#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
ACACA	31	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	35545400	35545400	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr17:35545400G>T	ENST00000394406.2	-	39	4672	c.4482C>A	c.(4480-4482)agC>agA	p.S1494R	ACACA_ENST00000335166.5_Missense_Mutation_p.S1416R|ACACA_ENST00000360679.3_Missense_Mutation_p.S1436R|ACACA_ENST00000353139.5_Missense_Mutation_p.S1531R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1494					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.S1436R(1)|p.S1531R(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GCATTACCATGCTCCGCACGG	0.458																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)												2	Substitution - Missense(2)	kidney(2)											141.0	131.0	134.0					17																	35545400		2203	4300	6503	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.4482C>A	17.37:g.35545400G>T	ENSP00000377928:p.Ser1494Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619510	0.46736	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.6	4.63	0.57726	Acetyl-CoA carboxylase, central domain (1);	0.203924	0.52532	D	0.000080	T	0.40297	0.1111	M	0.65975	2.015	0.80722	D	1	B;B;B;B	0.22211	0.066;0.021;0.011;0.021	B;B;B;B	0.23716	0.048;0.034;0.024;0.014	T	0.29458	-1.0011	10	0.38643	T	0.18	-17.5067	9.9396	0.41572	0.1528:0.0:0.8472:0.0	.	242;1531;1494;1436	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	R	1531;1436;1494;1518;1416;242	ENSP00000344789:S1531R;ENSP00000353898:S1436R;ENSP00000377928:S1494R;ENSP00000335323:S1416R	ENSP00000335323:S1416R	S	-	3	2	ACACA	32619513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.092000	0.57707	2.630000	0.89119	0.655000	0.94253	AGC		0.458	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1		NM_198836	
ADAMTS9	56999	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	64619448	64619448	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr3:64619448G>T	ENST00000498707.1	-	13	2306	c.1964C>A	c.(1963-1965)gCt>gAt	p.A655D	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.A627D	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	655	Cys-rich.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A655D(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GTCAAAGTGAGCACACTGTTC	0.458																																																	1	Substitution - Missense(1)	kidney(1)											190.0	171.0	177.0					3																	64619448		2203	4300	6503	SO:0001583	missense	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1964C>A	3.37:g.64619448G>T	ENSP00000418735:p.Ala655Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	G	33	5.271067	0.95429	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.03745	3.82;3.82	5.51	5.51	0.81932	.	0.064357	0.64402	D	0.000008	T	0.19208	0.0461	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.71674	0.957;0.975;0.998;0.957	P;P;D;P	0.68765	0.641;0.837;0.96;0.641	T	0.00074	-1.2123	10	0.87932	D	0	.	19.4315	0.94772	0.0:0.0:1.0:0.0	.	627;655;655;655	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	D	627;655	ENSP00000295903:A627D;ENSP00000418735:A655D	ENSP00000295903:A627D	A	-	2	0	ADAMTS9	64594488	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.518000	0.81795	2.600000	0.87896	0.655000	0.94253	GCT		0.458	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			
ANKRA2	57763	broad.mit.edu;hgsc.bcm.edu	37	5	72849308	72849308	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr5:72849308C>A	ENST00000296785.3	-	8	1467	c.809G>T	c.(808-810)aGt>aTt	p.S270I		NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	270						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)	p.S270I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		ATCAGCCCCACTTTCTATACC	0.358																																																	1	Substitution - Missense(1)	kidney(1)											68.0	63.0	64.0					5																	72849308		2203	4300	6503	SO:0001583	missense	57763			AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"""Ankyrin repeat domain containing"""	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.809G>T	5.37:g.72849308C>A	ENSP00000296785:p.Ser270Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000296785.3	37	CCDS4020.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.483680	0.26598	.	.	ENSG00000164331	ENST00000296785	T	0.65916	-0.18	6.04	3.53	0.40419	Ankyrin repeat-containing domain (4);	0.211922	0.56097	D	0.000023	T	0.56321	0.1977	L	0.48935	1.535	0.43007	D	0.994533	B	0.27380	0.177	B	0.34931	0.192	T	0.53872	-0.8377	10	0.54805	T	0.06	-10.7669	9.2438	0.37513	0.0:0.2221:0.0:0.7779	.	270	Q9H9E1	ANRA2_HUMAN	I	270	ENSP00000296785:S270I	ENSP00000296785:S270I	S	-	2	0	ANKRA2	72885064	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.923000	0.40055	0.521000	0.28445	-0.440000	0.05779	AGT		0.358	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2		NM_023039	
AQP12B	653437	hgsc.bcm.edu	37	2	241621800	241621800	+	Frame_Shift_Del	DEL	C	C	-	rs201917032	byFrequency	TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr2:241621800delC	ENST00000407834.3	-	1	517	c.455delG	c.(454-456)agcfs	p.S153fs		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	141						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S152fs*24(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CAGGGCCGAGCTGCAGCTCTG	0.697													|||unknown(ALL_OTHER_Ns)	1162	0.232029	0.2602	0.1859	5008	,	,		16428	0.3621		0.1372	False		,,,				2504	0.1902																2	Deletion - Frameshift(2)	ovary(1)|breast(1)								1107,2703		290,527,1088	3.0	5.0	4.0			2.8	1.0	2		5	1068,6184		219,630,2777	no	frameshift	AQP12B	NM_001102467.1		509,1157,3865	A1A1,A1R,RR		14.727,29.0551,19.6619			241621800	2175,8887	1826	3778	5604	SO:0001589	frameshift_variant	653437			BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.455delG	2.37:g.241621800delC	ENSP00000384894:p.Ser153fs	Somatic		WXS	Illumina HiSeq	Phase_I	A4QPB9	Frame_Shift_Del	DEL	ENST00000407834.3	37	CCDS46560.1																																																																																				0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			
ATG4D	84971	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	10663721	10663721	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr19:10663721C>A	ENST00000309469.4	+	10	1576	c.1403C>A	c.(1402-1404)tCt>tAt	p.S468Y	RNU7-140P_ENST00000459546.1_RNA|ATG4D_ENST00000540862.1_Missense_Mutation_p.S135Y|MIR1238_ENST00000408483.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	468					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)	p.S468Y(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CGCCCCAGCTCTGAGGACTTT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											31.0	35.0	33.0					19																	10663721		2203	4300	6503	SO:0001583	missense	84971			AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"""AUT-like 4, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog D (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog D (S. cerevisiae)"""	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.1403C>A	19.37:g.10663721C>A	ENSP00000311318:p.Ser468Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.073716	0.76415	.	.	ENSG00000130734	ENST00000309469;ENST00000540862	.	.	.	5.49	5.49	0.81192	.	0.320346	0.32918	N	0.005495	T	0.72977	0.3528	L	0.59436	1.845	0.49483	D	0.999791	P;D	0.58970	0.882;0.984	P;P	0.56700	0.534;0.804	T	0.75422	-0.3323	9	0.72032	D	0.01	-12.5461	18.1314	0.89603	0.0:1.0:0.0:0.0	.	405;468	B4DGM8;Q86TL0	.;ATG4D_HUMAN	Y	468;135	.	ENSP00000311318:S468Y	S	+	2	0	ATG4D	10524721	0.998000	0.40836	1.000000	0.80357	0.601000	0.36947	3.808000	0.55598	2.586000	0.87340	0.655000	0.94253	TCT		0.547	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1		NM_032885	
