#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
ABCA12	26154	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	215880269	215880269	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr2:215880269T>C	ENST00000272895.7	-	15	2120	c.1901A>G	c.(1900-1902)tAc>tGc	p.Y634C	ABCA12_ENST00000389661.4_Missense_Mutation_p.Y316C	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	634					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.Y634C(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCGATGAGGTAAGACTGCCG	0.393																																					Ovarian(66;664 1488 5121 34295)												1	Substitution - Missense(1)	kidney(1)											104.0	99.0	101.0					2																	215880269		2203	4300	6503	SO:0001583	missense	26154			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1901A>G	2.37:g.215880269T>C	ENSP00000272895:p.Tyr634Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	17.91	3.504550	0.64410	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.92446	-3.04;-2.91	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000014	D	0.92977	0.7765	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.93980	0.7257	10	0.87932	D	0	.	14.4069	0.67088	0.0:0.0:0.0:1.0	.	634;316	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	C	634;316	ENSP00000272895:Y634C;ENSP00000374312:Y316C	ENSP00000272895:Y634C	Y	-	2	0	ABCA12	215588514	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	4.852000	0.62904	2.279000	0.76181	0.533000	0.62120	TAC		0.393	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1		NM_173076	
ACTN4	81	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	39216363	39216363	+	Splice_Site	SNP	G	G	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr19:39216363G>A	ENST00000252699.2	+	17	2086		c.e17-1		ACTN4_ENST00000390009.3_Splice_Site|ACTN4_ENST00000424234.2_Splice_Site	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4						actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.?(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CACCCCCGTAGGAGATCGGGC	0.657																																					Colon(168;199 1940 10254 46213 46384)												1	Unknown(1)	kidney(1)											46.0	38.0	41.0					19																	39216363		2203	4300	6503	SO:0001630	splice_region_variant	81			D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.2011-1G>A	19.37:g.39216363G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A4K467|D6PXK4|O76048	Splice_Site	SNP	ENST00000252699.2	37	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575153	0.45902	.	.	ENSG00000130402	ENST00000252699;ENST00000424234;ENST00000390009;ENST00000440400	.	.	.	3.76	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8788	0.70516	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACTN4	43908203	1.000000	0.71417	0.997000	0.53966	0.455000	0.32408	9.601000	0.98297	2.098000	0.63641	0.561000	0.74099	.		0.657	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			Intron
ALDOB	229	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	104187311	104187312	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr9:104187311_104187312insA	ENST00000374855.4	-	8	936_937	c.812_813insT	c.(811-813)ttgfs	p.L271fs	ALDOB_ENST00000468981.3_5'Flank	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	271					carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose catabolic process (GO:0006001)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|NADH oxidation (GO:0006116)|positive regulation of ATPase activity (GO:0032781)|small molecule metabolic process (GO:0044281)|vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072)	centriolar satellite (GO:0034451)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)	ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-1-phosphate aldolase activity (GO:0061609)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(5)|prostate(2)|skin(4)|urinary_tract(1)	24		Acute lymphoblastic leukemia(62;0.0559)				TGCCACCAGACAAAAAGCAGAT	0.455																																																	0																																										SO:0001589	frameshift_variant	229			X01098	CCDS6756.1	9q21.3-q22.2	2008-02-05			ENSG00000136872	ENSG00000136872	4.1.2.13		417	protein-coding gene	gene with protein product		612724					Standard	NM_000035		Approved		uc004bbk.2	P05062	OTTHUMG00000020378	ENST00000374855.4:c.813dupT	9.37:g.104187316_104187316dupA	ENSP00000363988:p.Leu271fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q13741|Q13742|Q5T7D6	Frame_Shift_Ins	INS	ENST00000374855.4	37	CCDS6756.1																																																																																				0.455	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			
AMBRA1	55626	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	46567203	46567203	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr11:46567203G>A	ENST00000458649.2	-	5	920	c.502C>T	c.(502-504)Cgg>Tgg	p.R168W	AMBRA1_ENST00000534300.1_Missense_Mutation_p.R168W|AMBRA1_ENST00000533727.1_Missense_Mutation_p.R168W|AMBRA1_ENST00000314845.3_Missense_Mutation_p.R168W|AMBRA1_ENST00000426438.1_Missense_Mutation_p.R168W|AMBRA1_ENST00000528950.1_Missense_Mutation_p.R168W|AMBRA1_ENST00000298834.3_Missense_Mutation_p.R168W			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	168					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)		p.R168W(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		AAGGGTTCCCGTCGACTCCAG	0.562																																																	2	Substitution - Missense(2)	kidney(2)											133.0	108.0	117.0					11																	46567203		2201	4299	6500	SO:0001583	missense	55626			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.502C>T	11.37:g.46567203G>A	ENSP00000415327:p.Arg168Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	G	19.98	3.926423	0.73327	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.83	3.88	0.44766	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.139583	0.56097	D	0.000034	T	0.43942	0.1270	L	0.36672	1.1	0.48135	D	0.999593	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.999	P;D;D;D;D;D	0.66084	0.874;0.941;0.941;0.915;0.941;0.915	T	0.47195	-0.9136	10	0.87932	D	0	.	15.2216	0.73316	0.0:0.0:0.6383:0.3617	.	168;168;168;168;168;168	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	W	168	ENSP00000318313:R168W;ENSP00000433372:R168W;ENSP00000431926:R168W;ENSP00000410899:R168W;ENSP00000298834:R168W;ENSP00000415327:R168W;ENSP00000433945:R168W	ENSP00000298834:R168W	R	-	1	2	AMBRA1	46523779	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.796000	0.55507	1.437000	0.47472	0.591000	0.81541	CGG		0.562	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1		NM_017749	
