#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
AKAP3	10566	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	4747326	4747326	+	Nonsense_Mutation	SNP	C	C	A	rs570803135		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr12:4747326C>A	ENST00000545990.2	-	4	561	c.37G>T	c.(37-39)Gga>Tga	p.G13*	AKAP3_ENST00000228850.1_Nonsense_Mutation_p.G13*|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	13					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)	p.G13*(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TTGCATACTCCATTTTGGCTT	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		18372	0.0		0.0	False		,,,				2504	0.001																2	Substitution - Nonsense(2)	kidney(2)											240.0	238.0	239.0					12																	4747326		2203	4300	6503	SO:0001587	stop_gained	10566			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.37G>T	12.37:g.4747326C>A	ENSP00000440994:p.Gly13*	Somatic		WXS	Illumina HiSeq	Phase_I	O75945|Q86X01|Q9UM61	Nonsense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063108	0.93898	.	.	ENSG00000111254	ENST00000228850;ENST00000545990;ENST00000540967;ENST00000536414	.	.	.	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.959	16.4468	0.83936	0.0:1.0:0.0:0.0	.	.	.	.	X	13	.	ENSP00000228850:G13X	G	-	1	0	AKAP3	4617587	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	3.839000	0.55835	2.868000	0.98415	0.557000	0.71058	GGA		0.408	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2		NM_006422	
ASXL3	80816	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	31320355	31320355	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr18:31320355C>A	ENST00000269197.5	+	11	2987	c.2987C>A	c.(2986-2988)cCa>cAa	p.P996Q		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	996					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P703Q(1)|p.P996Q(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TCTAGCAGCCCACCTGAGAAA	0.443																																																	2	Substitution - Missense(2)	kidney(2)											33.0	33.0	33.0					18																	31320355		1852	4088	5940	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2987C>A	18.37:g.31320355C>A	ENSP00000269197:p.Pro996Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	7.562	0.664996	0.14710	.	.	ENSG00000141431	ENST00000269197	T	0.56103	0.48	5.93	5.05	0.67936	.	0.181679	0.38326	N	0.001728	T	0.30916	0.0780	N	0.03608	-0.345	0.21822	N	0.999522	B	0.13594	0.008	B	0.06405	0.002	T	0.23190	-1.0195	10	0.46703	T	0.11	.	14.0051	0.64459	0.2903:0.7097:0.0:0.0	.	996	Q9C0F0	ASXL3_HUMAN	Q	996	ENSP00000269197:P996Q	ENSP00000269197:P996Q	P	+	2	0	ASXL3	29574353	0.784000	0.28713	0.922000	0.36590	0.404000	0.30871	1.837000	0.39201	1.470000	0.48102	0.655000	0.94253	CCA		0.443	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			
C11orf63	79864	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	122817268	122817268	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr11:122817268A>T	ENST00000531316.1	+	5	1789	c.1697A>T	c.(1696-1698)cAg>cTg	p.Q566L	C11orf63_ENST00000227349.2_Missense_Mutation_p.Q566L			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	566					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.Q566L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		TGGCTCACCCAGATAATGGAG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											70.0	68.0	68.0					11																	122817268		2202	4299	6501	SO:0001583	missense	79864			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.1697A>T	11.37:g.122817268A>T	ENSP00000431669:p.Gln566Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6G0|Q96GB5|Q9H5D6	Missense_Mutation	SNP	ENST00000531316.1	37	CCDS8438.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.817648	0.32145	.	.	ENSG00000109944	ENST00000227349;ENST00000531316	T;T	0.26518	1.73;1.73	5.66	3.34	0.38264	.	0.574985	0.16897	N	0.195045	T	0.36166	0.0957	M	0.72118	2.19	0.09310	N	1	P	0.49090	0.919	P	0.51229	0.663	T	0.12578	-1.0542	10	0.39692	T	0.17	-1.9717	8.5272	0.33313	0.8467:0.0:0.1533:0.0	.	566	Q6NUN7	CK063_HUMAN	L	566	ENSP00000227349:Q566L;ENSP00000431669:Q566L	ENSP00000227349:Q566L	Q	+	2	0	C11orf63	122322478	0.066000	0.20996	0.140000	0.22221	0.396000	0.30629	1.662000	0.37418	0.427000	0.26145	0.533000	0.62120	CAG		0.468	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1		NM_024806	
CAPN11	11131	hgsc.bcm.edu	37	6	44140054	44140055	+	Frame_Shift_Ins	INS	-	-	GGCTGCC	rs397947482|rs57288791|rs111320370	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:44140054_44140055insGGCTGCC	ENST00000398776.1	+	5	463_464	c.425_426insGGCTGCC	c.(424-429)ctggctfs	p.-143fs	CAPN11_ENST00000542245.1_Frame_Shift_Ins_p.-143fs	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGCTGGCTGCTGGCTGCCATCG	0.584											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		330	0.0658946	0.1256	0.0519	5008	,	,		15212	0.0		0.0736	False		,,,				2504	0.0552																0										348,3260		52,244,1508						4.1	1.0		dbSNP_134	14	387,7195		36,315,3440	yes	frameshift	CAPN11	NM_007058.3		88,559,4948	A1A1,A1R,RR		5.1042,9.6452,6.5684				735,10455				SO:0001589	frameshift_variant	11131			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.426_432dupGGCTGCC	6.37:g.44140055_44140061dupGGCTGCC	ENSP00000381758:p.Ala143fs	Somatic	921	WXS	Illumina HiSeq	Phase_I	B2RA64|Q5T3G1|Q8N4R5	Frame_Shift_Ins	INS	ENST00000398776.1	37	CCDS47436.1																																																																																				0.584	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			
CCDC155	147872	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	49912528	49912528	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr19:49912528G>C	ENST00000447857.3	+	14	1339	c.1134G>C	c.(1132-1134)gaG>gaC	p.E378D		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	378						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.E378D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGGAGATCGAGGCCATTCGAC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											46.0	50.0	48.0					19																	49912528		2003	4168	6171	SO:0001583	missense	147872				CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1134G>C	19.37:g.49912528G>C	ENSP00000404220:p.Glu378Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	37	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.374342	0.42105	.	.	ENSG00000161609	ENST00000447857	T	0.34275	1.37	5.38	-0.205	0.13196	.	1.260350	0.05317	N	0.525946	T	0.33498	0.0865	M	0.62723	1.935	0.09310	N	0.999997	B;B	0.33238	0.403;0.403	B;B	0.25291	0.059;0.059	T	0.30475	-0.9977	10	0.48119	T	0.1	-16.6983	8.2631	0.31797	0.3872:0.0:0.6128:0.0	.	378;378	C9JGW3;Q8N6L0	.;CC155_HUMAN	D	378	ENSP00000404220:E378D	ENSP00000404220:E378D	E	+	3	2	CCDC155	54604340	0.972000	0.33761	0.050000	0.19076	0.816000	0.46133	0.764000	0.26532	-0.086000	0.12550	0.585000	0.79938	GAG		0.602	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2		NM_144688	
CENPE	1062	broad.mit.edu;ucsc.edu	37	4	104097155	104097155	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr4:104097155C>A	ENST00000265148.3	-	15	1530	c.1441G>T	c.(1441-1443)Gag>Tag	p.E481*	CENPE_ENST00000380026.3_Nonsense_Mutation_p.E481*	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	481					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.E481*(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CATTCTATCTCACTTAATGTA	0.279																																																	1	Substitution - Nonsense(1)	kidney(1)											109.0	111.0	110.0					4																	104097155		2203	4296	6499	SO:0001587	stop_gained	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.1441G>T	4.37:g.104097155C>A	ENSP00000265148:p.Glu481*	Somatic		WXS	Illumina GAIIx	Phase_I	A6NKY9|A8K2U7|Q4LE75	Nonsense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	37	6.000265	0.97189	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	15.295	0.73898	0.0:1.0:0.0:0.0	.	.	.	.	X	481	.	ENSP00000265148:E481X	E	-	1	0	CENPE	104316604	0.673000	0.27539	0.148000	0.22405	0.665000	0.39181	3.413000	0.52686	2.679000	0.91253	0.557000	0.71058	GAG		0.279	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
COCH	1690	hgsc.bcm.edu	37	14	31358882	31358883	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr14:31358882_31358883insT	ENST00000396618.3	+	12	1594_1595	c.1538_1539insT	c.(1537-1542)gcttctfs	p.S514fs	COCH_ENST00000382493.4_Frame_Shift_Ins_p.S365fs|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000460581.2_Frame_Shift_Ins_p.S402fs|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000475087.1_Intron|RP11-829H16.3_ENST00000468444.2_RNA|COCH_ENST00000216361.4_Frame_Shift_Ins_p.S514fs	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	514	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		AAAGATATGGCTTCTAAACCGA	0.396																																																	0																																										SO:0001589	frameshift_variant	1690				CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"""coagulation factor C (Limulus polyphemus homolog); cochlin"", ""coagulation factor C homolog, cochlin (Limulus polyphemus)"""	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.1540dupT	14.37:g.31358884_31358884dupT	ENSP00000379862:p.Ser514fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9K9|D3DS84|Q96IU6	Frame_Shift_Ins	INS	ENST00000396618.3	37	CCDS9640.1																																																																																				0.396	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1		NM_004086	
CYP8B1	1582	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	42916230	42916230	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:42916230A>G	ENST00000316161.4	-	1	1403	c.1079T>C	c.(1078-1080)gTt>gCt	p.V360A	RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Missense_Mutation_p.V360A|KRBOX1_ENST00000426937.1_Intron	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	360					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)	p.V360A(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		GTCTTCATGAACCAACCTGAG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											65.0	63.0	64.0					3																	42916230		2203	4300	6503	SO:0001583	missense	1582			AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1079T>C	3.37:g.42916230A>G	ENSP00000318867:p.Val360Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.859163	0.32884	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.01165	5.24;5.24	5.05	3.89	0.44902	.	0.081290	0.48767	N	0.000164	T	0.02610	0.0079	L	0.28054	0.825	0.49130	D	0.999753	D;D	0.71674	0.998;0.993	D;D	0.67382	0.951;0.951	T	0.64630	-0.6362	10	0.48119	T	0.1	-10.4425	9.9161	0.41434	0.9169:0.0:0.0831:0.0	.	360;360	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	A	360	ENSP00000404499:V360A;ENSP00000318867:V360A	ENSP00000318867:V360A	V	-	2	0	CYP8B1	42891234	1.000000	0.71417	0.003000	0.11579	0.001000	0.01503	9.224000	0.95209	0.756000	0.33013	-0.441000	0.05720	GTT		0.572	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1		NM_004391	