CACNA1S	779	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	201017771	201017771	+	Silent	SNP	T	T	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr1:201017771T>A	ENST00000362061.3	-	36	4606	c.4380A>T	c.(4378-4380)acA>acT	p.T1460T	CACNA1S_ENST00000367338.3_Silent_p.T1441T	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1460					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.T1460T(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGAAGGTGACTGTGCCGTCGC	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											131.0	100.0	110.0					1																	201017771		2203	4300	6503	SO:0001819	synonymous_variant	779			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4380A>T	1.37:g.201017771T>A		Somatic		WXS	Illumina HiSeq	Phase_I	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																				0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1		NM_000069	
CLPTM1	1209	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	45465320	45465320	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr19:45465320G>A	ENST00000337392.5	+	2	323	c.173G>A	c.(172-174)gGt>gAt	p.G58D	CLPTM1_ENST00000541297.2_Missense_Mutation_p.G44D|CLPTM1_ENST00000546079.1_5'UTR	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	58					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.G58D(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		GTCATCAAAGGTGTGCTGTTT	0.547																																																	2	Substitution - Missense(2)	kidney(2)											52.0	50.0	51.0					19																	45465320		2195	4298	6493	SO:0001583	missense	1209			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.173G>A	19.37:g.45465320G>A	ENSP00000336994:p.Gly58Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335892	0.81801	.	.	ENSG00000104853	ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.73418	0.3584	M	0.65498	2.005	0.58432	D	0.999998	D;D	0.55800	0.967;0.973	P;P	0.58721	0.758;0.844	T	0.74668	-0.3588	9	0.56958	D	0.05	-44.6437	14.4408	0.67314	0.0:0.0:1.0:0.0	.	44;58	F5H8J3;O96005	.;CLPT1_HUMAN	D	44;58;58	.	ENSP00000336994:G58D	G	+	2	0	CLPTM1	50157160	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.088000	0.64486	2.777000	0.95525	0.549000	0.68633	GGT		0.547	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1		NM_001294	
COL11A2	1302	hgsc.bcm.edu	37	6	33156155	33156155	+	Frame_Shift_Del	DEL	T	T	-	rs190156778		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr6:33156155delT	ENST00000374708.4	-	4	848	c.590delA	c.(589-591)gatfs	p.D197fs	COL11A2_ENST00000357486.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000395194.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000374712.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000395197.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000341947.2_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000374713.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000361917.1_Frame_Shift_Del_p.D197fs|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.D197fs	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	197	Laminin G-like.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GACTTCTTCATCCAGAATACG	0.527																																					Melanoma(1;90 116 3946 5341 17093)												0													120.0	127.0	125.0					6																	33156155		1511	2708	4219	SO:0001589	frameshift_variant	1302			U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.590delA	6.37:g.33156155delT	ENSP00000363840:p.Asp197fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000374708.4	37	CCDS43452.1																																																																																				0.527	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			
CSNK1A1L	122011	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	37678647	37678647	+	Silent	SNP	A	A	G			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr13:37678647A>G	ENST00000379800.3	-	1	1156	c.747T>C	c.(745-747)tgT>tgC	p.C249C		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.C249C(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GAAACCCCTTACATAAAACTT	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											122.0	121.0	122.0					13																	37678647		2203	4300	6503	SO:0001819	synonymous_variant	122011			BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.747T>C	13.37:g.37678647A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T2N2	Silent	SNP	ENST00000379800.3	37	CCDS9363.1																																																																																				0.453	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1		NM_145203	
DACT1	51339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	59113389	59113389	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr14:59113389C>A	ENST00000335867.4	+	4	2072	c.2048C>A	c.(2047-2049)gCc>gAc	p.A683D	DACT1_ENST00000395153.3_Missense_Mutation_p.A646D|DACT1_ENST00000556859.1_Missense_Mutation_p.A402D|DACT1_ENST00000541264.2_Missense_Mutation_p.A402D			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	683					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)	p.A683D(1)		endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						AAGTCCTCGGCCGAGATTTCC	0.701																																																	1	Substitution - Missense(1)	kidney(1)											13.0	14.0	14.0					14																	59113389		2171	4265	6436	SO:0001583	missense	51339			AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2048C>A	14.37:g.59113389C>A	ENSP00000337439:p.Ala683Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.862387	0.51482	.	.	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.63	4.74	0.60224	.	0.177981	0.49305	D	0.000156	T	0.68540	0.3012	M	0.74258	2.255	0.25110	N	0.990729	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.962	T	0.65813	-0.6077	10	0.72032	D	0.01	-19.9519	16.6668	0.85255	0.0:0.8702:0.1298:0.0	.	646;683	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	D	402;402;646;683;402	ENSP00000451598:A402D;ENSP00000378581:A402D;ENSP00000378582:A646D;ENSP00000337439:A683D;ENSP00000442850:A402D	ENSP00000337439:A683D	A	+	2	0	DACT1	58183142	0.128000	0.22383	0.111000	0.21465	0.613000	0.37349	1.072000	0.30678	1.365000	0.46057	0.563000	0.77884	GCC		0.701	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1		NM_016651	
EMG1	10436	hgsc.bcm.edu	37	12	7080210	7080211	+	Splice_Site	INS	-	-	G	rs60117710|rs374779752|rs200041551		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr12:7080210_7080211insG	ENST00000261406.6	+	2	266		c.e2-1		PHB2_ENST00000546111.1_5'Flank|PHB2_ENST00000544134.1_5'Flank|PHB2_ENST00000440277.1_5'Flank|PHB2_ENST00000535923.1_5'Flank|PHB2_ENST00000399433.2_5'Flank|PHB2_ENST00000542912.1_5'Flank|EMG1_ENST00000546220.1_3'UTR	NM_006331.7	NP_006322.4			EMG1 N1-specific pseudouridine methyltransferase																		CGGAGGCCGTAGTTTATTGTGG	0.569													GG|G|GG|deletion	5008	1.0	1.0	1.0	5008	,	,		18008	1.0		1.0	False		,,,				2504	1.0																0										3732,16		1865,2,7						3.0	1.0		dbSNP_129	28	7880,30		3934,12,9	no	frameshift	EMG1	NM_006331.7		5799,14,16	A1A1,A1R,RR		0.3793,0.4269,0.3946				11612,46				SO:0001630	splice_region_variant	10436			U72514	CCDS73430.1	12p13	2013-05-22	2013-05-22			ENSG00000126749			16912	protein-coding gene	gene with protein product		611531	"""EMG1 nucleolar protein homolog (S. cerevisiae)"""			9074930, 11935223, 19463982	Standard	NM_006331		Approved	C2F, NEP1, Grcc2f	uc001qsh.4	Q92979		ENST00000261406.6:c.124-1->G	12.37:g.7080211_7080211dupG		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000261406.6	37																																																																																					0.569	EMG1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_006331	Intron