C14orf1	11161	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	76118207	76118207	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr14:76118207A>T	ENST00000256319.6	-	4	695	c.250T>A	c.(250-252)Ttc>Atc	p.F84I	FLVCR2_ENST00000556241.1_Intron|FLVCR2_ENST00000553587.1_Intron	NM_007176.3	NP_009107.1	Q9UKR5	ERG28_HUMAN	chromosome 14 open reading frame 1	84					sterol biosynthetic process (GO:0016126)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.F84I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6		all_epithelial(191;0.125)|all_neural(303;0.13)|Myeloproliferative disorder(585;0.163)		BRCA - Breast invasive adenocarcinoma(234;0.00147)		GCAAGGAGGAAGGTCCAGAGT	0.483																																																	1	Substitution - Missense(1)	kidney(1)											116.0	113.0	114.0					14																	76118207		2203	4300	6503	SO:0001583	missense	11161			AF134159	CCDS9845.1	14q24.3	2012-08-16			ENSG00000133935	ENSG00000133935			1187	protein-coding gene	gene with protein product		604576				10449901, 12958361, 11160377	Standard	NM_007176		Approved	NET51, ERG28	uc001xrt.3	Q9UKR5	OTTHUMG00000171488	ENST00000256319.6:c.250T>A	14.37:g.76118207A>T	ENSP00000256319:p.Phe84Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q9P093|Q9UPI2	Missense_Mutation	SNP	ENST00000256319.6	37	CCDS9845.1	.	.	.	.	.	.	.	.	.	.	A	35	5.435212	0.96150	.	.	ENSG00000133935	ENST00000256319	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87646	0.2525	9	0.87932	D	0	-37.5025	15.5154	0.75818	1.0:0.0:0.0:0.0	.	84	Q9UKR5	ERG28_HUMAN	I	84	.	ENSP00000256319:F84I	F	-	1	0	C14orf1	75187960	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.857000	0.92250	2.144000	0.66660	0.496000	0.49642	TTC		0.483	C14orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413683.1		NM_007176	
COL5A2	1290	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	189962055	189962055	+	Splice_Site	SNP	C	C	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr2:189962055C>T	ENST00000374866.3	-	6	678	c.404G>A	c.(403-405)gGa>gAa	p.G135E	AC133106.2_ENST00000419029.1_RNA	NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	135					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.G135E(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TCCTGGAGGTCCCTAAAACAG	0.403																																																	1	Substitution - Missense(1)	kidney(1)											134.0	118.0	123.0					2																	189962055		2203	4300	6503	SO:0001630	splice_region_variant	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.403-1G>A	2.37:g.189962055C>T		Somatic		WXS	Illumina HiSeq	Phase_I	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.291196	0.80914	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.99353	-5.77	5.96	5.96	0.96718	.	0.000000	0.52532	D	0.000065	D	0.99718	0.9891	H	0.98802	4.335	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.97355	0.9966	9	.	.	.	.	17.336	0.87281	0.0:1.0:0.0:0.0	.	135	P05997	CO5A2_HUMAN	E	135;9	ENSP00000364000:G135E	.	G	-	2	0	COL5A2	189670300	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.778000	0.68940	2.831000	0.97527	0.650000	0.86243	GGA		0.403	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1		NM_000393	Missense_Mutation
ELOVL5	60481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	53135507	53135507	+	Missense_Mutation	SNP	T	T	C	rs200213620		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr6:53135507T>C	ENST00000542638.1	-	7	1087	c.640A>G	c.(640-642)Atc>Gtc	p.I214V	ELOVL5_ENST00000304434.6_Missense_Mutation_p.I214V|ELOVL5_ENST00000370918.4_Missense_Mutation_p.I204V|ELOVL5_ENST00000541407.1_Missense_Mutation_p.I241V			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5	214				YFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQL LQFVLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLIALFTN FYIQTYNKKGASRR -> SVCADNHPDQLRGHLAVHIPSWL VVFPDWIHDFPDCSLHKLLHSDLQQERGLPKERPPEGPPEW VHGCCEWTHQQLFTPGKQCEAKEAAEGLKSKN (in Ref. 4; BAD93035). {ECO:0000305}.	alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)	p.I214V(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					GTCTGGATGATTGTCAGCACA	0.522																																																	1	Substitution - Missense(1)	kidney(1)						T	VAL/ILE,SER/ASN,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	77.0	65.0	69.0		721,515,640	6.1	1.0	6		69	0,8600		0,0,4300	no	missense,missense,missense	ELOVL5	NM_001242828.1,NM_001242830.1,NM_021814.4	29,46,29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign	241/327,172/263,214/300	53135507	1,13005	2203	4300	6503	SO:0001583	missense	60481			AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.640A>G	6.37:g.53135507T>C	ENSP00000440728:p.Ile214Val	Somatic		WXS	Illumina HiSeq	Phase_I	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Missense_Mutation	SNP	ENST00000542638.1	37	CCDS4951.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.122647	0.56613	2.27E-4	0.0	ENSG00000012660	ENST00000370918;ENST00000304434;ENST00000542638;ENST00000541407	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	6.14	6.14	0.99180	.	.	.	.	.	T	0.13586	0.0329	.	.	.	0.46586	D	0.999111	B;B	0.17465	0.013;0.022	B;B	0.29267	0.009;0.1	T	0.03112	-1.1071	8	0.45353	T	0.12	-15.637	16.806	0.85666	0.0:0.0:0.0:1.0	.	241;214	F6SH78;Q9NYP7	.;ELOV5_HUMAN	V	204;214;214;241	ENSP00000359956:I204V;ENSP00000306640:I214V;ENSP00000440728:I214V;ENSP00000438095:I241V	ENSP00000306640:I214V	I	-	1	0	ELOVL5	53243466	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.940000	0.56599	2.367000	0.80283	0.529000	0.55759	ATC		0.522	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1		NM_021814	
