#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
ABCA7	10347	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	1048966	1048966	+	Missense_Mutation	SNP	A	A	T	rs145106069		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:1048966A>T	ENST00000263094.6	+	17	2573	c.2342A>T	c.(2341-2343)aAg>aTg	p.K781M	ABCA7_ENST00000433129.1_Missense_Mutation_p.K781M|ABCA7_ENST00000435683.2_Missense_Mutation_p.K643M	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	781					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)	p.K781M(1)		NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCCCCCCAAGAGTCCAGCC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											25.0	26.0	26.0					19																	1048966		2193	4297	6490	SO:0001583	missense	10347			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2342A>T	19.37:g.1048966A>T	ENSP00000263094:p.Lys781Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	10.97	1.502041	0.26949	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87650	-2.28;-2.28	4.08	1.87	0.25490	.	.	.	.	.	D	0.84266	0.5434	L	0.58354	1.805	0.09310	N	1	P;P	0.47604	0.898;0.65	P;B	0.46718	0.525;0.145	T	0.74315	-0.3705	9	0.52906	T	0.07	.	3.2217	0.06717	0.625:0.0:0.1943:0.1808	.	643;781	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	M	781	ENSP00000263094:K781M;ENSP00000414062:K781M	ENSP00000263094:K781M	K	+	2	0	ABCA7	999966	0.134000	0.22483	0.212000	0.23672	0.186000	0.23388	1.054000	0.30455	0.431000	0.26258	0.379000	0.24179	AAG		0.607	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1		NM_019112	
ACOX3	8310	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	8394072	8394072	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr4:8394072C>T	ENST00000356406.5	-	11	1365	c.1288G>A	c.(1288-1290)Ggc>Agc	p.G430S	ACOX3_ENST00000503233.1_Missense_Mutation_p.G430S|RNA5SP152_ENST00000365184.1_RNA|ACOX3_ENST00000413009.2_Missense_Mutation_p.G430S	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	430					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)	p.G430S(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GCCAGATAGCCGTGTCCTCCA	0.617																																																	1	Substitution - Missense(1)	kidney(1)											164.0	168.0	166.0					4																	8394072		2203	4300	6503	SO:0001583	missense	8310			Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1288G>A	4.37:g.8394072C>T	ENSP00000348775:p.Gly430Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890167	0.91889	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	D;D;D	0.97114	-4.25;-4.25;-4.25	4.14	4.14	0.48551	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.99086	0.9686	H	0.98577	4.27	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98855	1.0760	10	0.87932	D	0	-40.071	15.3608	0.74472	0.0:1.0:0.0:0.0	.	430;430;430	B2R856;O15254-2;O15254	.;.;ACOX3_HUMAN	S	430	ENSP00000413994:G430S;ENSP00000348775:G430S;ENSP00000421625:G430S	ENSP00000348775:G430S	G	-	1	0	ACOX3	8444972	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.558000	0.73942	2.143000	0.66587	0.655000	0.94253	GGC		0.617	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			
AIFM1	9131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	129265667	129265667	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chrX:129265667G>T	ENST00000287295.3	-	14	1786	c.1556C>A	c.(1555-1557)tCt>tAt	p.S519Y	AIFM1_ENST00000346424.2_Missense_Mutation_p.S232Y|AIFM1_ENST00000440263.1_Missense_Mutation_p.S167Y|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000460436.2_Missense_Mutation_p.S180Y|AIFM1_ENST00000319908.3_Missense_Mutation_p.S515Y	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	519					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.S515Y(1)|p.S519Y(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	CTCTGTGGCAGATTTGGGGTT	0.488																																																	2	Substitution - Missense(2)	kidney(2)											215.0	194.0	201.0					X																	129265667		2203	4300	6503	SO:0001583	missense	9131			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1556C>A	X.37:g.129265667G>T	ENSP00000287295:p.Ser519Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	37	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359174	0.61403	.	.	ENSG00000156709	ENST00000460436;ENST00000346424;ENST00000319908;ENST00000440263;ENST00000287295	T;T;D;T;T	0.83673	0.86;0.86;-1.75;0.86;-0.75	5.04	5.04	0.67666	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (1);	0.168777	0.53938	D	0.000052	D	0.82504	0.5051	N	0.19112	0.55	0.80722	D	1	D;D;D	0.69078	0.995;0.997;0.995	D;D;D	0.69654	0.965;0.965;0.923	T	0.79553	-0.1756	10	0.21540	T	0.41	-9.4587	13.5081	0.61495	0.0:0.2761:0.7239:0.0	.	232;515;519	O95831-2;O95831-3;O95831	.;.;AIFM1_HUMAN	Y	180;232;515;167;519	ENSP00000431222:S180Y;ENSP00000316320:S232Y;ENSP00000315122:S515Y;ENSP00000405879:S167Y;ENSP00000287295:S519Y	ENSP00000287295:S519Y	S	-	2	0	AIFM1	129093348	1.000000	0.71417	0.999000	0.59377	0.856000	0.48823	5.984000	0.70548	2.323000	0.78572	0.600000	0.82982	TCT		0.488	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			