FCGBP	8857	broad.mit.edu;hgsc.bcm.edu	37	19	40420153	40420153	+	Silent	SNP	G	G	C			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr19:40420153G>C	ENST00000221347.6	-	6	2848	c.2841C>G	c.(2839-2841)gtC>gtG	p.V947V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	947	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.V947V(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GATACTGAAGGACGTCATCCA	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											37.0	35.0	36.0					19																	40420153		2203	4299	6502	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.2841C>G	19.37:g.40420153G>C		Somatic		WXS	Illumina HiSeq	Phase_I	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1		NM_003890	
FZD10	11211	broad.mit.edu;hgsc.bcm.edu	37	12	130648146	130648146	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr12:130648146G>A	ENST00000229030.4	+	1	1143	c.659G>A	c.(658-660)aGc>aAc	p.S220N	FZD10_ENST00000539839.1_Silent_p.E187E|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	220					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S220N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		GTGTACTGGAGCCGCGAGGAC	0.692																																																	1	Substitution - Missense(1)	kidney(1)											58.0	47.0	51.0					12																	130648146		2203	4300	6503	SO:0001583	missense	11211			AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.659G>A	12.37:g.130648146G>A	ENSP00000229030:p.Ser220Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835963	0.71373	.	.	ENSG00000111432	ENST00000229030	D	0.82803	-1.65	5.26	3.44	0.39384	.	0.050614	0.85682	U	0.000000	T	0.81597	0.4856	M	0.64404	1.975	0.52099	D	0.999941	B	0.24092	0.097	B	0.32342	0.144	T	0.77935	-0.2401	10	0.62326	D	0.03	.	11.7902	0.52065	0.1421:0.0:0.8579:0.0	.	220	Q9ULW2	FZD10_HUMAN	N	220	ENSP00000229030:S220N	ENSP00000229030:S220N	S	+	2	0	FZD10	129214099	1.000000	0.71417	0.962000	0.40283	0.997000	0.91878	7.845000	0.86875	0.601000	0.29879	0.561000	0.74099	AGC		0.692	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
GRID2	2895	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	94693413	94693413	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr4:94693413A>T	ENST00000282020.4	+	16	3046	c.2788A>T	c.(2788-2790)Aca>Tca	p.T930S	GRID2_ENST00000510992.1_Missense_Mutation_p.T835S	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	930	Interaction with AP4M1. {ECO:0000250}.				cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.T930S(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TATTACCACAACAACCTTTAT	0.483																																																	1	Substitution - Missense(1)	kidney(1)											146.0	137.0	140.0					4																	94693413		2203	4300	6503	SO:0001583	missense	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2788A>T	4.37:g.94693413A>T	ENSP00000282020:p.Thr930Ser	Somatic		WXS	Illumina HiSeq	Phase_I	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.877890	0.33162	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.15256	2.5;2.44	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.23330	0.0564	N	0.20986	0.625	0.80722	D	1	P;P	0.52842	0.956;0.956	P;P	0.62184	0.899;0.899	T	0.04551	-1.0943	10	0.10636	T	0.68	.	15.4652	0.75394	1.0:0.0:0.0:0.0	.	835;930	E9PH24;O43424	.;GRID2_HUMAN	S	930;835	ENSP00000282020:T930S;ENSP00000421257:T835S	ENSP00000282020:T930S	T	+	1	0	GRID2	94912436	1.000000	0.71417	0.958000	0.39756	0.995000	0.86356	8.918000	0.92759	2.047000	0.60756	0.528000	0.53228	ACA		0.483	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			
IKBKAP	8518	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	111659236	111659236	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr9:111659236G>A	ENST00000374647.5	-	24	2891	c.2584C>T	c.(2584-2586)Caa>Taa	p.Q862*	IKBKAP_ENST00000537196.1_Nonsense_Mutation_p.Q513*	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	862					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)	p.Q862*(1)		NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TCTCTACCTTGAAGCTCGTGT	0.443																																																	1	Substitution - Nonsense(1)	kidney(1)											114.0	111.0	112.0					9																	111659236		2203	4300	6503	SO:0001587	stop_gained	8518			AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2584C>T	9.37:g.111659236G>A	ENSP00000363779:p.Gln862*	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JSV2|Q9H327|Q9UG87	Nonsense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	G	41	8.962568	0.99018	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	.	.	.	5.59	5.59	0.84812	.	0.083020	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0846	0.53690	0.0:0.0:0.8282:0.1718	.	.	.	.	X	862;513	.	ENSP00000363779:Q862X	Q	-	1	0	IKBKAP	110699057	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.719000	0.54926	2.625000	0.88918	0.467000	0.42956	CAA		0.443	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			
INPP5B	3633	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	38343913	38343913	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr1:38343913T>C	ENST00000373026.1	-	15	1864	c.1864A>G	c.(1864-1866)Atg>Gtg	p.M622V	INPP5B_ENST00000373027.1_Missense_Mutation_p.M378V|INPP5B_ENST00000458109.2_3'UTR|INPP5B_ENST00000373024.3_Missense_Mutation_p.M542V|INPP5B_ENST00000373023.2_Missense_Mutation_p.M622V			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	622	5-phosphatase. {ECO:0000250}.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)	p.M622V(1)		breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TTCAGGGCCATGTGGCTCTGG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											100.0	103.0	102.0					1																	38343913		2059	4209	6268	SO:0001583	missense	3633			M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.1864A>G	1.37:g.38343913T>C	ENSP00000362117:p.Met622Val	Somatic		WXS	Illumina HiSeq	Phase_I	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	T	19.37	3.814690	0.70912	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	5.43	5.43	0.79202	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.96056	0.8715	M	0.77103	2.36	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.843	D	0.94674	0.7859	10	0.21540	T	0.41	.	12.068	0.53598	0.0:0.0:0.1437:0.8563	.	622;542	P32019;P32019-2	I5P2_HUMAN;.	V	378;622;622;622;542	ENSP00000362118:M378V;ENSP00000362114:M622V;ENSP00000362117:M622V;ENSP00000362115:M542V	ENSP00000362114:M622V	M	-	1	0	INPP5B	38116500	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.827000	0.69300	2.078000	0.62432	0.460000	0.39030	ATG		0.527	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1		NM_005540	