FAM13A	10144	hgsc.bcm.edu;ucsc.edu	37	4	89912229	89912229	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr4:89912229delA	ENST00000264344.5	-	4	707	c.500delT	c.(499-501)ctcfs	p.L168fs	FAM13A_ENST00000509094.1_Frame_Shift_Del_p.L168fs|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000515600.1_Frame_Shift_Del_p.L168fs	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	168	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						GTACTTGAGGAGGCAGTAGTG	0.413																																																	0													101.0	97.0	99.0					4																	89912229		2203	4300	6503	SO:0001589	frameshift_variant	10144			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.500delT	4.37:g.89912229delA	ENSP00000264344:p.Leu168fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Frame_Shift_Del	DEL	ENST00000264344.5	37	CCDS34029.1																																																																																				0.413	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr9:70427685delG	ENST00000377413.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)								GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TGCCCGCCCAGCACCGCGCCC	0.677																																																	0																																										SO:0001589	frameshift_variant	349334				CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	ENST00000377413.1:c.1215delC	9.37:g.70427685delG	ENSP00000366630:p.Cys405fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5RIB4	Frame_Shift_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																				0.677	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2			
GPR75	10936	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	54081819	54081819	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr2:54081819G>C	ENST00000394705.2	-	2	345	c.75C>G	c.(73-75)aaC>aaG	p.N25K	ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	25					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)	p.N25K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GAGAGGTGCTGTTTCCTTCCT	0.532																																																	1	Substitution - Missense(1)	kidney(1)											113.0	106.0	109.0					2																	54081819		2203	4300	6503	SO:0001583	missense	10936			AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"""GPCR / Class A : Orphans"""	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.75C>G	2.37:g.54081819G>C	ENSP00000378195:p.Asn25Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RC02|Q6NWR2	Missense_Mutation	SNP	ENST00000394705.2	37	CCDS1849.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.724155	0.30593	.	.	ENSG00000119737	ENST00000394705	T	0.64085	-0.08	5.33	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.54759	0.1878	.	.	.	0.41956	D	0.990685	P	0.43750	0.816	B	0.39068	0.289	T	0.59778	-0.7390	9	0.66056	D	0.02	-13.8216	11.097	0.48150	0.0886:0.0:0.9114:0.0	.	25	O95800	GPR75_HUMAN	K	25	ENSP00000378195:N25K	ENSP00000378195:N25K	N	-	3	2	GPR75	53935323	0.987000	0.35691	0.455000	0.27031	0.821000	0.46438	1.859000	0.39418	1.214000	0.43395	0.561000	0.74099	AAC		0.532	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			
IPP	3652	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	46212019	46212019	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr1:46212019A>T	ENST00000396478.3	-	2	167	c.65T>A	c.(64-66)cTc>cAc	p.L22H		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	22						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.L22H(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					GGCCAAGATGAGTTGGGCATG	0.428																																																	1	Substitution - Missense(1)	kidney(1)											116.0	104.0	108.0					1																	46212019		2203	4300	6503	SO:0001583	missense	3652			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"""Kelch-like"", ""BTB/POZ domain containing"""	6108	protein-coding gene	gene with protein product	"""kelch-like family member 27"""	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.65T>A	1.37:g.46212019A>T	ENSP00000379739:p.Leu22His	Somatic		WXS	Illumina HiSeq	Phase_I	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.909828	0.33721	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.70631	-0.5;-0.5	5.65	4.51	0.55191	BTB/POZ fold (2);	0.194612	0.45126	N	0.000382	T	0.58424	0.2121	N	0.20807	0.61	0.52099	D	0.999945	B;D	0.58620	0.008;0.983	B;P	0.45712	0.006;0.491	T	0.56920	-0.7899	10	0.35671	T	0.21	.	11.8102	0.52179	0.8618:0.0:0.0:0.1382	.	22;22	Q9Y573;A2A6V3	IPP_HUMAN;.	H	22	ENSP00000353024:L22H;ENSP00000379739:L22H	ENSP00000353024:L22H	L	-	2	0	IPP	45984606	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	6.872000	0.75536	0.933000	0.37291	0.533000	0.62120	CTC		0.428	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3		NM_005897	
KHDRBS2	202559	broad.mit.edu;ucsc.edu	37	6	62604655	62604655	+	Missense_Mutation	SNP	G	G	T	rs201374549	byFrequency	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr6:62604655G>T	ENST00000281156.4	-	6	973	c.695C>A	c.(694-696)gCg>gAg	p.A232E		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	232	Pro-rich.			A -> V (in Ref. 1; AAL77219). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)	p.A232E(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		CACTGGAAGCGCTCCACGGGT	0.632																																																	1	Substitution - Missense(1)	kidney(1)											48.0	49.0	48.0					6																	62604655		2203	4300	6503	SO:0001583	missense	202559			BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.695C>A	6.37:g.62604655G>T	ENSP00000281156:p.Ala232Glu	Somatic		WXS	Illumina GAIIx	Phase_I	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721925	0.48728	.	.	ENSG00000112232	ENST00000281156;ENST00000539571	T	0.45276	0.9	5.52	5.52	0.82312	.	0.220525	0.38959	N	0.001517	T	0.15478	0.0373	N	0.19112	0.55	0.30651	N	0.755468	B	0.22800	0.075	B	0.25506	0.061	T	0.05451	-1.0884	10	0.30078	T	0.28	-3.6431	14.0284	0.64599	0.0726:0.0:0.9274:0.0	.	232	Q5VWX1	KHDR2_HUMAN	E	232	ENSP00000281156:A232E	ENSP00000281156:A232E	A	-	2	0	KHDRBS2	62662614	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.998000	0.70653	2.734000	0.93682	0.655000	0.94253	GCG		0.632	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2		NM_152688	