DNAH2	146754	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7667223	7667223	+	Missense_Mutation	SNP	C	C	T	rs559459258		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr17:7667223C>T	ENST00000572933.1	+	19	4513	c.3053C>T	c.(3052-3054)tCg>tTg	p.S1018L	DNAH2_ENST00000389173.2_Missense_Mutation_p.S1018L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1018	Stem. {ECO:0000250}.				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.S1018L(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGGACTGTTCGCACCTCAAG	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		20782	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	kidney(1)											118.0	102.0	108.0					17																	7667223		2203	4300	6503	SO:0001583	missense	146754			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3053C>T	17.37:g.7667223C>T	ENSP00000458355:p.Ser1018Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402290	0.62288	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.46819	0.86	4.57	4.57	0.56435	.	0.327444	0.25283	N	0.031781	T	0.45337	0.1337	M	0.75447	2.3	0.80722	D	1	P	0.36974	0.576	B	0.31869	0.137	T	0.49153	-0.8969	10	0.38643	T	0.18	.	12.1091	0.53830	0.0:0.8261:0.1739:0.0	.	1018	Q9P225	DYH2_HUMAN	L	1018	ENSP00000373825:S1018L	ENSP00000353818:S1018L	S	+	2	0	DNAH2	7607948	0.999000	0.42202	0.947000	0.38551	0.985000	0.73830	5.115000	0.64655	2.075000	0.62263	0.555000	0.69702	TCG		0.562	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1		NM_020877	
DYRK3	8444	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	206822222	206822222	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:206822222G>T	ENST00000367109.2	+	3	1847	c.1679G>T	c.(1678-1680)gGa>gTa	p.G560V	DYRK3_ENST00000367106.1_Missense_Mutation_p.G540V|DYRK3_ENST00000367108.3_Missense_Mutation_p.G540V|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	560					erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.G560V(1)|p.G525V(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CCAGTTGTTGGAATAGCCAAT	0.448																																					Melanoma(164;427 2622 26826 51707)												2	Substitution - Missense(2)	kidney(2)											91.0	83.0	86.0					1																	206822222		2203	4300	6503	SO:0001583	missense	8444			Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"""regulatory erythroid kinase"", ""dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5"", ""protein kinase Dyrk3"""	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1679G>T	1.37:g.206822222G>T	ENSP00000356076:p.Gly560Val	Somatic		WXS	Illumina HiSeq	Phase_I	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	37	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481840	0.44147	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000367106	T;T;T	0.71222	-0.55;-0.45;-0.45	5.44	5.44	0.79542	.	0.047684	0.85682	D	0.000000	T	0.70430	0.3223	L	0.58101	1.795	0.80722	D	1	B;B	0.29085	0.232;0.045	B;B	0.34590	0.186;0.142	T	0.68746	-0.5327	10	0.46703	T	0.11	.	15.6041	0.76649	0.0:0.1375:0.8624:0.0	.	560;540	O43781;O43781-2	DYRK3_HUMAN;.	V	560;540;540	ENSP00000356076:G560V;ENSP00000356075:G540V;ENSP00000356073:G540V	ENSP00000356073:G540V	G	+	2	0	DYRK3	204888845	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.346000	0.79347	2.834000	0.97654	0.650000	0.86243	GGA		0.448	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1		NM_003582	
E2F7	144455	broad.mit.edu;ucsc.edu	37	12	77424037	77424037	+	Silent	SNP	G	G	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr12:77424037G>T	ENST00000322886.7	-	10	1693	c.1458C>A	c.(1456-1458)ctC>ctA	p.L486L	E2F7_ENST00000416496.2_Silent_p.L486L	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	486					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.L486L(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GGTCAACAGAGAGGACAGGGA	0.473																																																	2	Substitution - coding silent(2)	kidney(2)											113.0	124.0	121.0					12																	77424037		2203	4300	6503	SO:0001819	synonymous_variant	144455			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.1458C>A	12.37:g.77424037G>T		Somatic		WXS	Illumina GAIIx	Phase_I	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																				0.473	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1		XM_084871	
ELAC1	55520	broad.mit.edu;ucsc.edu	37	18	48510776	48510776	+	Silent	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr18:48510776C>A	ENST00000269466.3	+	3	575	c.468C>A	c.(466-468)atC>atA	p.I156I	ELAC1_ENST00000588577.1_Intron|RP11-729L2.2_ENST00000588256.1_Intron|ELAC1_ENST00000591429.1_Silent_p.I156I|SMAD4_ENST00000452201.2_Intron|RP11-729L2.2_ENST00000590722.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	156					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)	p.I156I(1)		kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GAAGAACTATCCTGTTAGACT	0.398																																																	1	Substitution - coding silent(1)	kidney(1)											80.0	75.0	77.0					18																	48510776		2203	4300	6503	SO:0001819	synonymous_variant	55520			AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"""tRNA Z (short form)"", ""RNaseZ(S)"""	608079	"""elaC (E. coli) homolog 1"", ""elaC homolog 1 (E. coli)"""			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.468C>A	18.37:g.48510776C>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q9NS99	Silent	SNP	ENST00000269466.3	37	CCDS11949.1																																																																																				0.398	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			
ESPN	83715	broad.mit.edu;hgsc.bcm.edu	37	1	6504722	6504722	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:6504722A>G	ENST00000377828.1	+	6	1340	c.1172A>G	c.(1171-1173)aAg>aGg	p.K391R	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	391					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)	p.K391R(1)		NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TCCAGCATCAAGGGCCAGCAC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											81.0	67.0	72.0					1																	6504722		2203	4300	6503	SO:0001583	missense	83715			AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.1172A>G	1.37:g.6504722A>G	ENSP00000367059:p.Lys391Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	a	8.685	0.906166	0.17760	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	D;D	0.88046	-2.33;-2.33	3.6	2.44	0.29823	.	0.186932	0.35235	N	0.003351	T	0.71426	0.3338	N	0.17082	0.46	0.80722	D	1	B	0.19445	0.036	B	0.16289	0.015	T	0.63589	-0.6603	10	0.32370	T	0.25	-20.9527	3.3627	0.07193	0.6337:0.0:0.3663:0.0	.	391	B1AK53	ESPN_HUMAN	R	391;176	ENSP00000367059:K391R;ENSP00000401793:K176R	ENSP00000367059:K391R	K	+	2	0	ESPN	6427309	1.000000	0.71417	0.954000	0.39281	0.117000	0.20001	3.639000	0.54339	1.514000	0.48869	0.398000	0.26397	AAG		0.617	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3		NM_031475	
FBXL4	26235	hgsc.bcm.edu;ucsc.edu	37	6	99365322	99365322	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:99365322delA	ENST00000369244.2	-	5	1214	c.786delT	c.(784-786)cttfs	p.L262fs	FBXL4_ENST00000229971.1_Frame_Shift_Del_p.L262fs	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	262					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		ACTTTTTGTTAAGACTGTCCA	0.393																																																	0													151.0	141.0	145.0					6																	99365322		2203	4299	6502	SO:0001589	frameshift_variant	26235			AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.786delT	6.37:g.99365322delA	ENSP00000358247:p.Leu262fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Frame_Shift_Del	DEL	ENST00000369244.2	37	CCDS5041.1																																																																																				0.393	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			
FBXL4	26235	hgsc.bcm.edu;ucsc.edu	37	6	99365325	99365326	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:99365325_99365326delAC	ENST00000369244.2	-	5	1210_1211	c.782_783delGT	c.(781-783)agtfs	p.S261fs	FBXL4_ENST00000229971.1_Frame_Shift_Del_p.S261fs	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	261					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TTTTGTTAAGACTGTCCATTCC	0.401																																																	0																																										SO:0001589	frameshift_variant	26235			AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.782_783delGT	6.37:g.99365325_99365326delAC	ENSP00000358247:p.Ser261fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Frame_Shift_Del	DEL	ENST00000369244.2	37	CCDS5041.1																																																																																				0.401	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			
GRM4	2914	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	33996013	33996013	+	Missense_Mutation	SNP	C	C	T	rs371727193		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:33996013C>T	ENST00000538487.2	-	10	3016	c.2573G>A	c.(2572-2574)cGc>cAc	p.R858H	GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Missense_Mutation_p.R725H|GRM4_ENST00000544773.2_Missense_Mutation_p.R689H|GRM4_ENST00000455714.2_Missense_Mutation_p.R718H|GRM4_ENST00000374181.4_Missense_Mutation_p.R858H|GRM4_ENST00000374177.3_Missense_Mutation_p.R742H|GRM4_ENST00000609222.1_Missense_Mutation_p.R725H	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	858					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.R858H(2)|p.R742H(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTTGAGGCTGCGCTTGCGCTT	0.602																																																	3	Substitution - Missense(3)	kidney(3)						C	HIS/ARG	0,4406		0,0,2203	110.0	92.0	98.0		2573	4.3	1.0	6		98	1,8599	1.2+/-3.3	0,1,4299	no	missense	GRM4	NM_000841.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	858/913	33996013	1,13005	2203	4300	6503	SO:0001583	missense	2914			U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2573G>A	6.37:g.33996013C>T	ENSP00000440556:p.Arg858His	Somatic		WXS	Illumina HiSeq	Phase_I	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628904	0.87560	0.0	1.16E-4	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.89196	-2.46;-2.48;-2.22;-2.26;-2.28;-2.46;-2.3	4.28	4.28	0.50868	GPCR, family 3, C-terminal (1);	0.230852	0.36555	N	0.002526	D	0.92028	0.7474	M	0.72353	2.195	0.58432	D	0.999999	B;B;D;D;B	0.76494	0.029;0.029;0.999;0.998;0.071	B;B;D;P;B	0.63113	0.009;0.023;0.911;0.818;0.023	D	0.92524	0.6027	10	0.56958	D	0.05	.	16.8937	0.86094	0.0:1.0:0.0:0.0	.	