double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.E213K(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TGAGAGAATCGAAATCCCAAT	0.438																																																	1	Substitution - Missense(1)	kidney(1)											90.0	76.0	80.0					X																	154344345		1937	4124	6061	SO:0001583	missense	79184			X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"""Lys-63-specific deubiquitinase"""	300617	"""chromosome X open reading frame 53"""	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.637G>A	X.37:g.154344345G>A	ENSP00000358474:p.Glu213Lys	Somatic		WXS	Illumina GAIIx	Phase_I	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Missense_Mutation	SNP	ENST00000369462.1	37	CCDS56611.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932228	0.73442	.	.	ENSG00000185515	ENST00000340647;ENST00000330045;ENST00000369462;ENST00000411985;ENST00000399042	T;T;T;T;T	0.58210	0.61;0.64;0.36;0.75;0.35	4.68	4.68	0.58851	.	0.048580	0.85682	D	0.000000	T	0.55114	0.1900	M	0.78456	2.415	0.80722	D	1	B;B	0.26902	0.104;0.163	B;B	0.20384	0.029;0.013	T	0.59958	-0.7356	10	0.54805	T	0.06	-10.84	15.9187	0.79542	0.0:0.0:1.0:0.0	.	188;213	P46736-2;P46736	.;BRCC3_HUMAN	K	189;188;213;189;213	ENSP00000344103:E189K;ENSP00000328641:E188K;ENSP00000358474:E213K;ENSP00000413170:E189K;ENSP00000381998:E213K	ENSP00000328641:E188K	E	+	1	0	BRCC3	153997539	1.000000	0.71417	0.984000	0.44739	0.995000	0.86356	9.361000	0.97122	2.255000	0.74692	0.594000	0.82650	GAA		0.438	BRCC3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058788.4		NM_024332	
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	lincRNA	SNP	C	C	T	rs367060	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTCAGCCTTCCGCCGGGCCAG	0.672													.|||	253	0.0505192	0.115	0.0533	5008	,	,		65734	0.0119		0.0437	False		,,,				2504	0.0082																0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946434C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
CROCCP2	84809	broad.mit.edu	37	1	16946438	16946438	+	lincRNA	SNP	G	G	A	rs28392876	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr1:16946438G>A	ENST00000412962.1	-	0	1081				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GCCTTCCGCCGGGCCAGCAGC	0.672																																																	0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946438G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
Unknown	0	broad.mit.edu	37	13	19411895	19411895	+	IGR	SNP	A	A	G	rs7334605	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr13:19411895A>G								LINC00418 (118026 upstream) : RP11-38M15.11 (22071 downstream)																							cagagatcccaccactgcact	0.507													.|||	1572	0.313898	0.4856	0.2622	5008	,	,		14522	0.2282		0.2266	False		,,,				2504	0.2965																0																																										SO:0001628	intergenic_variant	0																															13.37:g.19411895A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.507									
S1PR4	8698	broad.mit.edu	37	19	3179916	3179916	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr19:3179916T>C	ENST00000246115.3	+	1	1181	c.1126T>C	c.(1126-1128)Tcc>Ccc	p.S376P		NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	376					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.S376P(2)		breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						GGAGCCCCTGTCCAGCATCTC	0.652																																					GBM(82;318 1638 33279 49708)												2	Substitution - Missense(2)	kidney(2)											50.0	59.0	56.0					19																	3179916		2144	4192	6336	SO:0001583	missense	8698			AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3170	protein-coding gene	gene with protein product		603751	"""endothelial differentiation, G-protein-coupled receptor 6"", ""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"""	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.1126T>C	19.37:g.3179916T>C	ENSP00000246115:p.Ser376Pro	Somatic		WXS	Illumina GAIIx	Phase_I	D6W612	Missense_Mutation	SNP	ENST00000246115.3	37	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.537162	0.45176	.	.	ENSG00000125910	ENST00000246115	D	0.82526	-1.62	3.94	0.423	0.16463	.	0.833523	0.10513	N	0.665950	T	0.71400	0.3335	N	0.24115	0.695	0.37565	D	0.919227	B	0.02656	0.0	B	0.04013	0.001	T	0.59963	-0.7355	10	0.62326	D	0.03	.	9.411	0.38491	0.6353:0.0:0.0:0.3647	.	376	O95977	S1PR4_HUMAN	P	376	ENSP00000246115:S376P	ENSP00000246115:S376P	S	+	1	0	S1PR4	3130916	0.999000	0.42202	0.997000	0.53966	0.971000	0.66376	0.607000	0.24209	-0.218000	0.10018	0.459000	0.35465	TCC		0.652	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1		NM_003775	
CAPN15	6650	broad.mit.edu	37	16	603028	603063	+	Splice_Site	DEL	CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	-	rs370987722|rs373525992|rs560177562	byFrequency	TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr16:603028_603063delCCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	ENST00000219611.2	+	13	3433_3446	c.3070_3083delCCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC	c.(3070-3084)ccacccctgcacagg>g	p.PPLHR1024del	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	1024					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1028W(1)|p.?(1)									GGATAGCGTGCCACCCCTGCACAGGTGcgcccccgcccctgcccccccacccctgc	0.708																																																	2	Substitution - Missense(1)|Unknown(1)	lung(2)																																								SO:0001630	splice_region_variant	6650			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.3083+1CCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC>-	16.37:g.603028_603063delCCACCCCTGCACAGGTGCGCCCCCGCCCCTGCCCCC		Somatic		WXS	Illumina GAIIx	Phase_I	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Splice_Site	DEL	ENST00000219611.2	37	CCDS10410.1																																																																																				0.708	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1		NM_005632	In_Frame_Del
SMG1P4	100507526	broad.mit.edu	37	16	21902088	21902089	+	RNA	DNP	CA	CA	TG	rs55647608|rs56214519		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr16:21902088_21902089CA>TG	ENST00000540706.1	-	0	0				snoU13_ENST00000459388.1_RNA														p.A694A(7)|p.D695N(3)									GTCTTACTGTCAGCTAAAAGGC	0.376																																																	10	Substitution - coding silent(7)|Substitution - Missense(3)	endometrium(5)|kidney(5)																																										0																														Exception_encountered	16.37:g.21902088_21902089delinsTG		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000540706.1	37																																																																																					0.376	RP11-645C24.2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000402428.1			
MIR4477B	100616194	broad.mit.edu	37	9	68414338	68414338	+	RNA	SNP	G	G	T	rs62545747		TCGA-B0-5691-01A-11D-1534-10	TCGA-B0-5691-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ac2e1d29-e239-4dab-9d81-77c8d45970eb	732d3bc7-b0c9-4999-9e3a-3f831f437d85	g.chr9:68414338G>T	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		gcttagtgaagatgtagaatt	0.413																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68414338G>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581659.1	37																																																																																					0.413	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