CEP170B	283638	hgsc.bcm.edu	37	14	105352885	105352890	+	In_Frame_Del	DEL	GCAGGA	GCAGGA	-	rs60001925|rs150426191	byFrequency	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	GCAGGA	GCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr14:105352885_105352890delGCAGGA	ENST00000414716.3	+	12	2537_2542	c.2309_2314delGCAGGA	c.(2308-2316)cgcaggagc>cgc	p.RS771del	CEP170B_ENST00000418279.1_In_Frame_Del_p.RS701del|CEP170B_ENST00000453495.1_In_Frame_Del_p.RS772del|CEP170B_ENST00000556508.1_In_Frame_Del_p.RS701del	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	771						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GACAGCAGACGCAGGAGCCCCCAGGA	0.694														358	0.0714856	0.0061	0.1196	5008	,	,		13278	0.1091		0.0775	False		,,,				2504	0.0808																0									,	62,3458		5,52,1703					,	3.2	0.0		dbSNP_129	9	575,7107		59,457,3325	no	coding,coding	KIAA0284	NM_015005.2,NM_001112726.2	,	64,509,5028	A1A1,A1R,RR		7.485,1.7614,5.6865	,	,		637,10565				SO:0001651	inframe_deletion	0			AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.2309_2314delGCAGGA	14.37:g.105352885_105352890delGCAGGA	ENSP00000404151:p.Arg771_Ser772del	Somatic		WXS	Illumina HiSeq	Phase_I	Q2KHR7|Q86TI7	In_Frame_Del	DEL	ENST00000414716.3	37	CCDS45175.1																																																																																				0.694	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2		NM_001112726	
ICE1	23379	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	5462477	5462477	+	Silent	SNP	G	G	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr5:5462477G>T	ENST00000296564.7	+	13	3252	c.3030G>T	c.(3028-3030)gtG>gtT	p.V1010V		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1010					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)	p.V1010V(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AAGTGACTGTGTCAGGAGGGT	0.542																																																	2	Substitution - coding silent(2)	kidney(2)											72.0	75.0	74.0					5																	5462477		2004	4189	6193	SO:0001819	synonymous_variant	23379																														ENST00000296564.7:c.3030G>T	5.37:g.5462477G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																				0.542	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662																																																	4	Substitution - Missense(4)	endometrium(3)|kidney(1)											6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240			AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val	Somatic		WXS	Illumina GAIIx	Phase_I	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			
LATS2	26524	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	21557681	21557681	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr13:21557681C>A	ENST00000382592.4	-	5	2569	c.2164G>T	c.(2164-2166)Gag>Tag	p.E722*	LATS2_ENST00000542899.1_Nonsense_Mutation_p.E722*	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2									p.E722*(2)		breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TTGTCTGCCTCGGCCAGGATG	0.542																																																	2	Substitution - Nonsense(2)	kidney(2)											155.0	148.0	150.0					13																	21557681		2203	4300	6503	SO:0001587	stop_gained	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2164G>T	13.37:g.21557681C>A	ENSP00000372035:p.Glu722*	Somatic		WXS	Illumina HiSeq	Phase_I		Nonsense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	C	42	9.389594	0.99156	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	.	.	.	5.19	4.34	0.51931	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	13.9931	0.64378	0.0:0.9274:0.0:0.0726	.	.	.	.	X	722	.	ENSP00000372035:E722X	E	-	1	0	LATS2	20455681	1.000000	0.71417	0.889000	0.34880	0.829000	0.46940	5.877000	0.69675	1.426000	0.47256	0.555000	0.69702	GAG		0.542	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			
LGALS14	56891	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	40199946	40199946	+	Missense_Mutation	SNP	G	G	A	rs528408473		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr19:40199946G>A	ENST00000392052.3	+	4	636	c.413G>A	c.(412-414)aGc>aAc	p.S138N	LGALS14_ENST00000360675.3_Missense_Mutation_p.S167N	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	138	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)	p.S138N(1)|p.S167N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			GTGCTTATCAGCGATTGAGGG	0.483													G|||	1	0.000199681	0.0	0.0014	5008	,	,		22839	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)											99.0	87.0	91.0					19																	40199946		2203	4300	6503	SO:0001583	missense	56891			AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.413G>A	19.37:g.40199946G>A	ENSP00000375905:p.Ser138Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	.	.	.	.	.	.	.	.	.	.	.	1.592	-0.528888	0.04112	.	.	ENSG00000006659	ENST00000392052;ENST00000360675	T;T	0.17370	2.28;2.28	0.902	-1.8	0.07907	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (2);	.	.	.	.	T	0.07773	0.0195	N	0.19112	0.55	0.09310	N	1	B;B	0.10296	0.003;0.0	B;B	0.10450	0.005;0.001	T	0.40831	-0.9542	9	0.16896	T	0.51	.	2.5026	0.04637	0.2534:0.3139:0.4327:0.0	.	138;167	Q8TCE9;A8MPV8	PPL13_HUMAN;.	N	138;167	ENSP00000375905:S138N;ENSP00000353893:S167N	ENSP00000353893:S167N	S	+	2	0	LGALS14	44891786	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.960000	0.00673	-0.722000	0.04922	-0.657000	0.03884	AGC		0.483	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1		NM_020129	
LIPE	3991	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	42910438	42910438	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr19:42910438T>A	ENST00000244289.4	-	7	2516	c.2240A>T	c.(2239-2241)gAt>gTt	p.D747V	LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000599276.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	747					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)	p.D747V(1)		breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CATGATGCCATCTGGCACCCG	0.662																																																	1	Substitution - Missense(1)	kidney(1)											55.0	52.0	53.0					19																	42910438		2203	4300	6503	SO:0001583	missense	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2240A>T	19.37:g.42910438T>A	ENSP00000244289:p.Asp747Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232362	0.79688	.	.	ENSG00000079435	ENST00000244289	T	0.09911	2.93	5.09	4.06	0.47325	Alpha/beta hydrolase fold-3 (1);	0.205939	0.39475	N	0.001343	T	0.19685	0.0473	L	0.47016	1.485	0.80722	D	1	P	0.49783	0.928	P	0.58780	0.845	T	0.00359	-1.1791	10	0.54805	T	0.06	-14.8539	9.6433	0.39853	0.0:0.0847:0.0:0.9153	.	747	Q05469	LIPS_HUMAN	V	747	ENSP00000244289:D747V	ENSP00000244289:D747V	D	-	2	0	LIPE	47602278	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.084000	0.64462	2.047000	0.60756	0.524000	0.50904	GAT		0.662	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1		NM_005357	