811;689;718;858;725	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	H	858;742;550;725;689;858;718	ENSP00000363296:R858H;ENSP00000363292:R742H;ENSP00000445533:R550H;ENSP00000437925:R725H;ENSP00000437730:R689H;ENSP00000440556:R858H;ENSP00000398456:R718H	ENSP00000363292:R742H	R	-	2	0	GRM4	34103991	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.871000	0.69628	2.218000	0.71995	0.478000	0.44815	CGC		0.602	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376925	168376926	+	lincRNA	INS	-	-	T	rs2516606|rs71305247|rs35001101|rs66632147	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:168376925_168376926insT	ENST00000538528.1	-	0	693_694																											TGCAGTGTGTGGGGAAGGAGGA	0.634													?|-|T|unsure	1595	0.31849	0.2579	0.3199	5008	,	,		19949	0.3998		0.2535	False		,,,				2504	0.3824																0										559,21,2008		29,0,501,4,13,747							0.0		dbSNP_130	23	1115,56,3729		66,2,981,3,48,1350	no	codingComplex	HGC6.3	NM_001129895.2		95,2,1482,7,61,2097	A1A1,A1A2,A1R,A2A2,A2R,RR		23.898,22.4111,23.3841				1674,77,5737						100128124																															6.37:g.168376925_168376926insT		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																					0.634	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376967	168376968	+	lincRNA	INS	-	-	G	rs74216590|rs200262961		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:168376967_168376968insG	ENST00000538528.1	-	0	651_652																											CTGCAGTGTGTTGGGAGGAGGA	0.634																																																	0																																												100128124																															6.37:g.168376967_168376968insG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																					0.634	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376968	168376969	+	lincRNA	INS	-	-	G	rs74216590|rs200262961		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:168376968_168376969insG	ENST00000538528.1	-	0	650_651																											TGCAGTGTGTTGGGAGGAGGAG	0.639																																																	0																																												100128124																															6.37:g.168376971_168376971dupG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																					0.639	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
IMPG2	50939	broad.mit.edu;ucsc.edu	37	3	101038458	101038458	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:101038458C>A	ENST00000193391.7	-	2	491	c.304G>T	c.(304-306)Gca>Tca	p.A102S		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	102					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.A102S(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	ACATGATTTGCCACAGCCTCT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											146.0	142.0	143.0					3																	101038458		2203	4300	6503	SO:0001583	missense	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.304G>T	3.37:g.101038458C>A	ENSP00000193391:p.Ala102Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.748695	0.89753	.	.	ENSG00000081148	ENST00000193391	T	0.75367	-0.93	5.52	5.52	0.82312	.	0.073561	0.56097	D	0.000031	D	0.84379	0.5459	M	0.64170	1.965	0.36187	D	0.849795	D	0.89917	1.0	D	0.68765	0.96	D	0.88276	0.2933	10	0.87932	D	0	-15.039	17.6116	0.88055	0.0:1.0:0.0:0.0	.	102	Q9BZV3	IMPG2_HUMAN	S	102	ENSP00000193391:A102S	ENSP00000193391:A102S	A	-	1	0	IMPG2	102521148	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.565000	0.67365	2.590000	0.87494	0.563000	0.77884	GCA		0.388	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs367746100|rs111905975	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr19:8389893_8389895delTCC	ENST00000593649.1	-	8	2087_2089	c.2022_2024delGGA	c.(2020-2025)gaggac>gac	p.E674del	KANK3_ENST00000330915.3_In_Frame_Del_p.E674del			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	674										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CACAGCCATGTCCTCCTCTTCCT	0.626														770	0.153754	0.2958	0.1383	5008	,	,		19550	0.0655		0.1223	False		,,,				2504	0.0961																0										1092,3172		142,808,1182						3.3	1.0		dbSNP_132	62	1089,7165		100,889,3138	no	coding	KANK3	NM_198471.2		242,1697,4320	A1A1,A1R,RR		13.1936,25.6098,17.4229				2181,10337				SO:0001651	inframe_deletion	256949			AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.2022_2024delGGA	19.37:g.8389896_8389898delTCC	ENSP00000470728:p.Glu674del	Somatic		WXS	Illumina HiSeq	Phase_I	Q6NZI1|Q6ZQR3|Q8IUV2	In_Frame_Del	DEL	ENST00000593649.1	37																																																																																					0.626	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1		NM_198471	
KCNC1	3746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	17793557	17793557	+	Missense_Mutation	SNP	G	G	A	rs369830206		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr11:17793557G>A	ENST00000379472.3	+	2	946	c.916G>A	c.(916-918)Gtg>Atg	p.V306M	KCNC1_ENST00000265969.6_Missense_Mutation_p.V306M	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	306					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.V306M(2)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	AGCCAAGGACGTGCTGGGCTT	0.617																																																	2	Substitution - Missense(2)	kidney(2)											97.0	87.0	90.0					11																	17793557		2200	4293	6493	SO:0001583	missense	3746			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.916G>A	11.37:g.17793557G>A	ENSP00000368785:p.Val306Met	Somatic		WXS	Illumina HiSeq	Phase_I	K4DI87	Missense_Mutation	SNP	ENST00000379472.3	37	CCDS7827.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799698	0.70567	.	.	ENSG00000129159	ENST00000265969;ENST00000379472	D;D	0.98493	-4.96;-4.96	4.95	4.95	0.65309	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98516	0.9505	L	0.55103	1.725	0.80722	D	1	P;D	0.76494	0.901;0.999	P;D	0.76575	0.588;0.988	D	0.99881	1.1113	10	0.62326	D	0.03	.	18.1947	0.89817	0.0:0.0:1.0:0.0	.	306;306	Q3KNS8;P48547	.;KCNC1_HUMAN	M	306	ENSP00000265969:V306M;ENSP00000368785:V306M	ENSP00000265969:V306M	V	+	1	0	KCNC1	17750133	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.869000	0.99810	2.290000	0.77057	0.561000	0.74099	GTG		0.617	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1		NM_004976	
KIAA1107	23285	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	92643949	92643949	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:92643949G>C	ENST00000370378.4	+	7	1306	c.1208G>C	c.(1207-1209)gGa>gCa	p.G403A	KIAA1107_ENST00000409154.4_Missense_Mutation_p.G458A	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	458								p.G403A(1)		breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						ACTAGCAATGGATGTACTGCA	0.368																																																	1	Substitution - Missense(1)	kidney(1)											155.0	144.0	147.0					1																	92643949		692	1591	2283	SO:0001583	missense	23285			AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.1208G>C	1.37:g.92643949G>C	ENSP00000359404:p.Gly403Ala	Somatic		WXS	Illumina HiSeq	Phase_I	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737275	0.30774	.	.	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.05199	3.48;3.48	5.01	5.01	0.66863	.	0.474517	0.21905	N	0.067398	T	0.07683	0.0193	L	0.55481	1.735	0.09310	N	1	D	0.61697	0.99	P	0.59424	0.857	T	0.20505	-1.0273	10	0.32370	T	0.25	.	10.6096	0.45415	0.0:0.1416:0.7124:0.1461	.	403	E9PEZ5	.	A	458;403	ENSP00000386957:G458A;ENSP00000359404:G403A	ENSP00000359404:G403A	G	+	2	0	KIAA1107	92416537	0.938000	0.31826	0.864000	0.33941	0.103000	0.19146	1.916000	0.39986	2.712000	0.92718	0.561000	0.74099	GGA		0.368	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3		XM_034086	
KIAA1429	25962	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	95530150	95530150	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr8:95530150G>A	ENST00000297591.5	-	10	2609	c.2534C>T	c.(2533-2535)tCa>tTa	p.S845L	KIAA1429_ENST00000421249.2_Missense_Mutation_p.S845L|KIAA1429_ENST00000437199.1_Missense_Mutation_p.S845L	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	845					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S845L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ATAAGCTACTGACTTCTTAGA	0.313																																																	1	Substitution - Missense(1)	kidney(1)											91.0	79.0	83.0					8																	95530150		2203	4300	6503	SO:0001583	missense	25962			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2534C>T	8.37:g.95530150G>A	ENSP00000297591:p.Ser845Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	G	32	5.168237	0.94768	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.60920	0.15;0.19;0.18	5.33	5.33	0.75918	.	0.225119	0.39083	N	0.001480	T	0.60077	0.2241	L	0.32530	0.975	0.80722	D	1	P;P	0.50819	0.939;0.939	P;P	0.50934	0.58;0.654	T	0.64313	-0.6437	10	0.72032	D	0.01	-11.8486	19.0493	0.93036	0.0:0.0:1.0:0.0	.	845;845	Q69YN4-4;Q69YN4	.;VIR_HUMAN	L	845	ENSP00000297591:S845L;ENSP00000395600:S845L;ENSP00000398390:S845L	ENSP00000297591:S845L	S	-	2	0	KIAA1429	95599326	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.624000	0.98398	2.490000	0.84030	0.655000	0.94253	TCA		0.313	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2		NM_015496	
LATS2	26524	hgsc.bcm.edu;ucsc.edu	37	13	21557772	21557773	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr13:21557772_21557773insT	ENST00000382592.4	-	5	2477_2478	c.2072_2073insA	c.(2071-2073)cacfs	p.H691fs	LATS2_ENST00000542899.1_Frame_Shift_Ins_p.H691fs	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CGTACAGGGCGTGAGTGTCCAC	0.535																																																	0																																										SO:0001589	frameshift_variant	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2073dupA	13.37:g.21557773_21557773dupT	ENSP00000372035:p.His691fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000382592.4	37	CCDS9294.1																																																																																				0.535	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			
LGI2	55203	hgsc.bcm.edu	37	4	25032135	25032135	+	Missense_Mutation	SNP	C	C	T	rs74901868	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr4:25032135C>T	ENST00000382114.4	-	1	366	c.181G>A	c.(181-183)Ggc>Agc	p.G61S		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	61	LRRNT.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CTGATGTCGCCCGGCACGATC	0.721													C|||	901	0.179912	0.1611	0.2133	5008	,	,		8134	0.2262		0.1879	False		,,,				2504	0.1258																0								C	SER/GLY	692,3688		54,584,1552	16.0	20.0	19.0		181	3.4	1.0	4	dbSNP_131	19	1686,6888		183,1320,2784	yes	missense	LGI2	NM_018176.3	56	237,1904,4336	TT,TC,CC		19.6641,15.7991,18.3573	benign	61/546	25032135	2378,10576	2190	4287	6477	SO:0001583	missense	55203			AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.181G>A	4.37:g.25032135C>T	ENSP00000371548:p.Gly61Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	37	CCDS3431.1	470	0.21520146520146521	83	0.16869918699186992	91	0.2513812154696133	151	0.263986013986014	145	0.19129287598944592	C	10.22	1.290577	0.23564	0.157991	0.196641	ENSG00000153012	ENST00000382114	T	0.61158	0.13	4.23	3.38	0.38709	.	0.300464	0.35677	N	0.003060	T	0.00012	0.0000	N	0.04880	-0.145	0.26571	P	0.9735612	B	0.06786	0.001	B	0.08055	0.003	T	0.13791	-1.0496	9	0.13108	T	0.6	-21.4882	11.5814	0.50894	0.0:0.9076:0.0:0.0924	.	61	Q8N0V4	LGI2_HUMAN	S	61	ENSP00000371548:G61S	ENSP00000371548:G61S	G	-	1	0	LGI2	24641233	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.122000	0.31295	0.880000	0.35969	0.561000	0.74099	GGC		0.721	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			