MICALCL	84953	broad.mit.edu;ucsc.edu	37	11	12316166	12316166	+	Silent	SNP	T	T	G			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr11:12316166T>G	ENST00000256186.2	+	3	1479	c.1188T>G	c.(1186-1188)ctT>ctG	p.L396L		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	396					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.L396L(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		GAATCTCACTTTTTTCCTCCC	0.458																																																	1	Substitution - coding silent(1)	kidney(1)											124.0	127.0	126.0					11																	12316166		1858	4102	5960	SO:0001819	synonymous_variant	84953			BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1188T>G	11.37:g.12316166T>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																				0.458	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1		NM_032867	
KDM4D	55693	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	94731985	94731985	+	Silent	SNP	T	T	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr11:94731985T>A	ENST00000335080.5	+	3	2281	c.1449T>A	c.(1447-1449)gcT>gcA	p.A483A	KDM4D_ENST00000536741.1_Silent_p.A483A	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	483					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.A483A(1)		endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CATGCACAGCTTCGGGCCCAG	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											31.0	34.0	33.0					11																	94731985		2201	4298	6499	SO:0001819	synonymous_variant	55693			AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"""Chromatin-modifying enzymes / K-demethylases"""	25498	protein-coding gene	gene with protein product		609766	"""jumonji domain containing 2D"""	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.1449T>A	11.37:g.94731985T>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Silent	SNP	ENST00000335080.5	37	CCDS8302.1																																																																																				0.617	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2		NM_018039	
NMT2	9397	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	15151770	15151770	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr10:15151770A>T	ENST00000378165.4	-	11	1487	c.1407T>A	c.(1405-1407)ttT>ttA	p.F469L	NMT2_ENST00000466201.1_5'UTR|NMT2_ENST00000535341.1_Missense_Mutation_p.F456L|NMT2_ENST00000378150.1_Missense_Mutation_p.F456L|NMT2_ENST00000540259.1_Missense_Mutation_p.F281L|RPP38_ENST00000451677.1_Intron	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	469					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)	p.F469L(1)		breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						CTCCTATACCAAACTTGAGTT	0.328																																					Melanoma(117;1345 1645 4130 12688 30625)												1	Substitution - Missense(1)	kidney(1)											128.0	126.0	126.0					10																	15151770		2203	4299	6502	SO:0001583	missense	9397			AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.1407T>A	10.37:g.15151770A>T	ENSP00000367407:p.Phe469Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.423211	0.83559	.	.	ENSG00000152465	ENST00000441445;ENST00000378165;ENST00000378150;ENST00000378143;ENST00000540259;ENST00000535341	T	0.66460	-0.21	5.51	5.51	0.81932	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, conserved site (1);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87585	0.6214	H	0.96142	3.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91538	0.5247	10	0.87932	D	0	-22.7366	15.925	0.79609	1.0:0.0:0.0:0.0	.	456;469	Q5VUC6;O60551	.;NMT2_HUMAN	L	33;469;456;500;281;456	ENSP00000367407:F469L	ENSP00000367385:F500L	F	-	3	2	NMT2	15191776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.817000	0.55668	2.225000	0.72522	0.533000	0.62120	TTT		0.328	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2		NM_004808	
NUP50	10762	broad.mit.edu;hgsc.bcm.edu	37	22	45574718	45574718	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr22:45574718T>G	ENST00000347635.4	+	5	1406	c.940T>G	c.(940-942)Tct>Gct	p.S314A	NUP50_ENST00000425733.2_Missense_Mutation_p.S64A|NUP50_ENST00000407019.2_Missense_Mutation_p.S286A|NUP50_ENST00000396096.2_Missense_Mutation_p.S286A|CTA-268H5.12_ENST00000610217.1_RNA	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	314	Ser-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S314A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TAAACCAGTCTCTTCACCATT	0.463																																																	1	Substitution - Missense(1)	kidney(1)											54.0	51.0	52.0					22																	45574718		2200	4296	6496	SO:0001583	missense	10762			AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"""nucleoporin 50kD"""	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.940T>G	22.37:g.45574718T>G	ENSP00000345895:p.Ser314Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Missense_Mutation	SNP	ENST00000347635.4	37	CCDS14062.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.814949	0.32053	.	.	ENSG00000093000	ENST00000347635;ENST00000407019;ENST00000425733;ENST00000396096	.	.	.	5.26	-2.78	0.05859	.	0.886299	0.09866	N	0.745537	T	0.28101	0.0693	L	0.60455	1.87	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.34428	-0.9829	9	0.15952	T	0.53	-2.3389	0.4935	0.00567	0.237:0.2802:0.2209:0.2619	.	64;314	B4E2D3;Q9UKX7	.;NUP50_HUMAN	A	314;286;64;286	.	ENSP00000345895:S314A	S	+	1	0	NUP50	43953382	0.000000	0.05858	0.000000	0.03702	0.476000	0.33039	-0.592000	0.05747	-0.915000	0.03823	0.533000	0.62120	TCT		0.463	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52610643	52610643	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr3:52610643G>T	ENST00000296302.7	-	22	3606	c.3605C>A	c.(3604-3606)aCa>aAa	p.T1202K	PBRM1_ENST00000409767.1_Missense_Mutation_p.T1217K|PBRM1_ENST00000410007.1_Missense_Mutation_p.T1177K|PBRM1_ENST00000409057.1_Missense_Mutation_p.T1202K|PBRM1_ENST00000356770.4_Missense_Mutation_p.T1170K|PBRM1_ENST00000409114.3_Missense_Mutation_p.T1217K|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000337303.4_Missense_Mutation_p.T1202K|PBRM1_ENST00000394830.3_Missense_Mutation_p.T1177K			Q86U86	PB1_HUMAN	polybromo 1	1202	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.T1202K(2)|p.T1170K(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)		CTCATGCTCTGTTTCTTCTGG	0.383			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Missense(3)	kidney(3)											120.0	116.0	118.0					3																	52610643		2203	4300	6503	SO:0001583	missense	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.3605C>A	3.37:g.52610643G>T	ENSP00000296302:p.Thr1202Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	29.7	5.024274	0.93462	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	D;D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	5.62	5.62	0.85841	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	D	0.95201	0.8444	M	0.90977	3.165	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.996;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.997;0.99;0.996;0.994;0.998;1.0;0.996;0.996	D	0.95533	0.8605	10	0.66056	D	0.02	.	19.6678	0.95900	0.0:0.0:1.0:0.0	.	1177;1177;1202;1217;1217;1202;1170;1202	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	K	1170;1177;1202;1202;1202;1177;1217;1217;1201	ENSP00000349213:T1170K;ENSP00000378307:T1177K;ENSP00000296302:T1202K;ENSP00000338302:T1202K;ENSP00000386593:T1202K;ENSP00000386529:T1177K;ENSP00000386643:T1217K;ENSP00000386601:T1217K;ENSP00000387775:T1201K	ENSP00000296302:T1202K	T	-	2	0	PBRM1	52585683	1.000000	0.71417	0.976000	0.42696	0.972000	0.66771	9.796000	0.99103	2.659000	0.90383	0.585000	0.79938	ACA		0.383	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PIWIL2	55124	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	22167480	22167480	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr8:22167480G>A	ENST00000454009.2	+	15	2202	c.1693G>A	c.