MCM3AP	8888	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	47663535	47663535	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr21:47663535G>T	ENST00000397708.1	-	25	5394	c.5140C>A	c.(5140-5142)Ctc>Atc	p.L1714I	MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.L1714I|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1714	Acetyltransferase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.L1714I(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GTTCTGTGGAGCAGGTTCTCC	0.612																																																	1	Substitution - Missense(1)	kidney(1)											60.0	56.0	57.0					21																	47663535		2203	4300	6503	SO:0001583	missense	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.5140C>A	21.37:g.47663535G>T	ENSP00000380820:p.Leu1714Ile	Somatic		WXS	Illumina HiSeq	Phase_I	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304771	0.60305	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.14893	2.47;2.47	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.32436	0.0829	L	0.36672	1.1	0.46279	D	0.998968	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	T	0.02047	-1.1223	10	0.72032	D	0.01	-22.3182	14.5261	0.67890	0.0724:0.0:0.9276:0.0	.	1714;209	O60318;B3KT88	MCM3A_HUMAN;.	I	1714;1714;209	ENSP00000380820:L1714I;ENSP00000291688:L1714I	ENSP00000291688:L1714I	L	-	1	0	MCM3AP	46487963	1.000000	0.71417	0.990000	0.47175	0.152000	0.21847	7.100000	0.76989	2.551000	0.86045	0.655000	0.94253	CTC		0.612	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1		NM_003906	
MEFV	4210	broad.mit.edu;ucsc.edu	37	16	3293876	3293876	+	Silent	SNP	G	G	A	rs104895161		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr16:3293876G>A	ENST00000219596.1	-	9	1815	c.1776C>T	c.(1774-1776)ggC>ggT	p.G592G	MEFV_ENST00000536379.1_Silent_p.G381G|MEFV_ENST00000339854.4_Silent_p.G412G|MEFV_ENST00000541159.1_Missense_Mutation_p.R440C	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	592	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.R440C(1)|p.G592G(1)		NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GTGCCTGAGCGCCAATCAGCT	0.507																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)											47.0	49.0	49.0					16																	3293876		2197	4300	6497	SO:0001819	synonymous_variant	4210			AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1776C>T	16.37:g.3293876G>A		Somatic		WXS	Illumina GAIIx	Phase_I	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	G	6.424	0.446391	0.12223	.	.	ENSG00000103313	ENST00000541159	T	0.63744	-0.06	4.92	-7.28	0.01456	.	.	.	.	.	T	0.47040	0.1424	.	.	.	0.33568	D	0.598242	.	.	.	.	.	.	T	0.52518	-0.8565	6	0.40728	T	0.16	-32.6299	2.5339	0.04710	0.3649:0.1124:0.3807:0.142	.	.	.	.	C	440	ENSP00000438711:R440C	ENSP00000438711:R440C	R	-	1	0	MEFV	3233877	0.000000	0.05858	0.003000	0.11579	0.014000	0.08584	-1.373000	0.02568	-1.096000	0.03046	-1.127000	0.01993	CGC		0.507	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1		NM_000243	
MEP1B	4225	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	29788192	29788192	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr18:29788192A>T	ENST00000269202.6	+	9	924	c.877A>T	c.(877-879)Agg>Tgg	p.R293W	MEP1B_ENST00000581447.1_Missense_Mutation_p.R293W	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	293	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R293W(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						ACAGGTTCCCAGGGGGCCAGA	0.483																																																	1	Substitution - Missense(1)	kidney(1)											93.0	95.0	95.0					18																	29788192		1913	4117	6030	SO:0001583	missense	4225			X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.877A>T	18.37:g.29788192A>T	ENSP00000269202:p.Arg293Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454528	0.63290	.	.	ENSG00000141434	ENST00000269202	T	0.02015	4.5	5.48	-7.71	0.01254	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	1.563340	0.03383	N	0.200600	T	0.05090	0.0136	L	0.36672	1.1	0.09310	N	1	D	0.56521	0.976	P	0.56474	0.799	T	0.29549	-1.0008	10	0.72032	D	0.01	6.1214	12.1096	0.53831	0.2593:0.0:0.6553:0.0854	.	293	Q16820	MEP1B_HUMAN	W	293	ENSP00000269202:R293W	ENSP00000269202:R293W	R	+	1	2	MEP1B	28042190	0.000000	0.05858	0.000000	0.03702	0.512000	0.34134	0.169000	0.16641	-1.869000	0.01141	-0.375000	0.07067	AGG		0.483	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1		NM_005925	
Unknown	0	broad.mit.edu	37	1	16974224	16974224	+	IGR	SNP	C	C	G	rs368571421		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	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									
MYO5B	4645	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	47438527	47438527	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr18:47438527A>C	ENST00000285039.7	-	18	2406	c.2107T>G	c.(2107-2109)Ttt>Gtt	p.F703V		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	703	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.F703V(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CGGTTGAAAAAGTCATGGTAG	0.547																																																	1	Substitution - Missense(1)	kidney(1)											142.0	138.0	139.0					18																	47438527		1964	4171	6135	SO:0001583	missense	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.2107T>G	18.37:g.47438527A>C	ENSP00000285039:p.Phe703Val	Somatic		WXS	Illumina HiSeq	Phase_I	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.645282	0.87859	.	.	ENSG00000167306	ENST00000285039	D	0.89746	-2.56	5.38	5.38	0.77491	Myosin head, motor domain (2);	0.057917	0.64402	D	0.000001	D	0.95354	0.8492	M	0.94063	3.49	0.80722	D	1	D	0.67145	0.996	P	0.62382	0.901	D	0.96494	0.9366	10	0.87932	D	0	.	15.3533	0.74405	1.0:0.0:0.0:0.0	.	703	Q9ULV0	MYO5B_HUMAN	V	703	ENSP00000285039:F703V	ENSP00000285039:F703V	F	-	1	0	MYO5B	45692525	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.157000	0.94714	2.161000	0.67846	0.460000	0.39030	TTT		0.547	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			