MAP3K4	4216	hgsc.bcm.edu	37	6	161519378	161519378	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr6:161519378C>T	ENST00000392142.4	+	17	3741	c.3593C>T	c.(3592-3594)gCt>gTt	p.A1198V	MAP3K4_ENST00000366919.2_Intron|MAP3K4_ENST00000366920.2_Missense_Mutation_p.A1194V|MAP3K4_ENST00000348824.7_Intron	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1198	Poly-Ala.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		gctgctgctgctgctgttgct	0.597																																																	0													93.0	92.0	92.0					6																	161519378		2203	4299	6502	SO:0001583	missense	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3593C>T	6.37:g.161519378C>T	ENSP00000375986:p.Ala1198Val	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.360800	0.01245	.	.	ENSG00000085511	ENST00000392142;ENST00000366920	T;T	0.71103	-0.54;-0.53	2.29	2.29	0.28610	.	0.754387	0.11657	N	0.542271	T	0.51227	0.1662	N	0.19112	0.55	0.26345	N	0.977309	B;D	0.57571	0.073;0.98	B;D	0.65443	0.037;0.935	T	0.39354	-0.9618	10	0.10377	T	0.69	-7.006	8.5531	0.33465	0.0:1.0:0.0:0.0	.	1194;1198	F5H538;Q9Y6R4	.;M3K4_HUMAN	V	1198;1194	ENSP00000375986:A1198V;ENSP00000355887:A1194V	ENSP00000355887:A1194V	A	+	2	0	MAP3K4	161439368	0.010000	0.17322	0.105000	0.21289	0.511000	0.34104	0.116000	0.15561	1.726000	0.51525	0.366000	0.22137	GCT		0.597	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			
MMS19	64210	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	99229886	99229886	+	Splice_Site	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr10:99229886C>T	ENST00000438925.2	-	10	1181	c.846G>A	c.(844-846)ctG>ctA	p.L282L	MMS19_ENST00000327277.7_5'UTR|MMS19_ENST00000483626.1_5'UTR|MMS19_ENST00000327238.10_Splice_Site_p.L282L|MMS19_ENST00000370782.2_Splice_Site_p.L282L|MMS19_ENST00000355839.6_Splice_Site_p.L239L	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	282					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)	p.L282L(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AATCACTCACCAGAGTCTGTA	0.463								Direct reversal of damage																																									1	Substitution - coding silent(1)	kidney(1)											86.0	74.0	78.0					10																	99229886		2203	4300	6503	SO:0001630	splice_region_variant	64210			AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.846+1G>A	10.37:g.99229886C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Silent	SNP	ENST00000438925.2	37	CCDS7464.1																																																																																				0.463	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2			Silent
MYCBP2	23077	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	77785318	77785318	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr13:77785318A>G	ENST00000544440.2	-	23	3303	c.3286T>C	c.(3286-3288)Tat>Cat	p.Y1096H	MYCBP2_ENST00000407578.2_Missense_Mutation_p.Y1134H|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.Y1096H					MYC binding protein 2, E3 ubiquitin protein ligase									p.Y1096H(2)|p.Y1134H(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATTACATCATATACAGGATCA	0.323																																																	3	Substitution - Missense(3)	kidney(3)											83.0	77.0	79.0					13																	77785318		2203	4299	6502	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.3286T>C	13.37:g.77785318A>G	ENSP00000444596:p.Tyr1096His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	A	16.27	3.076215	0.55646	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.36340	1.27;1.26;1.27	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000001	T	0.23492	0.0568	N	0.20574	0.59	0.51482	D	0.999928	B	0.06786	0.001	B	0.08055	0.003	T	0.05451	-1.0884	10	0.38643	T	0.18	.	10.076	0.42360	0.9245:0.0:0.0755:0.0	.	1096	O75592	MYCB2_HUMAN	H	1096;1134;1096	ENSP00000349892:Y1096H;ENSP00000384288:Y1134H;ENSP00000444596:Y1096H	ENSP00000349892:Y1096H	Y	-	1	0	MYCBP2	76683319	1.000000	0.71417	0.994000	0.49952	0.960000	0.62799	7.068000	0.76748	2.151000	0.67156	0.383000	0.25322	TAT		0.323	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1		NM_015057	
ODF1	4956	hgsc.bcm.edu	37	8	103573015	103573015	+	Missense_Mutation	SNP	A	A	G	rs568456031|rs62523271|rs386728346	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr8:103573015A>G	ENST00000285402.3	+	2	812	c.656A>G	c.(655-657)aAc>aGc	p.N219S	ODF1_ENST00000518835.1_Missense_Mutation_p.N12S	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	219	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			agcccctgcaacccctgcagc	0.552																																																	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)											61.0	58.0	59.0					8																	103573015		2185	4223	6408	SO:0001583	missense	4956			M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.656A>G	8.37:g.103573015A>G	ENSP00000285402:p.Asn219Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	615	0.2815934065934066	93	0.18902439024390244	136	0.3756906077348066	192	0.3356643356643357	194	0.2559366754617414	A	0.009	-1.843056	0.00568	.	.	ENSG00000155087	ENST00000285402;ENST00000518835	D;T	0.84944	-1.92;1.98	4.92	-4.07	0.03975	.	0.911386	0.09516	N	0.791664	T	0.00012	0.0000	L	0.29908	0.895	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.02625	-1.1132	10	0.02654	T	1	-9.7732	11.9345	0.52866	0.5323:0.0:0.4677:0.0	rs62523271	219	Q14990	ODFP1_HUMAN	S	219;12	ENSP00000285402:N219S;ENSP00000430023:N12S	ENSP00000285402:N219S	N	+	2	0	ODF1	103642191	0.000000	0.05858	0.597000	0.28824	0.024000	0.10985	-2.116000	0.01327	-0.809000	0.04381	-1.969000	0.00466	AAC		0.552	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			
PABPC3	5042	hgsc.bcm.edu	37	13	25671786	25671786	+	Missense_Mutation	SNP	G	G	A	rs113301206	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr13:25671786G>A	ENST00000281589.3	+	1	1487	c.1450G>A	c.(1450-1452)Gtg>Atg	p.V484M		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	484					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AACACAGACAGTGGGTCCACG	0.537													g|||	617	0.123203	0.1876	0.1081	5008	,	,		22365	0.0655		0.0666	False		,,,				2504	0.1646																0													64.0	58.0	60.0					13																	25671786		2203	4300	6503	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1450G>A	13.37:g.25671786G>A	ENSP00000281589:p.Val484Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	4.651	0.121106	0.08881	.	.	ENSG00000151846	ENST00000281589	T	0.26957	1.7	0.875	-0.771	0.11002	.	0.098881	0.40908	N	0.000987	T	0.04363	0.0120	N	0.00197	-1.87	0.23421	N	0.997711	B	0.02656	0.0	B	0.09377	0.004	T	0.38243	-0.9670	10	0.30854	T	0.27	.	4.3022	0.10930	0.7031:0.0:0.2969:0.0	.	484	Q9H361	PABP3_HUMAN	M	484	ENSP00000281589:V484M	ENSP00000281589:V484M	V	+	1	0	PABPC3	24569786	0.402000	0.25311	0.468000	0.27192	0.114000	0.19823	0.521000	0.22893	-0.307000	0.08804	0.313000	0.20887	GTG		0.537	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2		NM_030979	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52610695	52610695	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:52610695G>A	ENST00000296302.7	-	22	3554	c.3553C>T	c.(3553-3555)Cga>Tga	p.R1185*	PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R1153*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R1185*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R1185*|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R1160*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R1200*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R1200*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R1160*			Q86U86	PB1_HUMAN	polybromo 1	1185	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R1185*(3)|p.R1153*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GCTCCATCTCGAACCCATACT	0.338			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	4	Substitution - Nonsense(4)	kidney(4)											76.0	73.0	74.0					3																	52610695		2202	4300	6502	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3553C>T	3.37:g.52610695G>A	ENSP00000296302:p.Arg1185*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	41	8.826239	0.98968	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.1593	15.0475	0.71838	0.0:0.0:0.8573:0.1427	.	.	.	.	X	1153;1160;1185;1185;1185;1160;1200;1200;1184	.	ENSP00000296302:R1185X	R	-	1	2	PBRM1	52585735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.391000	0.66266	2.664000	0.90586	0.591000	0.81541	CGA		0.338	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDH15	65217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	55755498	55755499	+	Missense_Mutation	DNP	TA	TA	CT			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr10:55755498_55755499TA>CT	ENST00000320301.6	-	21	3172_3173	c.2778_2779TA>AG	c.(2776-2781)ttTAgt>ttAGgt	p.926_927FS>LG	PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.933_934FS>LG|PCDH15_ENST00000414778.1_Missense_Mutation_p.931_932FS>LG|PCDH15_ENST00000373965.2_Missense_Mutation_p.933_934FS>LG|PCDH15_ENST00000395430.1_Missense_Mutation_p.926_927FS>LG|PCDH15_ENST00000395433.1_Missense_Mutation_p.904_905FS>LG|PCDH15_ENST00000409834.1_Missense_Mutation_p.537_538FS>LG|PCDH15_ENST00000361849.3_Missense_Mutation_p.926_927FS>LG|PCDH15_ENST00000395438.1_Missense_Mutation_p.926_927FS>LG|PCDH15_ENST00000437009.1_Missense_Mutation_p.855_856FS>LG|PCDH15_ENST00000373955.1_Missense_Mutation_p.926_927FS>LG|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.889_890FS>LG|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	926	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.|Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.F926L(2)|p.S927G(2)|p.F931L(2)|p.S932G(2)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATTCGTTTACTAAAGACAGGAG	0.411										HNSCC(58;0.16)																																							8	Substitution - Missense(8)	kidney(8)																																								SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2778_2779delinsCT	10.37:g.55755498_55755499delinsCT	ENSP00000322604:p.F926_S927delinsLG	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.411	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2		NM_033056	