(1693-1695)Gga>Aga	p.G565R	PIWIL2_ENST00000521356.1_Missense_Mutation_p.G565R|PIWIL2_ENST00000356766.6_Missense_Mutation_p.G565R	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	565					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.G565R(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		TTAGATTGAAGGACGTGTTCT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											118.0	119.0	119.0					8																	22167480		2203	4300	6503	SO:0001583	missense	55124			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"""Argonaute/PIWI family"""	17644	protein-coding gene	gene with protein product	"""Hiwi-like"", ""cancer/testis antigen 80"""	610312	"""piwi-like 2 (Drosophila)"""			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.1693G>A	8.37:g.22167480G>A	ENSP00000406956:p.Gly565Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.606076	0.87157	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.07216	3.21;3.21;3.21	6.03	6.03	0.97812	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.31199	0.0789	M	0.81341	2.54	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.64506	0.926;0.926	T	0.00780	-1.1569	10	0.87932	D	0	6.0E-4	17.4736	0.87653	0.0:0.0:1.0:0.0	.	565;565	E7ECA4;Q8TC59	.;PIWL2_HUMAN	R	565	ENSP00000349208:G565R;ENSP00000428267:G565R;ENSP00000406956:G565R	ENSP00000349208:G565R	G	+	1	0	PIWIL2	22223425	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.267000	0.78462	2.861000	0.98227	0.655000	0.94253	GGA		0.388	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1			
PLEKHH2	130271	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	43934682	43934682	+	Missense_Mutation	SNP	G	G	A	rs200629095		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr2:43934682G>A	ENST00000282406.4	+	11	2074	c.1964G>A	c.(1963-1965)cGa>cAa	p.R655Q		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	655	Ser-rich.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)	p.R655Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCCATGAAACGAGGTGAGGGA	0.478																																																	1	Substitution - Missense(1)	kidney(1)						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	54.0	58.0	56.0		1964	4.7	1.0	2		56	0,8600		0,0,4300	no	missense	PLEKHH2	NM_172069.3	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	655/1494	43934682	1,13005	2203	4300	6503	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.1964G>A	2.37:g.43934682G>A	ENSP00000282406:p.Arg655Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	33	5.260171	0.95368	2.27E-4	0.0	ENSG00000152527	ENST00000282406	T	0.13778	2.56	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000001	T	0.31199	0.0789	L	0.43923	1.385	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.999;0.986;0.999	T	0.02431	-1.1160	10	0.56958	D	0.05	-6.1912	17.7253	0.88363	0.0:0.0:1.0:0.0	.	655;92;655	Q8IVE3;Q8IVE3-2;Q8IVE3-3	PKHH2_HUMAN;.;.	Q	655	ENSP00000282406:R655Q	ENSP00000282406:R655Q	R	+	2	0	PLEKHH2	43788186	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.526000	0.90588	2.430000	0.82344	0.460000	0.39030	CGA		0.478	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1		NM_172069	
PRG4	10216	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	186278973	186278973	+	Nonsense_Mutation	SNP	T	T	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr1:186278973T>A	ENST00000445192.2	+	8	3515	c.3470T>A	c.(3469-3471)tTg>tAg	p.L1157*	RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Nonsense_Mutation_p.L1116*|PRG4_ENST00000367485.4_Nonsense_Mutation_p.L1064*|PRG4_ENST00000367486.3_Nonsense_Mutation_p.L1114*|PRG4_ENST00000367484.3_Nonsense_Mutation_p.L686*	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1157					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.L1157*(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTGACTACTTTGCGCAATGGG	0.358																																																	1	Substitution - Nonsense(1)	kidney(1)											209.0	189.0	196.0					1																	186278973		2203	4300	6503	SO:0001587	stop_gained	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3470T>A	1.37:g.186278973T>A	ENSP00000399679:p.Leu1157*	Somatic		WXS	Illumina HiSeq	Phase_I	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Nonsense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	T	38	7.100329	0.98063	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	.	.	.	4.69	4.69	0.59074	.	0.000000	0.35040	U	0.003493	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.8862	13.9049	0.63828	0.0:0.0:0.0:1.0	.	.	.	.	X	1114;686;1116;1064;1157	.	ENSP00000356453:L1116X	L	+	2	0	PRG4	184545596	1.000000	0.71417	0.800000	0.32199	0.334000	0.28698	6.349000	0.73013	1.772000	0.52199	0.524000	0.50904	TTG		0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1		NM_005807	
RIN2	54453	hgsc.bcm.edu;ucsc.edu	37	20	19955468	19955468	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr20:19955468G>T	ENST00000255006.6	+	8	1095	c.946G>T	c.(946-948)Ggg>Tgg	p.G316W	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	267					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)	p.G316W(1)|p.G267W(1)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CCAGACCAACGGGGCCCTGTG	0.557																																																	2	Substitution - Missense(2)	kidney(2)											65.0	71.0	69.0					20																	19955468		1935	4114	6049	SO:0001583	missense	54453			AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.946G>T	20.37:g.19955468G>T	ENSP00000255006:p.Gly316Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711051	0.68730	.	.	ENSG00000132669	ENST00000255006	T	0.27402	1.67	5.44	4.48	0.54585	.	0.173050	0.50627	D	0.000109	T	0.54743	0.1877	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.56872	-0.7907	9	.	.	.	-5.6604	15.7583	0.78054	0.0:0.1372:0.8628:0.0	.	267	Q8WYP3	RIN2_HUMAN	W	316	ENSP00000255006:G316W	.	G	+	1	0	RIN2	19903468	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.762000	0.85270	1.267000	0.44247	0.655000	0.94253	GGG		0.557	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			
SIX1	6495	hgsc.bcm.edu	37	14	61113204	61113204	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr14:61113204C>T	ENST00000247182.6	-	2	924	c.652G>A	c.(652-654)Gag>Aag	p.E218K	SIX1_ENST00000554986.1_Missense_Mutation_p.E45K	NM_005982.3	NP_005973.1	Q15475	SIX1_HUMAN	SIX homeobox 1	218					aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|branching involved in ureteric bud morphogenesis (GO:0001658)|cochlea morphogenesis (GO:0090103)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial cell differentiation (GO:0030855)|facial nerve morphogenesis (GO:0021610)|generation of neurons (GO:0048699)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesonephric tubule formation (GO:0072172)|metanephric mesenchyme development (GO:0072075)|middle ear morphogenesis (GO:0042474)|myoblast migration (GO:0051451)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|organ induction (GO:0001759)|otic vesicle development (GO:0071599)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|protein localization to nucleus (GO:0034504)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of neuron differentiation (GO:0045664)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		GAGAATTCCTCTTCTGAGCTG	0.532																																																	0													105.0	93.0	97.0					14																	61113204		2203	4300	6503	SO:0001583	missense	6495			X91868	CCDS9748.1	14q23.1	2011-06-20	2007-07-13		ENSG00000126778	ENSG00000126778		"""Homeoboxes / SINE class"""	10887	protein-coding gene	gene with protein product		601205	"""sine oculis homeobox (Drosophila) homolog 1"", ""sine oculis homeobox homolog 1 (Drosophila)"", ""deafness, autosomal dominant 23"""	DFNA23		8617500, 15141091	Standard	NM_005982		Approved		uc001xfb.4	Q15475	OTTHUMG00000140334	ENST00000247182.6:c.652G>A	14.37:g.61113204C>T	ENSP00000247182:p.Glu218Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q53Y16|Q96H64	Missense_Mutation	SNP	ENST00000247182.6	37	CCDS9748.1	.	