NAB2	4665	broad.mit.edu	37	12	57485457	57485457	+	Silent	SNP	T	T	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr12:57485457T>C	ENST00000300131.3	+	2	1011	c.633T>C	c.(631-633)ccT>ccC	p.P211P	NAB2_ENST00000342556.6_Silent_p.P211P|NAB2_ENST00000554718.1_3'UTR|NAB2_ENST00000357680.4_Silent_p.P211P	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	211					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.P211P(3)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TCTCCCCCCCTGCAGGGGGAG	0.711																																																	3	Substitution - coding silent(3)	prostate(1)|lung(1)|kidney(1)																																								SO:0001819	synonymous_variant	4665			BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.633T>C	12.37:g.57485457T>C		Somatic		WXS	Illumina GAIIx	Phase_I	B2RAK3|O76006|Q14797	Silent	SNP	ENST00000300131.3	37	CCDS8930.1																																																																																				0.711	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1		NM_005967	
NPL	80896	hgsc.bcm.edu;ucsc.edu	37	1	182794926	182794926	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr1:182794926delA	ENST00000367553.1	+	11	793	c.749delA	c.(748-750)cagfs	p.Q250fs	NPL_ENST00000258317.2_Frame_Shift_Del_p.Q250fs|NPL_ENST00000367554.3_Frame_Shift_Del_p.Q231fs|NPL_ENST00000367552.2_Frame_Shift_Del_p.Q206fs|NPL_ENST00000367555.1_Frame_Shift_Del_p.Q206fs|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	250					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						TTTTGTATCCAGAGATTTATC	0.328																																																	0													144.0	153.0	150.0					1																	182794926		2203	4300	6503	SO:0001589	frameshift_variant	80896			AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.749delA	1.37:g.182794926delA	ENSP00000356524:p.Gln250fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Frame_Shift_Del	DEL	ENST00000367553.1	37	CCDS1350.1																																																																																				0.328	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1		NM_030769	
OR10C1	442194	broad.mit.edu;hgsc.bcm.edu	37	6	29407843	29407843	+	Silent	SNP	C	C	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr6:29407843C>T	ENST00000444197.2	+	1	761	c.51C>T	c.(49-51)tcC>tcT	p.S17S	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S17S(1)		NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TCGGCTTCTCCCACCTGGCCG	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											142.0	123.0	130.0					6																	29407843		1511	2709	4220	SO:0001819	synonymous_variant	442194				CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.51C>T	6.37:g.29407843C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q5SUN7|Q96R18	Silent	SNP	ENST00000444197.2	37	CCDS34364.1																																																																																				0.507	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			
OR2AG1	144125	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	6806283	6806283	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr11:6806283C>A	ENST00000307401.4	+	1	36	c.15C>A	c.(13-15)aaC>aaA	p.N5K		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N5K(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGCTCTGGAACTTCACCTTGG	0.428																																																	1	Substitution - Missense(1)	kidney(1)											107.0	103.0	104.0					11																	6806283		2201	4296	6497	SO:0001583	missense	144125			AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.15C>A	11.37:g.6806283C>A	ENSP00000307447:p.Asn5Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	37	CCDS31414.1	.	.	.	.	.	.	.	.	.	.	C	8.803	0.933330	0.18131	.	.	ENSG00000170803	ENST00000307401	T	0.64085	-0.08	4.25	1.32	0.21799	.	0.475888	0.19469	N	0.113503	T	0.78559	0.4302	M	0.92268	3.29	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66428	-0.5926	10	0.87932	D	0	.	3.3044	0.06994	0.1836:0.5233:0.0:0.2931	.	5	Q9H205	O2AG1_HUMAN	K	5	ENSP00000307447:N5K	ENSP00000307447:N5K	N	+	3	2	OR2AG1	6762859	0.000000	0.05858	0.557000	0.28306	0.056000	0.15407	-0.541000	0.06099	0.190000	0.20209	-0.237000	0.12165	AAC		0.428	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1		NM_001004489	
PAPL	390928	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	39597629	39597629	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr19:39597629C>T	ENST00000331256.5	+	12	1430	c.1156C>T	c.(1156-1158)Ccc>Tcc	p.P386S	PAPL_ENST00000594229.1_Intron	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		386						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)	p.P386S(1)									CTTCCCGAGGCCCTGGAGTGC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											67.0	52.0	57.0					19																	39597629		2203	4300	6503	SO:0001583	missense	390928																														ENST00000331256.5:c.1156C>T	19.37:g.39597629C>T	ENSP00000327557:p.Pro386Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	37	CCDS33018.1	.	.	.	.	.	.	.	.	.	.	c	11.39	1.623609	0.28889	.	.	ENSG00000183760	ENST00000331256	.	.	.	4.61	4.61	0.57282	.	0.299519	0.32687	N	0.005769	T	0.39036	0.1063	N	0.25245	0.725	0.26276	N	0.978351	P	0.41131	0.739	P	0.50617	0.646	T	0.20773	-1.0265	9	0.42905	T	0.14	-36.5983	10.1356	0.42704	0.1994:0.8006:0.0:0.0	.	386	Q6ZNF0	PAPL_HUMAN	S	386	.	ENSP00000327557:P386S	P	+	1	0	AC011443.1	44289469	1.000000	0.71417	1.000000	0.80357	0.386000	0.30323	2.289000	0.43523	2.425000	0.82216	0.538000	0.68166	CCC		0.647	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52643898	52643898	+	Nonsense_Mutation	SNP	A	A	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr3:52643898A>T	ENST00000296302.7	-	16	1999	c.1998T>A	c.(1996-1998)taT>taA	p.Y666*	PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y666*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y681*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y666*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y681*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y666*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y666*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y634*			Q86U86	PB1_HUMAN	polybromo 1	666					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.Y666*(2)|p.Y634*(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)		TTACAGCTTCATAGACCTCAT	0.398			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											111.0	128.0	122.0					3																	52643898		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1998T>A	3.37:g.52643898A>T	ENSP00000296302:p.Tyr666*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	A	38	6.880800	0.97908	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	6.17	2.59	0.31030	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-39.4605	10.1694	0.42900	0.7583:0.0:0.2417:0.0	.	.	.	.	