PEX26	55670	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	18566476	18566476	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr22:18566476G>C	ENST00000329627.7	+	4	851	c.645G>C	c.(643-645)gaG>gaC	p.E215D	PEX26_ENST00000428061.2_Missense_Mutation_p.E215D|PEX26_ENST00000399744.3_Missense_Mutation_p.E215D	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	215					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.E215D(1)		breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GCTCTGAGGAGGCCCAGAAGC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											74.0	70.0	71.0					22																	18566476		2203	4300	6503	SO:0001583	missense	55670			AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"""peroxisome biogenesis factor 26"""			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.645G>C	22.37:g.18566476G>C	ENSP00000331106:p.Glu215Asp	Somatic		WXS	Illumina HiSeq	Phase_I	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.530590	0.64860	.	.	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.95853	-3.83;-3.83;-3.83	5.18	1.59	0.23543	.	0.728570	0.12078	U	0.501528	D	0.94437	0.8210	M	0.68317	2.08	0.09310	N	0.999998	P;P	0.43392	0.787;0.805	B;P	0.45753	0.23;0.492	D	0.87100	0.2178	10	0.37606	T	0.19	-5.23	10.0502	0.42210	0.0:0.2761:0.5816:0.1424	.	215;215	F6UBB5;Q7Z412	.;PEX26_HUMAN	D	215	ENSP00000331106:E215D;ENSP00000382648:E215D;ENSP00000412441:E215D	ENSP00000331106:E215D	E	+	3	2	PEX26	16946476	0.941000	0.31946	0.387000	0.26183	0.607000	0.37147	1.734000	0.38166	0.639000	0.30564	0.555000	0.69702	GAG		0.567	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3		NM_017929	
PIP4K2B	8396	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	36935738	36935738	+	Silent	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr17:36935738C>A	ENST00000269554.3	-	5	1032	c.552G>T	c.(550-552)ctG>ctT	p.L184L	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	184	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)	p.L184L(3)		endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GGTACATGCCCAGGAACTGTG	0.517																																																	3	Substitution - coding silent(3)	lung(2)|kidney(1)											144.0	103.0	117.0					17																	36935738		2203	4300	6503	SO:0001819	synonymous_variant	8396			U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.552G>T	17.37:g.36935738C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																				0.517	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1		NM_003559	
SCUBE1	80274	broad.mit.edu;hgsc.bcm.edu	37	22	43614319	43614319	+	Silent	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr22:43614319C>T	ENST00000360835.4	-	15	1959	c.1833G>A	c.(1831-1833)aaG>aaA	p.K611K		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	611					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.K611K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CCTCCAGCGCCTTGGCTGGCC	0.632																																																	1	Substitution - coding silent(1)	kidney(1)											93.0	93.0	93.0					22																	43614319		2203	4300	6503	SO:0001819	synonymous_variant	80274				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1833G>A	22.37:g.43614319C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																				0.632	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3		NM_173050	
SDR16C5	195814	broad.mit.edu;ucsc.edu	37	8	57214061	57214061	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr8:57214061A>G	ENST00000303749.3	-	7	1545	c.908T>C	c.(907-909)gTt>gCt	p.V303A	SDR16C5_ENST00000522671.1_3'UTR|SDR16C5_ENST00000396721.2_Missense_Mutation_p.V259A	NM_138969.2	NP_620419.2	Q8N3Y7	RDHE2_HUMAN	short chain dehydrogenase/reductase family 16C, member 5	303					detection of light stimulus involved in visual perception (GO:0050908)|keratinocyte proliferation (GO:0043616)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	retinol dehydrogenase activity (GO:0004745)	p.V303A(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)	16						CTTTTGGTCAACAAAGCCATC	0.383																																																	1	Substitution - Missense(1)	kidney(1)											228.0	211.0	217.0					8																	57214061		2203	4300	6503	SO:0001583	missense	195814				CCDS6167.1	8q12.1	2011-09-20			ENSG00000170786	ENSG00000170786	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	30311	protein-coding gene	gene with protein product		608989				12372410	Standard	NM_138969		Approved	RDHE2, RDH-E2	uc003xsy.1	Q8N3Y7	OTTHUMG00000164311	ENST00000303749.3:c.908T>C	8.37:g.57214061A>G	ENSP00000307607:p.Val303Ala	Somatic		WXS	Illumina GAIIx	Phase_I	B4DGK2|Q330K3|Q8TDV9|Q96LX1	Missense_Mutation	SNP	ENST00000303749.3	37	CCDS6167.1	.	.	.	.	.	.	.	.	.	.	A	8.721	0.914268	0.17907	.	.	ENSG00000170786	ENST00000396721;ENST00000303749	T;D	0.81499	-1.26;-1.5	5.63	-8.2	0.01045	.	1.141100	0.06472	N	0.731352	T	0.64594	0.2612	L	0.47016	1.485	0.09310	N	1	B;B	0.21225	0.053;0.0	B;B	0.25405	0.06;0.001	T	0.51052	-0.8754	10	0.19590	T	0.45	.	0.8634	0.01198	0.2193:0.2:0.3662:0.2145	.	259;303	Q8N3Y7-2;Q8N3Y7	.;RDHE2_HUMAN	A	259;303	ENSP00000379947:V259A;ENSP00000307607:V303A	ENSP00000307607:V303A	V	-	2	0	SDR16C5	57376615	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.474000	0.06607	-0.911000	0.03843	-0.408000	0.06270	GTT		0.383	SDR16C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378235.1		NM_138969	
SERPINA4	5267	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	95029883	95029883	+	Silent	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr14:95029883C>T	ENST00000557004.1	+	2	485	c.64C>T	c.(64-66)Ctg>Ttg	p.L22L	SERPINA4_ENST00000555095.1_Silent_p.L22L|SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Silent_p.L22L			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	22					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L22L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		TCATGGCCAGCTGCACGTTGA	0.562																																																	1	Substitution - coding silent(1)	kidney(1)											77.0	75.0	76.0					14																	95029883		2203	4300	6503	SO:0001819	synonymous_variant	5267			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"""Serine (or cysteine) peptidase inhibitors"""	8948	protein-coding gene	gene with protein product		147935	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"""	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.64C>T	14.37:g.95029883C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	37	CCDS9927.1																																																																																				0.562	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1		NM_006215	
SETD2	29072	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	47158115	47158115	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:47158115T>A	ENST00000409792.3	-	4	4626	c.4584A>T	c.(4582-4584)gaA>gaT	p.E1528D		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1528	AWS. {ECO:0000255|PROSITE- ProRule:PRU00562}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.E1025D(1)|p.E1528D(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTACTTACCATTCAATCATGA	0.338			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Missense(2)	kidney(2)											123.0	124.0	124.0					3																	47158115		2203	4300	6503	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4584A>T	3.37:g.47158115T>A	ENSP00000386759:p.Glu1528Asp	Somatic		WXS	Illumina HiSeq	Phase_I	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	22.7	4.329269	0.81690	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.87729	-2.29	5.93	0.849	0.18972	AWS (2);	0.000000	0.56097	D	0.000021	D	0.94703	0.8291	H	0.96996	3.92	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.988	D	0.93412	0.6769	10	0.87932	D	0	.	10.2808	0.43539	0.0:0.3729:0.0:0.6271	.	1528;1528	F2Z317;Q9BYW2	.;SETD2_HUMAN	D	1528	ENSP00000386759:E1528D	ENSP00000386759:E1528D	E	-	3	2	SETD2	47133119	0.994000	0.37717	0.998000	0.56505	0.988000	0.76386	0.251000	0.18257	-0.071000	0.12886	0.482000	0.46254	GAA		0.338	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC12A2	6558	broad.mit.edu;ucsc.edu	37	5	127488499	127488499	+	Splice_Site	SNP	T	T	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr5:127488499T>G	ENST00000262461.2	+	15	2552		c.e15+2		SLC12A2_ENST00000343225.4_Splice_Site	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2						ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)	p.?(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	AAACTTTAGGTAAGTGATAAA	0.393																																																	1	Unknown(1)	kidney(1)											82.0	79.0	80.0					5																	127488499		2203	4300	6503	SO:0001630	splice_region_variant	6558				CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.2363+2T>G	5.37:g.127488499T>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q8N713|Q8WWH7	Splice_Site	SNP	ENST00000262461.2	37	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.761328	0.49468	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0912	0.72195	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A2	127516398	1.000000	0.71417	0.936000	0.37596	0.295000	0.27426	7.453000	0.80700	2.147000	0.66899	0.377000	0.23210	.		0.393	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1		NM_001046	Intron
TCHH	7062	broad.mit.edu;ucsc.edu	37	1	152084846	152084846	+	Silent	SNP	G	G	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:152084846G>T	ENST00000368804.1	-	2	846	c.847C>A	c.(847-849)Cgg>Agg	p.R283R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	283					keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.R283R(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTCTTGCCGCTCCAGCTTC	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											78.0	89.0	85.0					1																	152084846		2122	4250	6372	SO:0001819	synonymous_variant	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.847C>A	1.37:g.152084846G>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																				0.617	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TEK	7010	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	27109633	27109633	+	Silent	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:27109633C>T	ENST00000380036.4	+	1	487	c.45C>T	c.(43-45)ctC>ctT	p.L15L	TEK_ENST00000519097.1_Silent_p.L15L|TEK_ENST00000406359.4_Silent_p.L15L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	15					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L15L(1)		breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TCAGCTTGCTCCTTTCTGGTA	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											222.0	203.0	210.0					9																	27109633		2203	4300	6503	SO:0001819	synonymous_variant	7010			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.45C>T	9.37:g.27109633C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																				0.418	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			