.	.	.	.	.	.	.	.	.	C	36	5.762504	0.96906	.	.	ENSG00000126778	ENST00000247182;ENST00000555955;ENST00000553535	D;D;D	0.87334	-2.18;-2.24;-2.24	5.19	5.19	0.71726	.	0.047554	0.85682	D	0.000000	T	0.78748	0.4332	N	0.19112	0.55	0.58432	D	0.999998	B	0.20887	0.049	B	0.16289	0.015	T	0.72984	-0.4125	10	0.12430	T	0.62	-15.8859	18.9138	0.92496	0.0:1.0:0.0:0.0	.	218	Q15475	SIX1_HUMAN	K	218;34;34	ENSP00000247182:E218K;ENSP00000450952:E34K;ENSP00000450739:E34K	ENSP00000247182:E218K	E	-	1	0	SIX1	60182957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.320000	0.79064	2.695000	0.91970	0.655000	0.94253	GAG		0.532	SIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276951.3			
SLC10A3	8273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	153716013	153716013	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chrX:153716013C>G	ENST00000393587.4	-	3	1530	c.1267G>C	c.(1267-1269)Gtg>Ctg	p.V423L	UBL4A_ENST00000477777.1_5'Flank|SLC10A3_ENST00000263512.4_Missense_Mutation_p.V423L|UBL4A_ENST00000369653.4_5'Flank|UBL4A_ENST00000369660.4_5'Flank|SLC10A3_ENST00000369649.4_Missense_Mutation_p.V394L|SLC10A3_ENST00000393586.1_Missense_Mutation_p.V478L	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	423					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)	p.V423L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGTTCTGCACCCCTACCTCA	0.642																																																	1	Substitution - Missense(1)	kidney(1)											57.0	47.0	50.0					X																	153716013		2203	4300	6503	SO:0001583	missense	8273			X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"""Solute carriers"""	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.1267G>C	X.37:g.153716013C>G	ENSP00000377212:p.Val423Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5HY79|Q9BSL2	Missense_Mutation	SNP	ENST00000393587.4	37	CCDS14755.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.118243	0.56505	.	.	ENSG00000126903	ENST00000369649;ENST00000393586;ENST00000263512;ENST00000393587	T;T;T;T	0.08720	3.15;3.06;3.08;3.08	5.4	4.53	0.55603	.	0.085351	0.46442	U	0.000293	T	0.06735	0.0172	N	0.16037	0.36	0.47905	D	0.99954	P;P	0.45672	0.864;0.776	B;B	0.42851	0.4;0.4	T	0.33394	-0.9870	10	0.59425	D	0.04	-7.4072	12.5398	0.56163	0.0:0.9136:0.0:0.0864	.	394;423	Q9BSL2;P09131	.;P3_HUMAN	L	394;478;423;423	ENSP00000358663:V394L;ENSP00000377211:V478L;ENSP00000263512:V423L;ENSP00000377212:V423L	ENSP00000263512:V423L	V	-	1	0	SLC10A3	153369207	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.209000	0.51122	2.244000	0.73946	0.513000	0.50165	GTG		0.642	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3		NM_019848	
SLC1A5	6510	broad.mit.edu;hgsc.bcm.edu	37	19	47285647	47285647	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr19:47285647T>C	ENST00000542575.2	-	4	1445	c.817A>G	c.(817-819)Atc>Gtc	p.I273V	SLC1A5_ENST00000434726.2_Missense_Mutation_p.I71V|SLC1A5_ENST00000594991.1_Missense_Mutation_p.I97V|SLC1A5_ENST00000412532.2_Missense_Mutation_p.I45V	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	273					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)	p.I273V(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	TACCACATGATCCAGGAGACC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											68.0	64.0	65.0					19																	47285647		2203	4300	6503	SO:0001583	missense	6510			U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.817A>G	19.37:g.47285647T>C	ENSP00000444408:p.Ile273Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Missense_Mutation	SNP	ENST00000542575.2	37	CCDS12692.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527848	0.44969	.	.	ENSG00000105281	ENST00000542575;ENST00000434726;ENST00000412532;ENST00000306894	T;T;T	0.55234	0.53;0.53;0.53	5.23	5.23	0.72850	.	0.107037	0.64402	D	0.000007	T	0.41719	0.1171	L	0.31294	0.92	0.53005	D	0.999967	P;B;B	0.35982	0.531;0.139;0.139	B;B;B	0.34931	0.192;0.122;0.122	T	0.37888	-0.9686	10	0.41790	T	0.15	-22.8124	14.163	0.65459	0.0:0.0:0.0:1.0	.	71;273;273	E9PC01;Q15758;Q71UA6	.;AAAT_HUMAN;.	V	273;71;45;280	ENSP00000444408:I273V;ENSP00000406532:I71V;ENSP00000397924:I45V	ENSP00000303623:I280V	I	-	1	0	SLC1A5	51977487	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.960000	0.87893	1.996000	0.58369	0.456000	0.33151	ATC		0.622	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1			
SPARCL1	8404	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	88394938	88394938	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr4:88394938G>C	ENST00000282470.6	-	11	2454	c.1984C>G	c.(1984-1986)Ctc>Gtc	p.L662V	SPARCL1_ENST00000503414.1_Missense_Mutation_p.L537V|SPARCL1_ENST00000418378.1_Missense_Mutation_p.L662V	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	662					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.L662V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		CAAAACAAGAGATTTTCATCT	0.343																																																	1	Substitution - Missense(1)	kidney(1)											94.0	102.0	99.0					4																	88394938		2203	4300	6503	SO:0001583	missense	8404			X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1984C>G	4.37:g.88394938G>C	ENSP00000282470:p.Leu662Val	Somatic		WXS	Illumina HiSeq	Phase_I	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784142	0.70222	.	.	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	T;T;T	0.34859	1.89;1.89;1.34	4.86	4.86	0.63082	EF-hand-like domain (1);	0.078077	0.49305	D	0.000151	T	0.58148	0.2102	M	0.73962	2.25	0.40257	D	0.978138	D	0.69078	0.997	D	0.64237	0.923	T	0.63673	-0.6584	10	0.72032	D	0.01	-9.6608	15.5793	0.76422	0.0:0.0:1.0:0.0	.	662	Q14515	SPRL1_HUMAN	V	662;662;537;537	ENSP00000282470:L662V;ENSP00000414856:L662V;ENSP00000422903:L537V	ENSP00000282470:L662V	L	-	1	0	SPARCL1	88613962	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.493000	0.66899	2.619000	0.88677	0.655000	0.94253	CTC		0.343	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2			
SSPO	23145	broad.mit.edu;hgsc.bcm.edu	37	7	149486417	149486417	+	RNA	SNP	C	C	G			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr7:149486417C>G	ENST00000378016.2	+	0	4393							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGGACGCTGCCTGCCGCCGGC	0.677																																																	0													21.0	24.0	23.0					7																	149486417		2198	4293	6491			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486417C>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				