X	634;666;666;666;666;666;681;681;666;625	.	ENSP00000296302:Y666X	Y	-	3	2	PBRM1	52618938	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.948000	0.29096	0.221000	0.20879	0.533000	0.62120	TAT		0.398	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PEAK1	79834	hgsc.bcm.edu;ucsc.edu	37	15	77471481	77471481	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr15:77471481delT	ENST00000560626.2	-	4	3263	c.2788delA	c.(2788-2790)agcfs	p.S930fs	PEAK1_ENST00000558305.1_Frame_Shift_Del_p.S930fs|PEAK1_ENST00000312493.4_Frame_Shift_Del_p.S930fs			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	930					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CGGAAGAAGCTTTTAAATGAT	0.502																																																	0													102.0	111.0	108.0					15																	77471481		1932	4128	6060	SO:0001589	frameshift_variant	79834				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2788delA	15.37:g.77471481delT	ENSP00000452796:p.Ser930fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Frame_Shift_Del	DEL	ENST00000560626.2	37	CCDS42062.1																																																																																				0.502	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			
PEAK1	79834	hgsc.bcm.edu	37	15	77471485	77471485	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr15:77471485A>C	ENST00000560626.2	-	4	3259	c.2784T>G	c.(2782-2784)ttT>ttG	p.F928L	PEAK1_ENST00000558305.1_Missense_Mutation_p.F928L|PEAK1_ENST00000312493.4_Missense_Mutation_p.F928L			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	928					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGAAGCTTTTAAATGATATCC	0.507																																																	0													100.0	108.0	105.0					15																	77471485		1922	4119	6041	SO:0001583	missense	79834				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2784T>G	15.37:g.77471485A>C	ENSP00000452796:p.Phe928Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.266067	0.80358	.	.	ENSG00000173517	ENST00000312493	T	0.78003	-1.14	5.91	0.898	0.19264	.	0.000000	0.64402	D	0.000007	T	0.63426	0.2510	L	0.34521	1.04	0.44956	D	0.997975	P	0.43750	0.816	B	0.36766	0.232	T	0.62746	-0.6789	10	0.72032	D	0.01	-10.4191	11.1486	0.48444	0.6189:0.0:0.3811:0.0	.	928	Q9H792	PEAK1_HUMAN	L	928	ENSP00000309230:F928L	ENSP00000309230:F928L	F	-	3	2	AC087465.1	75258540	0.988000	0.35896	0.992000	0.48379	0.998000	0.95712	0.455000	0.21843	0.134000	0.18681	0.533000	0.62120	TTT		0.507	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			
RNMT	8731	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	13737037	13737037	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr18:13737037G>T	ENST00000383314.2	+	5	822	c.582G>T	c.(580-582)aaG>aaT	p.K194N	RNMT_ENST00000535051.1_5'UTR|RNMT_ENST00000543302.2_Missense_Mutation_p.K194N|RNMT_ENST00000592764.1_Missense_Mutation_p.K194N|RNMT_ENST00000262173.3_Missense_Mutation_p.K194N|RNMT_ENST00000589866.1_Missense_Mutation_p.K194N			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	194	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)	p.K194N(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						TACGACAGAAGAAAAAACGTG	0.348																																					GBM(29;474 594 19092 36647 41529)												1	Substitution - Missense(1)	kidney(1)											119.0	120.0	120.0					18																	13737037		2203	4300	6503	SO:0001583	missense	8731			AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.582G>T	18.37:g.13737037G>T	ENSP00000372804:p.Lys194Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Missense_Mutation	SNP	ENST00000383314.2	37	CCDS11867.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002105	0.35320	.	.	ENSG00000101654	ENST00000383314;ENST00000543302;ENST00000544744;ENST00000262173	.	.	.	5.62	4.47	0.54385	.	0.238609	0.49305	D	0.000141	T	0.33527	0.0866	N	0.19112	0.55	0.80722	D	1	P;P	0.44344	0.692;0.833	B;P	0.45971	0.366;0.499	T	0.06197	-1.0840	9	0.15499	T	0.54	-22.9506	7.891	0.29677	0.7081:0.0:0.2919:0.0	.	194;194	O43148-2;O43148	.;MCES_HUMAN	N	194;194;16;194	.	ENSP00000262173:K194N	K	+	3	2	RNMT	13727037	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	0.902000	0.28459	0.964000	0.38108	-0.312000	0.09012	AAG		0.348	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1		NM_003799	
SCAF4	57466	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	33067196	33067196	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr21:33067196G>A	ENST00000286835.7	-	10	1548	c.1166C>T	c.(1165-1167)cCa>cTa	p.P389L	SCAF4_ENST00000434667.3_Missense_Mutation_p.P374L|SCAF4_ENST00000399804.1_Missense_Mutation_p.P389L	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	389						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P389L(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CTGCTGCACTGGTGGAGTTGG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											115.0	106.0	109.0					21																	33067196		2203	4300	6503	SO:0001583	missense	0			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.1166C>T	21.37:g.33067196G>A	ENSP00000286835:p.Pro389Leu	Somatic		WXS	Illumina HiSeq	Phase_I	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.669778	0.67814	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.46063	0.89;0.88;0.88	6.17	6.17	0.99709	.	0.244180	0.42548	D	0.000698	T	0.45756	0.1358	M	0.64997	1.995	0.80722	D	1	B;B;B;B	0.23377	0.03;0.084;0.05;0.03	B;B;B;B	0.26770	0.033;0.07;0.073;0.033	T	0.32824	-0.9892	10	0.59425	D	0.04	-2.3914	16.376	0.83392	0.0:0.0:0.8677:0.1323	.	374;389;389;389	C9JLZ0;C9J1W7;O95104-2;O95104	.;.;.;SFR15_HUMAN	L	374;389;389	ENSP00000402377:P374L;ENSP00000286835:P389L;ENSP00000382703:P389L	ENSP00000286835:P389L	P	-	2	0	SCAF4	31989067	0.999000	0.42202	0.977000	0.42913	0.971000	0.66376	5.673000	0.68109	2.941000	0.99782	0.655000	0.94253	CCA		0.458	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1		XM_047889	