TESC	54997	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	117477015	117477015	+	Splice_Site	SNP	T	T	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr12:117477015T>A	ENST00000335209.7	-	8	754	c.568A>T	c.(568-570)Atc>Ttc	p.I190F	TESC_ENST00000392545.4_Splice_Site_p.I243F|TESC_ENST00000541210.1_Splice_Site_p.I163F			Q96BS2	CHP3_HUMAN	tescalcin	190					cell differentiation (GO:0030154)|cellular response to retinoic acid (GO:0071300)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell proliferation (GO:0008285)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of sodium:proton antiporter activity (GO:0032417)|positive regulation of transcription, DNA-templated (GO:0045893)|protein maturation (GO:0051604)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of cell adhesion mediated by integrin (GO:0033628)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphatase inhibitor activity (GO:0019212)|protein homodimerization activity (GO:0042803)|protein kinase inhibitor activity (GO:0004860)	p.I243F(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		CCCTGCCAGATCTGGAAGGGA	0.642																																																	1	Substitution - Missense(1)	kidney(1)											84.0	94.0	90.0					12																	117477015		2203	4299	6502	SO:0001630	splice_region_variant	54997			AF443207	CCDS9183.2, CCDS9183.3, CCDS53835.1	12q24.22	2013-01-10			ENSG00000088992	ENSG00000088992		"""EF-hand domain containing"""	26065	protein-coding gene	gene with protein product	"""calcineurin-like EF hand protein 3"""	611585				11145610, 11696366, 12809501, 14661968	Standard	NM_017899		Approved	TSC, FLJ20607, CHP3	uc001twh.3	Q96BS2	OTTHUMG00000144168	ENST00000335209.7:c.568-1A>T	12.37:g.117477015T>A		Somatic		WXS	Illumina HiSeq	Phase_I	F5H1Y5|Q9NWT9	Missense_Mutation	SNP	ENST00000335209.7	37	CCDS9183.3	.	.	.	.	.	.	.	.	.	.	T	18.30	3.593982	0.66219	.	.	ENSG00000088992	ENST00000335209;ENST00000392545;ENST00000541210;ENST00000549210	T;T;T	0.54479	0.57;0.57;1.23	5.93	5.93	0.95920	EF-hand-like domain (1);	5.160780	0.00166	N	0.000000	T	0.54481	0.1861	L	0.50333	1.59	0.58432	D	0.999997	P	0.44946	0.846	B	0.36186	0.219	T	0.52472	-0.8571	10	0.66056	D	0.02	-37.8532	15.3655	0.74519	0.0:0.0:0.0:1.0	.	190	Q96BS2	TESC_HUMAN	F	190;243;163;57	ENSP00000334785:I190F;ENSP00000376328:I243F;ENSP00000445689:I163F	ENSP00000334785:I190F	I	-	1	0	TESC	115961398	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	3.405000	0.52630	2.271000	0.75665	0.459000	0.35465	ATC		0.642	TESC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291363.2		NM_017899	Missense_Mutation
THSD7B	80731	broad.mit.edu;ucsc.edu	37	2	138421031	138421031	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr2:138421031C>A	ENST00000409968.1	+	26	4715	c.4537C>A	c.(4537-4539)Cca>Aca	p.P1513T	THSD7B_ENST00000272643.3_Missense_Mutation_p.P1516T|THSD7B_ENST00000413152.2_Missense_Mutation_p.P1485T			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1515						integral component of membrane (GO:0016021)		p.P1485T(1)|p.P1516T(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CATGAAAGTACCAGGCTCAGA	0.363																																																	2	Substitution - Missense(2)	kidney(2)											79.0	74.0	76.0					2																	138421031		1841	4096	5937	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.4537C>A	2.37:g.138421031C>A	ENSP00000387145:p.Pro1513Thr	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	.	24.4	4.531564	0.85706	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.26067	2.28;2.15;1.76	6.02	5.14	0.70334	.	0.049873	0.85682	D	0.000000	T	0.45617	0.1351	M	0.67397	2.05	0.80722	D	1	D	0.71674	0.998	P	0.61722	0.893	T	0.26503	-1.0101	10	0.51188	T	0.08	.	14.7748	0.69724	0.0:0.9315:0.0:0.0685	.	1485	C9JKN6	.	T	1513;1516;1485	ENSP00000387145:P1513T;ENSP00000272643:P1516T;ENSP00000413841:P1485T	ENSP00000272643:P1516T	P	+	1	0	THSD7B	138137501	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.519000	0.60517	2.866000	0.98385	0.650000	0.86243	CCA		0.363	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2		XM_046570.9	
TMEM86A	144110	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	18722527	18722527	+	Silent	SNP	C	C	T	rs551911585	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr11:18722527C>T	ENST00000280734.2	+	2	165	c.69C>T	c.(67-69)tgC>tgT	p.C23C	TMEM86A_ENST00000527002.1_3'UTR	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	23						integral component of membrane (GO:0016021)		p.C23C(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						AGGCCACCTGCGTGTATTTTG	0.572													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18955	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											217.0	193.0	201.0					11																	18722527		2199	4293	6492	SO:0001819	synonymous_variant	144110			BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4		ENST00000280734.2:c.69C>T	11.37:g.18722527C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q96AJ0	Silent	SNP	ENST00000280734.2	37	CCDS7844.1																																																																																				0.572	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1		NM_153347	
TXNIP	10628	broad.mit.edu;hgsc.bcm.edu	37	1	145438828	145438828	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:145438828C>A	ENST00000369317.4	+	1	360	c.26C>A	c.(25-27)tCt>tAt	p.S9Y	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	9					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)	p.S9Y(2)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAGATCAAGTCTTTTGAGGTG	0.458																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											97.0	94.0	95.0					1																	145438828		2203	4300	6503	SO:0001583	missense	10628			S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"""upregulated by 1,25-dihydroxyvitamin D-3"", ""thioredoxin binding protein 2"""	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.26C>A	1.37:g.145438828C>A	ENSP00000358323:p.Ser9Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B4E3D3|Q16226|Q6PML0|Q9BXG9	Missense_Mutation	SNP	ENST00000369317.4	37	CCDS913.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032784	0.54790	.	.	ENSG00000117289	ENST00000369317	T	0.09538	2.97	5.64	5.64	0.86602	.	0.657828	0.16039	N	0.232503	T	0.05273	0.0140	L	0.39898	1.24	0.36127	D	0.845887	B	0.25955	0.138	B	0.19391	0.025	T	0.10086	-1.0645	10	0.66056	D	0.02	-29.6416	12.861	0.57913	0.0:0.8362:0.1638:0.0	.	9	Q9H3M7	TXNIP_HUMAN	Y	9	ENSP00000358323:S9Y	ENSP00000358323:S9Y	S	+	2	0	TXNIP	144150185	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	0.621000	0.24418	2.665000	0.90641	0.655000	0.94253	TCT		0.458	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1		NM_006472	
TYW1	55253	broad.mit.edu;hgsc.bcm.edu	37	7	66532334	66532334	+	Silent	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr7:66532334C>T	ENST00000359626.5	+	10	1382	c.1218C>T	c.(1216-1218)cgC>cgT	p.R406R		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	406					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.R406R(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				AGAGCCATCGCTGCATGGAAA	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											156.0	141.0	146.0					7																	66532334		2203	4300	6503	SO:0001819	synonymous_variant	55253			AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1218C>T	7.37:g.66532334C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																				0.418	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2		NM_018264	
USP20	10868	hgsc.bcm.edu;ucsc.edu	37	9	132636882	132636883	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:132636882_132636883insT	ENST00000315480.4	+	18	1926_1927	c.1768_1769insT	c.(1768-1770)cggfs	p.R590fs	USP20_ENST00000372429.3_Frame_Shift_Ins_p.R590fs|USP20_ENST00000358355.1_Frame_Shift_Ins_p.R590fs			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	590	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AAAGCGCTTTCGGCACGAGGTG	0.609																																																	0																																										SO:0001589	frameshift_variant	10868			AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	Exception_encountered	9.37:g.132636882_132636883insT	ENSP00000313811:p.Arg590fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Frame_Shift_Ins	INS	ENST00000315480.4	37	CCDS43892.1																																																																																				0.609	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			
USP20	10868	hgsc.bcm.edu	37	9	132636883	132636883	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:132636883G>T	ENST00000315480.4	+	18	1927	c.1769G>T	c.(1768-1770)cGg>cTg	p.R590L	USP20_ENST00000372429.3_Missense_Mutation_p.R590L|USP20_ENST00000358355.1_Missense_Mutation_p.R590L			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	590	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AAGCGCTTTCGGCACGAGGTG	0.607																																																	0													65.0	70.0	69.0					9																	132636883		2117	4233	6350	SO:0001583	missense	10868			AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1769G>T	9.37:g.132636883G>T	ENSP00000313811:p.Arg590Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290845	0.80914	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.31247	1.5;1.5;1.5	4.95	4.95	0.65309	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.069553	0.64402	D	0.000006	T	0.47469	0.1447	M	0.85859	2.78	0.80722	D	1	B	0.29988	0.264	B	0.37780	0.258	T	0.55522	-0.8128	10	0.72032	D	0.01	.	17.1774	0.86844	0.0:0.0:1.0:0.0	.	590	Q9Y2K6	UBP20_HUMAN	L	590	ENSP00000361506:R590L;ENSP00000313811:R590L;ENSP00000351122:R590L	ENSP00000313811:R590L	R	+	2	0	USP20	131676704	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.430000	0.97488	2.251000	0.74343	0.650000	0.86243	CGG		0.607	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188205	10188205	+	Silent	SNP	T	T	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:10188205T>C	ENST00000256474.2	+	2	1188	c.348T>C	c.(346-348)ctT>ctC	p.L116L	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	116	Involved in binding to CCT complex.		L -> V (in VHLD). {ECO:0000269|PubMed:8730290}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(2)|p.H115fs*41(1)|p.L116L(1)|p.W117fs*40(1)|p.H115fs*42(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TAGGTCACCTTTGGCTCTTCA	0.527		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	6	Deletion - Frameshift(3)|Unknown(2)|Substitution - coding silent(1)	kidney(6)											174.0	161.0	165.0					3																	10188205		2203	4300	6503	SO:0001819	synonymous_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.348T>C	3.37:g.10188205T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Silent	SNP	ENST00000256474.2	37	CCDS2597.1																																																																																				0.527	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188208	10188208	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:10188208G>C	ENST00000256474.2	+	2	1191	c.351G>C	c.