ST14	6768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	130066577	130066577	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr11:130066577T>A	ENST00000278742.5	+	11	1754	c.1336T>A	c.(1336-1338)Tcc>Acc	p.S446T		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	446	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S446T(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	TGAATACCTCTCCTACGACTC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											119.0	106.0	110.0					11																	130066577		2201	4297	6498	SO:0001583	missense	6768			AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1336T>A	11.37:g.130066577T>A	ENSP00000278742:p.Ser446Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.819098	0.50633	.	.	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.20332	2.08	5.04	5.04	0.67666	CUB (3);	0.000000	0.37715	N	0.001968	T	0.28234	0.0697	L	0.55990	1.75	0.50813	D	0.999898	P;P	0.52316	0.952;0.745	P;B	0.49477	0.612;0.231	T	0.02942	-1.1091	10	0.20046	T	0.44	.	14.4616	0.67453	0.0:0.0:0.0:1.0	.	256;446	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	T	446;348	ENSP00000278742:S446T	ENSP00000278742:S446T	S	+	1	0	ST14	129571787	1.000000	0.71417	0.937000	0.37676	0.574000	0.36063	2.871000	0.48459	1.896000	0.54893	0.459000	0.35465	TCC		0.562	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			
USP51	158880	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	55513238	55513238	+	Nonstop_Mutation	SNP	T	T	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chrX:55513238T>A	ENST00000500968.3	-	2	2217	c.2135A>T	c.(2134-2136)tAg>tTg	p.*712L	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	0					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.*712L(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CTGGTAAGACTAGTCTTTCTC	0.403																																																	1	Nonstop extension(1)	kidney(1)											60.0	50.0	53.0					X																	55513238		2203	4300	6503	SO:0001578	stop_lost	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.2135A>T	X.37:g.55513238T>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	9.036	0.988535	0.18966	.	.	ENSG00000247746	ENST00000500968	.	.	.	2.88	2.88	0.33553	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6549	0.34058	0.0:0.0:0.0:1.0	.	.	.	.	L	712	.	.	X	-	2	0	USP51	55529963	1.000000	0.71417	0.812000	0.32479	0.947000	0.59692	2.609000	0.46317	1.387000	0.46486	0.408000	0.27601	TAG		0.403	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2		NM_201286	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188320	10188324	+	Splice_Site	DEL	GGTAC	GGTAC	-	rs5030814|rs397516443	byFrequency	TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	GGTAC	GGTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr3:10188320_10188324delGGTAC	ENST00000256474.2	+	2	1303	c.463delGGTAC	c.(463-465)ggt>gt	p.G155fs	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	155	Involved in binding to CCT complex.		V -> G (in VHLD; type II). {ECO:0000269|Ref.41}.|V -> M (in VHLD; with RCC).		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.?(26)|p.V155L(6)|p.V155M(3)|p.V155fs*4(3)|p.L153fs*4(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)		CACACTGCCAGGTACTGACGTTTTA	0.41		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"""	39	Unknown(26)|Substitution - Missense(9)|Deletion - Frameshift(4)	kidney(38)|endometrium(1)	GRCh37	CM023999|CS003080|CS004297|CS951541|CS961707|CS961708	VHL	M|S	rs5030814|rs5030815																																			SO:0001630	splice_region_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.463+1GGTAC>-	3.37:g.10188320_10188324delGGTAC		Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.410	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	Frame_Shift_Del
ZFP37	7539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	115818875	115818875	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr9:115818875G>T	ENST00000374227.3	-	1	121	c.94C>A	c.(94-96)Ctg>Atg	p.L32M	ZFP37_ENST00000553380.1_Missense_Mutation_p.L32M|ZFP37_ENST00000555206.1_Missense_Mutation_p.L32M	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)	p.L32M(1)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						GCCATCTCCAGTGGTCGCCCG	0.632																																																	1	Substitution - Missense(1)	kidney(1)											155.0	161.0	159.0					9																	115818875		2203	4300	6503	SO:0001583	missense	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"""Zinc fingers, C2H2-type"", ""-"""	12863	protein-coding gene	gene with protein product		602951	"""zinc finger protein homologous to Zfp37 in mouse"", ""zinc finger protein 37 homolog (mouse)"""				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.94C>A	9.37:g.115818875G>T	ENSP00000363344:p.Leu32Met	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Missense_Mutation	SNP	ENST00000374227.3	37	CCDS6787.1	.	.	.	.	.	.	.	.	.	.	g	13.68	2.310440	0.40895	.	.	ENSG00000136866	ENST00000374227;ENST00000555206;ENST00000553380	T;T;T	0.05925	3.39;3.37;3.49	3.29	-2.3	0.06785	Krueppel-associated box (2);	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	P;P;B	0.36249	0.545;0.545;0.41	B;B;B	0.38755	0.281;0.281;0.146	T	0.37314	-0.9711	9	0.48119	T	0.1	33.741	1.9329	0.03331	0.1074:0.3336:0.2517:0.3073	.	32;32;32	G3V3L7;Q9Y6Q3-2;Q9Y6Q3	.;.;ZFP37_HUMAN	M	32	ENSP00000363344:L32M;ENSP00000451310:L32M;ENSP00000452552:L32M	ENSP00000363344:L32M	L	-	1	2	ZFP37	114858696	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.795000	0.04580	-0.537000	0.06290	-0.260000	0.10688	CTG		0.632	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1		NM_003408	
ZMYND8	23613	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	45853096	45853096	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr20:45853096T>C	ENST00000311275.7	-	19	3323	c.3070A>G	c.(3070-3072)Aag>Gag	p.K1024E	ZMYND8_ENST00000372023.3_Missense_Mutation_p.K946E|ZMYND8_ENST00000352431.2_Missense_Mutation_p.K998E|ZMYND8_ENST00000458360.2_Missense_Mutation_p.K892E|ZMYND8_ENST00000540497.1_Missense_Mutation_p.K972E|ZMYND8_ENST00000360911.3_Missense_Mutation_p.K973E|ZMYND8_ENST00000536340.1_Missense_Mutation_p.K1051E|ZMYND8_ENST00000471951.2_Missense_Mutation_p.K1044E|ZMYND8_ENST00000446994.2_Missense_Mutation_p.K915E|ZMYND8_ENST00000262975.4_Missense_Mutation_p.K978E|ZMYND8_ENST00000396281.4_Missense_Mutation_p.K1024E|ZMYND8_ENST00000461685.1_Missense_Mutation_p.K998E|ZMYND8_ENST00000355972.4_Missense_Mutation_p.K1024E	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	1024					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.K998E(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			CACTGCTTCTTCTTGGTCTCA	0.592																																																	1	Substitution - Missense(1)	kidney(1)											237.0	192.0	207.0					20																	45853096		2203	4300	6503	SO:0001583	missense	23613			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.3070A>G	20.37:g.45853096T>C	ENSP00000312237:p.Lys1024Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.1|28.1	4.888097|4.888097	0.91814|0.91814	.|.	.|.	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.57436	.|0.52;0.52;0.52;0.4;0.4;0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.73329|0.73329	0.3573|0.3573	M|M	0.78637|0.78637	2.42|2.42	0.53005|0.53005	D|D	0.999966|0.999966	.|D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D	.|0.76494	.|0.997;0.999;0.997;0.998;0.999;0.998;0.999;0.998;0.998;0.997;0.997;0.997;0.892;0.987;0.998;0.997	.|D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D	.|0.87578	.|0.985;0.998;0.995;0.991;0.998;0.998;0.996;0.996;0.998;0.995;0.995;0.995;0.613;0.97;0.991;0.995	T|T	0.77286|0.77286	-0.2644|-0.2644	5|10	.|0.72032	.|D	.|0.01	-14.8364|-14.8364	15.543|15.543	0.76070|0.76070	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|892;1051;946;953;1044;978;973;998;998;1024;915;973;972;917;926;1024	.|B7ZM62;F5H0X3;Q2HXV3;Q5TH11;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	G|E	905|973;1024;892;979;1045;998;1024;1051;1024;915;998;946;972	.|ENSP00000354166:K973E;ENSP00000312237:K1024E;ENSP00000392964:K892E;ENSP00000262975:K979E;ENSP00000420095:K1045E;ENSP00000335537:K998E;ENSP00000379577:K1024E;ENSP00000439800:K1051E;ENSP00000348246:K1024E;ENSP00000396725:K915E;ENSP00000418210:K998E;ENSP00000361093:K946E;ENSP00000443086:K972E	.|ENSP00000262975:K979E	E|K	-|-	2|1	0|0	ZMYND8|ZMYND8	45286503|45286503	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.988000|7.988000	0.88194|0.88194	2.060000|2.060000	0.61445|0.61445	0.533000|0.533000	0.62120|0.62120	GAA|AAG		0.592	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2		NM_183047	