SMC5	23137	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	72892386	72892386	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr9:72892386C>T	ENST00000361138.5	+	4	599	c.541C>T	c.(541-543)Cag>Tag	p.Q181*		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	181					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.Q181*(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						GTTTCTCCCTCAGGTATGAGA	0.338																																																	1	Substitution - Nonsense(1)	kidney(1)											65.0	70.0	68.0					9																	72892386		2203	4300	6503	SO:0001587	stop_gained	23137			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.541C>T	9.37:g.72892386C>T	ENSP00000354957:p.Gln181*	Somatic		WXS	Illumina HiSeq	Phase_I	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Nonsense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	C	36	5.973841	0.97162	.	.	ENSG00000198887	ENST00000361138	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.9262	19.5531	0.95330	0.0:1.0:0.0:0.0	.	.	.	.	X	181	.	ENSP00000354957:Q181X	Q	+	1	0	SMC5	72082206	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.487000	0.81328	2.634000	0.89283	0.460000	0.39030	CAG		0.338	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1		NM_015110	
SPEN	23013	broad.mit.edu	37	1	16258574	16258574	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr1:16258574A>C	ENST00000375759.3	+	11	6043	c.5839A>C	c.(5839-5841)Acc>Ccc	p.T1947P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1947					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.T1947P(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGTTCCCACCACCCCTCGGAG	0.592																																																	1	Substitution - Missense(1)	kidney(1)											38.0	43.0	41.0					1																	16258574		2202	4300	6502	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5839A>C	1.37:g.16258574A>C	ENSP00000364912:p.Thr1947Pro	Somatic		WXS	Illumina GAIIx	Phase_I	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	11.10	1.539612	0.27563	.	.	ENSG00000065526	ENST00000375759	T	0.10005	2.92	4.8	4.8	0.61643	.	.	.	.	.	T	0.21307	0.0513	L	0.35723	1.085	0.41730	D	0.989554	D	0.65815	0.995	D	0.72982	0.979	T	0.00978	-1.1493	9	0.48119	T	0.1	-14.5242	11.3246	0.49442	0.8478:0.1522:0.0:0.0	.	1947	Q96T58	MINT_HUMAN	P	1947	ENSP00000364912:T1947P	ENSP00000364912:T1947P	T	+	1	0	SPEN	16131161	0.261000	0.24063	0.566000	0.28421	0.483000	0.33249	3.667000	0.54547	1.921000	0.55644	0.260000	0.18958	ACC		0.592	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1		NM_015001	
SYNJ2	8871	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	158495714	158495714	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr6:158495714G>T	ENST00000355585.4	+	16	2311	c.2236G>T	c.(2236-2238)Gac>Tac	p.D746Y	SYNJ2_ENST00000367121.3_Missense_Mutation_p.D746Y|SYNJ2_ENST00000367112.1_5'Flank|SYNJ2_ENST00000367122.2_Missense_Mutation_p.D746Y	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	746					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.D746Y(1)		biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TAAACGCCAAGACTGGAAGAA	0.343																																																	1	Substitution - Missense(1)	kidney(1)											94.0	89.0	90.0					6																	158495714		2203	4300	6503	SO:0001583	missense	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.2236G>T	6.37:g.158495714G>T	ENSP00000347792:p.Asp746Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299158	0.81025	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585	D;D;D	0.95272	-3.66;-3.66;-3.66	5.8	5.8	0.92144	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.64402	D	0.000012	D	0.96889	0.8984	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97267	0.9908	10	0.87932	D	0	.	20.1109	0.97911	0.0:0.0:1.0:0.0	.	746;746	O15056;O15056-3	SYNJ2_HUMAN;.	Y	746	ENSP00000356089:D746Y;ENSP00000356088:D746Y;ENSP00000347792:D746Y	ENSP00000347792:D746Y	D	+	1	0	SYNJ2	158415702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.128000	0.77217	2.217000	0.71921	0.529000	0.55759	GAC		0.343	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			
SVILP1	645954	broad.mit.edu	37	10	30987274	30987274	+	RNA	SNP	C	C	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr10:30987274C>T	ENST00000435645.1	+	0	431									supervillin pseudogene 1																		AAATGTGATGCTCTCCTGTTG	0.403																																																	0																																												0					10p11.23	2012-12-20			ENSG00000234814	ENSG00000234814			44959	pseudogene	pseudogene							Standard	NR_036438		Approved				OTTHUMG00000017900		10.37:g.30987274C>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000435645.1	37																																																																																					0.403	SVILP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000331601.1			
DPPA3P2	400206	broad.mit.edu	37	14	36841025	36841025	+	RNA	SNP	G	G	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr14:36841025G>A	ENST00000557188.1	+	0	656									developmental pluripotency associated 3 pseudogene 2									p.C136Y(1)									TGCAGTTTCTGCGTGTCTAAT	0.428																																																	1	Substitution - Missense(1)	kidney(1)																																										0					14q13.3	2012-07-04			ENSG00000188831	ENSG00000188831			20417	pseudogene	pseudogene							Standard	NG_023379		Approved	STELLAR			OTTHUMG00000170728		14.37:g.36841025G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000557188.1	37																																																																																					0.428	DPPA3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000410122.1			
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191527	10191527	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	g.chr3:10191527delA	ENST00000256474.2	+	3	1360	c.520delA	c.(520-522)aatfs	p.N174fs	VHL_ENST00000345392.2_Frame_Shift_Del_p.N133fs|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	174					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.N174fs*28(2)|p.P172fs*39(2)|p.E173fs*26(1)|p.E173_R176del(1)|p.N174D(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)		CAAGCCTGAGAATTACAGGAG	0.532		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"""	7	Deletion - Frameshift(5)|Substitution - Missense(1)|Deletion - In frame(1)	kidney(7)											90.0	82.0	85.0					3																	10191527		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.520delA	3.37:g.10191527delA	ENSP00000256474:p.Asn174fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.532	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	RNA	SNP	G	G	A	rs201972834		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf09ae91-5523-494c-8f30-c26f6ba37624	bf8e0bcb-ce02-4b84-bd83-f34a5a14f4ea	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	