(349-351)tgG>tgC	p.W117C	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	117	Involved in binding to CCT complex.		W -> C (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911, ECO:0000269|PubMed:9829912}.		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.W117C(4)|p.W117*(2)|p.?(1)|p.W117fs*40(1)|p.W117fs*42(1)|p.W117fs*1(1)|p.H115fs*41(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)		GTCACCTTTGGCTCTTCAGAG	0.512		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	11	Substitution - Missense(4)|Deletion - Frameshift(4)|Substitution - Nonsense(2)|Unknown(1)	kidney(10)|upper_aerodigestive_tract(1)	GRCh37	CM951286|HM971481	VHL	M							178.0	165.0	169.0					3																	10188208		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.351G>C	3.37:g.10188208G>C	ENSP00000256474:p.Trp117Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.903601	0.52333	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99962	-9.39	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99961	0.9984	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.68483	0.958	D	0.94819	0.7985	10	0.87932	D	0	-0.0021	16.3181	0.82935	0.0:0.0:1.0:0.0	.	117	P40337	VHL_HUMAN	C	117;35	ENSP00000256474:W117C	ENSP00000256474:W117C	W	+	3	0	VHL	10163208	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	7.278000	0.78587	2.530000	0.85305	0.563000	0.77884	TGG		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VWF	7450	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	6091108	6091108	+	Silent	SNP	C	C	T	rs267607359|rs267607360		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr12:6091108C>T	ENST00000261405.5	-	42	7385	c.7131G>A	c.(7129-7131)ccG>ccA	p.P2377P		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2377					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.P2377P(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCAAACGGTGCGGGGGGCAGG	0.607																																																	1	Substitution - coding silent(1)	kidney(1)	GRCh37	CI983256	VWF	I	rs61750632						77.0	67.0	71.0					12																	6091108		2203	4300	6503	SO:0001819	synonymous_variant	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7131G>A	12.37:g.6091108C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.607	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1		NM_000552	
WBP2	23558	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73851365	73851365	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr17:73851365T>A	ENST00000591399.1	-	2	438	c.14A>T	c.(13-15)aAg>aTg	p.K5M	WBP2_ENST00000590221.1_Missense_Mutation_p.K5M|WBP2_ENST00000433525.2_Missense_Mutation_p.K5M|WBP2_ENST00000585462.1_De_novo_Start_OutOfFrame|WBP2_ENST00000254806.3_Missense_Mutation_p.K5M|WBP2_ENST00000344296.4_De_novo_Start_InFrame|WBP2_ENST00000590450.1_5'UTR			Q969T9	WBP2_HUMAN	WW domain binding protein 2	5	GRAM.				cellular response to estrogen stimulus (GO:0071391)|establishment of protein localization (GO:0045184)|positive regulation of gene expression, epigenetic (GO:0045815)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nuclear chromatin (GO:0000790)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription coactivator activity (GO:0001105)	p.K5M(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7			all cancers(21;2.61e-06)|Epithelial(20;2.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGAGTGATTCTTGTTGAGCGC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											141.0	143.0	142.0					17																	73851365		2203	4300	6503	SO:0001583	missense	23558			U79458	CCDS11731.1	17q25	2008-02-01				ENSG00000132471			12738	protein-coding gene	gene with protein product		606962				7644498	Standard	NM_012478		Approved	WBP-2	uc002jps.3	Q969T9		ENST00000591399.1:c.14A>T	17.37:g.73851365T>A	ENSP00000467579:p.Lys5Met	Somatic		WXS	Illumina HiSeq	Phase_I	O95638	Missense_Mutation	SNP	ENST00000591399.1	37	CCDS11731.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287238	0.80803	.	.	ENSG00000132471	ENST00000254806;ENST00000433525;ENST00000431190;ENST00000416574	T;D	0.88277	1.3;-2.36	4.21	3.13	0.36017	GRAM (1);	0.153419	0.56097	D	0.000021	D	0.88127	0.6353	L	0.39898	1.24	0.80722	D	1	D;P;P;P	0.57571	0.98;0.921;0.921;0.921	P;P;P;P	0.60345	0.873;0.671;0.671;0.671	D	0.86528	0.1820	10	0.52906	T	0.07	-11.9478	5.5684	0.17182	0.0:0.2939:0.0:0.7061	.	5;5;5;5	B4DV07;B4DFG2;Q7Z511;Q969T9	.;.;.;WBP2_HUMAN	M	5	ENSP00000254806:K5M;ENSP00000415251:K5M	ENSP00000254806:K5M	K	-	2	0	WBP2	71362960	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.886000	0.39688	1.891000	0.54761	0.460000	0.39030	AAG		0.562	WBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448862.1		NM_012478	
ZAN	7455	hgsc.bcm.edu	37	7	100371476	100371477	+	RNA	INS	-	-	G	rs148800656|rs200325383|rs372381708	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr7:100371476_100371477insG	ENST00000348028.3	+	0	5932_5933				ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546213.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCTGCTCCGTTTCGGGCCTCAG	0.624													G|-|G|deletion	2230	0.445288	0.2133	0.5418	5008	,	,		17915	0.7867		0.3419	False		,,,				2504	0.4448																1	Unknown(1)	upper_aerodigestive_tract(1)							,	906,2950		139,628,1161					,	4.6	0.9		dbSNP_134	33	2934,5018		557,1820,1599	no	frameshift,frameshift	ZAN	NM_173059.1,NM_003386.1	,	696,2448,2760	A1A1,A1R,RR		36.8964,23.4959,32.5203	,	,		3840,7968						7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100371476_100371477insG		Somatic		WXS	Illumina HiSeq	Phase_I	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Frame_Shift_Ins	INS	ENST00000348028.3	37																																																																																					0.624	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1		NM_003386	
ZNF2	7549	hgsc.bcm.edu	37	2	95847047	95847047	+	Silent	SNP	G	G	A	rs112887855		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr2:95847047G>A	ENST00000340539.5	+	5	936	c.474G>A	c.(472-474)cgG>cgA	p.R158R	ZNF2_ENST00000398107.2_Silent_p.R116R|ZNF2_ENST00000295210.6_Silent_p.R120R|ZNF2_ENST00000425369.1_Silent_p.R78R|ZNF2_ENST00000453539.2_Silent_p.R171R	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		GCTTGCGGCGGCGACGGTCAG	0.537																																																	0													49.0	55.0	53.0					2																	95847047		1976	4170	6146	SO:0001819	synonymous_variant	7549			X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"""Zinc fingers, C2H2-type"", ""-"""	12991	protein-coding gene	gene with protein product		194500	"""zinc finger protein 2 (A1-5)"""			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.474G>A	2.37:g.95847047G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Silent	SNP	ENST00000340539.5	37	CCDS42712.1																																																																																				0.537	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2		NM_021088	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692936	187692937	+	In_Frame_Ins	INS	-	-	GGG			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr2:187692936_187692937insGGG	ENST00000295131.2	-	9	1715_1716	c.1676_1677insCCC	c.(1675-1677)cct>ccCCCt	p.559_559P>PP		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	559					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TTTTAGTGGCAGGAGTCTTCTT	0.381																																																	0																																										SO:0001652	inframe_insertion	151112			AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1676_1677insCCC	2.37:g.187692936_187692937insGGG	ENSP00000295131:p.Pro559dup	Somatic		WXS	Illumina HiSeq	Phase_I	B3KXV6|Q53SI3|Q57ZY3	In_Frame_Ins	INS	ENST00000295131.2	37	CCDS33348.1																																																																																				0.381	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1		NM_182521	
ABO	28	broad.mit.edu	37	9	136131057	136131057	+	RNA	DEL	G	G	-	rs8176750|rs56392308	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:136131057delG	ENST00000453660.2	-	0	1071				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)	p.P353fs?(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		AGCCGCTCACGGGTTCCGGAC	0.662													GGG|GGG|GG|deletion	242	0.0483227	0.0658	0.0432	5008	,	,		13669	0.0		0.0954	False		,,,				2504	0.0297																1	Deletion - Frameshift(1)	central_nervous_system(1)								234,3304		17,200,1552	9.0	10.0	10.0			-7.1	0.0	9	dbSNP_129	10	533,7273		35,463,3405	no	frameshift	ABO	NM_020469.2		52,663,4957	A1A1,A1R,RR		6.8281,6.6139,6.7613			136131057	767,10577	1853	4054	5907			28			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"""Blood group antigens"", ""Glycosyltransferase family 6 domain containing"""	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136131057delG		Somatic		WXS	Illumina GAIIx	Phase_I	B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	Frame_Shift_Del	DEL	ENST00000453660.2	37																																																																																					0.662	ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4		NM_020469	
IGHD3-10	28499	broad.mit.edu	37	14	106372754	106372754	+	RNA	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr14:106372754C>T	ENST00000390583.1	-	0	0				IGHD2-8_ENST00000390585.1_RNA|IGHD3-9_ENST00000390584.1_RNA					immunoglobulin heavy diversity 3-10																		TGATCTCGAACACCAGTTTAT	0.547																																																	0																																												8755			X13972		14q32.33	2012-02-08			ENSG00000211923	ENSG00000211923		"""Immunoglobulins / IGH locus"""	5495	other	immunoglobulin gene						3243276	Standard	NG_001019		Approved	IGHD310, DXP'1			OTTHUMG00000152354		14.37:g.106372754C>T		Somatic		WXS	Illumina GAIIx	Phase_I		Splice_Site	SNP	ENST00000390583.1	37																																																																																					0.547	IGHD3-10-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_D_gene	IG_D_gene	OTTHUMT00000325960.3		NG_001019	
GOLGA6L10	647042	broad.mit.edu	37	15	82635163	82635163	+	Silent	SNP	C	C	G	rs28429808	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr15:82635163C>G	ENST00000439287.4	-	9	1506	c.1407G>C	c.(1405-1407)gcG>gcC	p.A469A		NM_001164465.1	NP_001157937.1	A6NI86	GG6LA_HUMAN	golgin A6 family-like 10	469								p.A469A(10)		endometrium(1)|kidney(4)	5						CCCTGTTCTCCGCAGCCCGAA	0.478																																																	10	Substitution - coding silent(10)	kidney(8)|endometrium(2)																																								SO:0001819	synonymous_variant	647042				CCDS45325.1	15q25.2	2014-08-13	2010-02-12		ENSG00000278662				37228	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 10"", ""golgin A6 family-like 18"""	GOLGA6L18			Standard	XM_006720643		Approved		uc021ssn.1	A6NI86	OTTHUMG00000172580	ENST00000439287.4:c.1407G>C	15.37:g.82635163C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000439287.4	37	CCDS45325.1																																																																																				0.478	GOLGA6L10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419403.2		NM_001164465	