FAM115C	285966	broad.mit.edu	37	7	143417404	143417405	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr7:143417404_143417405delCT	ENST00000441159.2	+	3	1318_1319	c.1252_1253delCT	c.(1252-1254)ctcfs	p.L418fs	FAM115C_ENST00000409703.3_Frame_Shift_Del_p.L254fs|FAM115C_ENST00000444908.2_Frame_Shift_Del_p.L418fs|FAM115C_ENST00000411497.2_Frame_Shift_Del_p.L137fs|FAM115C_ENST00000425618.2_Frame_Shift_Del_p.L137fs|FAM115C_ENST00000357344.4_Frame_Shift_Del_p.L418fs|FAM115C_ENST00000411935.1_Frame_Shift_Del_p.L254fs			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	418					hematopoietic progenitor cell differentiation (GO:0002244)					endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						CCGCAAGGCGCTCTCTCAATTC	0.53																																																	0									,,	39,207		18,3,102					,,	-7.1	0.0			1	22,442		10,2,220	no	frameshift,frameshift,frameshift	FAM115C	NM_173678.2,NM_001130026.2,NM_001130025.1	,,	28,5,322	A1A1,A1R,RR		4.7414,15.8537,8.5915	,,	,,		61,649				SO:0001589	frameshift_variant	285966			AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379			26878	protein-coding gene	gene with protein product			"""family with sequence similarity 139, member A"""	FAM139A			Standard	NM_173678		Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.1252_1253delCT	7.37:g.143417408_143417409delCT	ENSP00000404265:p.Leu418fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	Frame_Shift_Del	DEL	ENST00000441159.2	37																																																																																					0.530	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330287.1		NM_173678	
KRTAP4-9	100132386	broad.mit.edu	37	17	39261865	39261865	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr17:39261865C>A	ENST00000391415.1	+	1	282	c.225C>A	c.(223-225)tgC>tgA	p.C75*		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	75	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].		Missing (in allele KAP.9-v1).		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C75*(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						CCACCTGTTGCAGGACCACCT	0.647																																																	1	Substitution - Nonsense(1)	kidney(1)											18.0	26.0	24.0					17																	39261865		689	1590	2279	SO:0001587	stop_gained	100132386			AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.225C>A	17.37:g.39261865C>A	ENSP00000375234:p.Cys75*	Somatic		WXS	Illumina GAIIx	Phase_I		Nonsense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	17.06	3.293798	0.60086	.	.	ENSG00000212722	ENST00000391415;ENST00000333994	.	.	.	1.69	1.69	0.24217	.	0.000000	0.43579	U	0.000541	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4129	0.38503	0.0:1.0:0.0:0.0	.	.	.	.	X	75	.	ENSP00000334461:C75X	C	+	3	2	KRTAP4-9	36515391	0.042000	0.20092	0.003000	0.11579	0.584000	0.36387	0.202000	0.17295	1.265000	0.44215	0.306000	0.20318	TGC		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1		NM_001146041	
MAFA	389692	broad.mit.edu	37	8	144511954	144511956	+	In_Frame_Del	DEL	TGG	TGG	-	rs552049497|rs141816879		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr8:144511954_144511956delTGG	ENST00000333480.2	-	1	620_622	c.621_623delCCA	c.(619-624)caccat>cat	p.207_208HH>H	MAFA_ENST00000528185.1_5'UTR	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	207	His-rich.				insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H208delH(3)		breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			CGCGCCGCCAtggtggtggtggt	0.744										HNSCC(29;0.082)																																							3	Deletion - In frame(3)	upper_aerodigestive_tract(2)|breast(1)																																								SO:0001651	inframe_deletion	389692			AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.621_623delCCA	8.37:g.144511963_144511965delTGG	ENSP00000328364:p.His208del	Somatic		WXS	Illumina GAIIx	Phase_I		In_Frame_Del	DEL	ENST00000333480.2	37	CCDS34955.1																																																																																				0.744	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2		NM_201589	
Unknown	0	broad.mit.edu	37	1	16974224	16974224	+	IGR	SNP	C	C	G	rs368571421		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr1:16974224C>G								CROCCP2 (13170 upstream) : RNU1-3 (19055 downstream)																							TTGGTCCCAGCCCCAGAGGGA	0.652																																																	0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16974224C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.652									
MST1L	11223	broad.mit.edu	37	1	17086183	17086183	+	RNA	SNP	T	T	G	rs61769735	byFrequency	TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr1:17086183T>G	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.?(2)									CCTCGGACCCTTAGATGGACC	0.652																																																	2	Unknown(2)	kidney(2)																																										0			U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17086183T>G		Somatic		WXS	Illumina GAIIx	Phase_I	B7WPB1|Q13209	Splice_Site	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.643	0.487109	0.12641	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	rs61769735	.	.	.	.	-1	.	.	.	-	.	.	MST1P9	16958770	0.699000	0.27786	0.000000	0.03702	0.000000	0.00434	0.557000	0.23454	0.000000	0.14550	0.000000	0.15137	.		0.652	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1		NM_001271733	
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	RNA	SNP	G	G	A	rs201972834		TCGA-BP-5186-01A-01D-1429-08	TCGA-BP-5186-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	02b98f85-07df-4fb2-b27e-efd368c84ec8	f874ff04-d379-4de4-9a87-c04c045a70ca	g.chr15:102515299G>A	ENST00000557932.1	+	0	1145				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.G374S(10)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						TGGGGGCATCGGCAAGGCCAA	0.652																																																	10	Substitution - Missense(10)	kidney(7)|prostate(2)|endometrium(1)																																										374666					15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515299G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000557932.1	37		.	.	.	.	.	.	.	.	.	.	g	2.376	-0.343229	0.05243	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-23.1056	7.9382	0.29941	0.0:0.0:1.0:0.0	.	.	.	.	S	383;374	.	.	G	+	1	0	WASH3P	100332822	1.000000	0.71417	0.997000	0.53966	0.230000	0.25150	8.205000	0.89743	0.863000	0.35553	0.184000	0.17185	GGC		0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1		NM_199163	