IL9R	3581	broad.mit.edu	37	X	155233148	155233148	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chrX:155233148C>A	ENST00000244174.5	+	3	356	c.177C>A	c.(175-177)aaC>aaA	p.N59K	IL9R_ENST00000369423.2_Missense_Mutation_p.N106K|IL9R_ENST00000424344.3_Missense_Mutation_p.N38K|IL9R_ENST00000540897.1_Missense_Mutation_p.N96K	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	59					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)	p.N59K(1)		NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	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)					GCCTCACCAACAACATTCTCA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											116.0	120.0	118.0					X																	155233148		2203	4296	6499	SO:0001583	missense	3581			M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"""Pseudoautosomal regions / PAR2"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.177C>A	X.37:g.155233148C>A	ENSP00000244174:p.Asn59Lys	Somatic		WXS	Illumina GAIIx	Phase_I	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	37	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	c	16.99	3.273116	0.59649	.	.	ENSG00000124334	ENST00000244174;ENST00000424344;ENST00000455739;ENST00000369423;ENST00000540897	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	1.29	1.29	0.21616	.	0.068863	0.56097	D	0.000029	T	0.63988	0.2558	.	.	.	0.09310	N	1	P;D;D	0.67145	0.933;0.976;0.996	P;P;D	0.75484	0.557;0.629;0.986	T	0.50074	-0.8870	9	0.72032	D	0.01	-20.6157	5.5447	0.17057	0.0:1.0:0.0:0.0	.	38;59;106	F5H3Z0;Q01113;B9ZVT0	.;IL9R_HUMAN;.	K	59;38;38;106;96	ENSP00000244174:N59K;ENSP00000388918:N38K;ENSP00000358431:N106K;ENSP00000438112:N96K	ENSP00000244174:N59K	N	+	3	2	IL9R	154886342	0.997000	0.39634	0.973000	0.42090	0.734000	0.41952	0.831000	0.27476	0.932000	0.37266	0.287000	0.19450	AAC		0.607	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1		NM_002186	
IMPG2	50939	broad.mit.edu	37	3	101038459	101038459	+	Silent	SNP	C	C	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr3:101038459C>A	ENST00000193391.7	-	2	490	c.303G>T	c.(301-303)gtG>gtT	p.V101V		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	101					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.V101V(1)		NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	CATGATTTGCCACAGCCTCTG	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											145.0	142.0	143.0					3																	101038459		2203	4300	6503	SO:0001819	synonymous_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.303G>T	3.37:g.101038459C>A		Somatic		WXS	Illumina GAIIx	Phase_I	A8MWT5|Q9UKD4|Q9UKK5	Silent	SNP	ENST00000193391.7	37	CCDS2940.1																																																																																				0.388	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			
LAMC3	10319	broad.mit.edu	37	9	133901946	133901947	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:133901946_133901947delCT	ENST00000361069.4	+	2	781_782	c.648_649delCT	c.(646-651)gcctacfs	p.Y217fs	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	217	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GGCCCAGCGCCTACAACTTCGA	0.668																																																	0																																										SO:0001589	frameshift_variant	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.648_649delCT	9.37:g.133901946_133901947delCT	ENSP00000354360:p.Tyr217fs	Somatic		WXS	Illumina GAIIx	Phase_I	B1APX9|B1APY0|Q59H72	Frame_Shift_Del	DEL	ENST00000361069.4	37	CCDS6938.1																																																																																				0.668	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3		NM_006059	
Unknown	0	broad.mit.edu	37	13	19419613	19419613	+	IGR	SNP	G	G	C	rs367865827		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr13:19419613G>C								LINC00418 (125744 upstream) : RP11-38M15.11 (14353 downstream)																							CAAGATAATTGTGAAAAATTC	0.284																																																	0																																										SO:0001628	intergenic_variant	0																															13.37:g.19419613G>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.284									
Unknown	0	broad.mit.edu	37	13	19419620	19419620	+	IGR	SNP	A	A	T	rs371589349		TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr13:19419620A>T								LINC00418 (125751 upstream) : RP11-38M15.11 (14346 downstream)																							ATTGTGAAAAATTCTTGCCTC	0.284																																																	0																																										SO:0001628	intergenic_variant	0																															13.37:g.19419620A>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.284									
Unknown	0	broad.mit.edu	37	1	13183480	13183480	+	IGR	SNP	A	A	G			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:13183480A>G								RP13-221M14.3 (19012 upstream) : PRAMEF26 (32875 downstream)																							GAGGAGGAGGAGGTACACGTG	0.507																																																	0													94.0	74.0	80.0					1																	13183480		692	1591	2283	SO:0001628	intergenic_variant	440563																															1.37:g.13183480A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP		37																																																																																				0	0.507									
TNKS1BP1	85456	broad.mit.edu	37	11	57088165	57088165	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr11:57088165delG	ENST00000532437.1	-	2	427	c.116delC	c.(115-117)cctfs	p.P39fs	TNKS1BP1_ENST00000358252.3_Frame_Shift_Del_p.P39fs			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	39	Arg/Glu/Lys/Pro-rich (charged).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GGGCTTGACAGGGGGTTTGGC	0.627																																																	0													15.0	18.0	17.0					11																	57088165		2185	4275	6460	SO:0001589	frameshift_variant	85456			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.116delC	11.37:g.57088165delG	ENSP00000437271:p.Pro39fs	Somatic		WXS	Illumina GAIIx	Phase_I	A7E2F8|Q6PJ35|Q6ZV74	Frame_Shift_Del	DEL	ENST00000532437.1	37	CCDS7951.1																																																																																				0.627	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1		NM_033396	
DDX11L1	100287102	broad.mit.edu	37	1	13418	13418	+	RNA	SNP	G	G	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:13418G>A	ENST00000456328.2	+	0	666					NR_046018.2|NR_051986.1				DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1																		CCACCACCCCGAGATCACATT	0.562																																																	0																																												0			AM992871		1p36.33	2012-02-23	2012-02-23		ENSG00000223972	ENSG00000223972			37102	pseudogene	pseudogene			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1"""			19476624	Standard	NR_046018		Approved		uc010nxq.1		OTTHUMG00000000961		1.37:g.13418G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000456328.2	37																																																																																					0.562	DDX11L1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000362751.1			
SMG1P7	100506060	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	G	A			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr16:70268081G>A	ENST00000459379.1	-	0	0																											TCTTACTGTTGGCTAAAAGGC	0.373																																																	0																																												0																															16.37:g.70268081G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.373	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
LOC63930	63930	broad.mit.edu	37	20	61715967	61715968	+	lincRNA	INS	-	-	C	rs541866112|rs139661993	byFrequency	TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr20:61715967_61715968insC	ENST00000607802.1	+	0	2952_2953					NR_033370.1																						CGGACCACCAGCCCCCCTTCAC	0.574													CCCCCC|CCCCCC|CCCCCCC|insertion	555	0.110823	0.2534	0.0893	5008	,	,		15970	0.006		0.1113	False		,,,				2504	0.0409																0																																												0																															20.37:g.61715973_61715973dupC		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000607802.1	37																																																																																					0.574	RP11-305P22.9-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470475.1			
LINC01410	103352539	broad.mit.edu	37	9	66454921	66454921	+	lincRNA	SNP	C	C	T			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr9:66454921C>T	ENST00000424345.1	+	0	0																											TGTGGGGCCCCAGAAACTTCC	0.517																																																	0																																												0																															9.37:g.66454921C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000424345.1	37																																																																																					0.517	RP11-262H14.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000128851.1			
ZMYM6	9204	broad.mit.edu	37	1	35453715	35453715	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5684-01A-11D-1534-10	TCGA-CJ-5684-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24ee4b71-c2e0-44c3-aaeb-3c488cd26ce7	81ad0b3a-02ce-44e3-b84d-fd03c7792bcb	g.chr1:35453715A>C	ENST00000357182.4	-	16	3195	c.2968T>G	c.(2968-2970)Tat>Gat	p.Y990D	ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000487874.1_Intron|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	990					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Y990D(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				aaaccagaatacctgccagtc	0.358																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001583	missense	9204			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2968T>G	1.37:g.35453715A>C	ENSP00000349708:p.Tyr990Asp	Somatic		WXS	Illumina GAIIx	Phase_I	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	A	8.629	0.893304	0.17613	.	.	ENSG00000163867	ENST00000357182	T	0.21932	1.98	4.36	4.36	0.52297	Ribonuclease H-like (1);	1.167690	0.06344	N	0.708515	T	0.20618	0.0496	L	0.39898	1.24	0.80722	D	1	P	0.36712	0.566	B	0.35727	0.209	T	0.04723	-1.0931	10	0.36615	T	0.2	2.1055	10.2456	0.43339	1.0:0.0:0.0:0.0	.	990	O95789	ZMYM6_HUMAN	D	990	ENSP00000349708:Y990D	ENSP00000349708:Y990D	Y	-	1	0	ZMYM6	35226302	0.995000	0.38212	0.999000	0.59377	0.914000	0.54420	1.376000	0.34306	2.193000	0.70182	0.533000	0.62120	TAT		0.358	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1		NM_007167	