ALS2CL	259173	broad.mit.edu;ucsc.edu	37	3	46721931	46721931	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr3:46721931C>A	ENST00000318962.4	-	14	1620	c.1537G>T	c.(1537-1539)Gac>Tac	p.D513Y	ALS2CL_ENST00000415953.1_Missense_Mutation_p.D513Y	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	513					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D513Y(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		ACCGTCTTGTCCGCCTGGAAG	0.642																																																	1	Substitution - Missense(1)	kidney(1)											111.0	105.0	107.0					3																	46721931		2203	4300	6503	SO:0001583	missense	259173			AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.1537G>T	3.37:g.46721931C>A	ENSP00000313670:p.Asp513Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	C	13.14	2.149116	0.37923	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.50001	0.76;0.76	4.77	4.77	0.60923	.	0.080274	0.52532	D	0.000080	T	0.72137	0.3423	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.77332	-0.2627	10	0.87932	D	0	.	8.8379	0.35123	0.0:0.8997:0.0:0.1003	.	513	Q60I27	AL2CL_HUMAN	Y	513	ENSP00000313670:D513Y;ENSP00000413223:D513Y	ENSP00000313670:D513Y	D	-	1	0	ALS2CL	46696935	0.998000	0.40836	0.963000	0.40424	0.043000	0.13939	3.696000	0.54757	2.473000	0.83533	0.462000	0.41574	GAC		0.642	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3		NM_147129	
AMBP	259	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	116840415	116840415	+	Silent	SNP	C	C	T	rs200238441	byFrequency	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr9:116840415C>T	ENST00000265132.3	-	1	337	c.75G>A	c.(73-75)ccG>ccA	p.P25P		NM_001633.3	NP_001624.1	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin precursor	25					cell adhesion (GO:0007155)|female pregnancy (GO:0007565)|heme catabolic process (GO:0042167)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of JNK cascade (GO:0046329)|protein catabolic process (GO:0030163)|protein-chromophore linkage (GO:0018298)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|calcium oxalate binding (GO:0046904)|heme binding (GO:0020037)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)|small molecule binding (GO:0036094)	p.P25P(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	11					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	TGTTGTCGGGCGGCGTTGGCA	0.617													C|||	6	0.00119808	0.0	0.0	5008	,	,		17510	0.003		0.0	False		,,,				2504	0.0031																2	Substitution - coding silent(2)	breast(1)|kidney(1)											111.0	121.0	117.0					9																	116840415		2203	4300	6503	SO:0001819	synonymous_variant	259			X04494	CCDS6800.1	9q32-q33	2014-01-22			ENSG00000106927	ENSG00000106927		"""Lipocalins"""	453	protein-coding gene	gene with protein product	"""growth-inhibiting protein 19"", ""uristatin"", ""complex-forming glycoprotein heterogeneous in charge"", ""bikunin"", ""inter-alpha-trypsin inhibitor light chain"", ""protein HC"", ""uronic-acid-rich protein"", ""trypstatin"""	176870		ITI, ITIL		1708673, 1385302	Standard	NM_001633		Approved	UTI, HCP, EDC1, HI30, IATIL, ITILC	uc004bie.4	P02760	OTTHUMG00000020534	ENST00000265132.3:c.75G>A	9.37:g.116840415C>T		Somatic		WXS	Illumina HiSeq	Phase_I	P00977|P02759|P78491|Q2TU33|Q5TBD7|Q9UC58|Q9UDI8	Silent	SNP	ENST00000265132.3	37	CCDS6800.1																																																																																				0.617	AMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053758.2		NM_001633	
ANKLE2	23141	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	133331594	133331594	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:133331594C>G	ENST00000357997.5	-	2	396	c.307G>C	c.(307-309)Gag>Cag	p.E103Q	ANKLE2_ENST00000337516.5_Missense_Mutation_p.E103Q|ANKLE2_ENST00000539605.1_Missense_Mutation_p.E41Q	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	103	LEM. {ECO:0000255|PROSITE- ProRule:PRU00313}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)	p.E103Q(1)		NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		AATTTTTTCTCAAAAATGAAC	0.458																																																	1	Substitution - Missense(1)	kidney(1)											75.0	74.0	74.0					12																	133331594		1889	4118	6007	SO:0001583	missense	23141			AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.307G>C	12.37:g.133331594C>G	ENSP00000350686:p.Glu103Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.894331	0.91889	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516	T;T;T	0.57752	0.38;0.38;0.38	5.4	5.4	0.78164	LEM-like domain (2);Lamino-associated polypeptide 2/emerin (2);	0.000000	0.85682	D	0.000000	T	0.72486	0.3466	M	0.68593	2.085	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.73842	-0.3855	10	0.59425	D	0.04	-6.6395	19.2348	0.93855	0.0:1.0:0.0:0.0	.	103;103	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	Q	41;103;103	ENSP00000446268:E41Q;ENSP00000350686:E103Q;ENSP00000337651:E103Q	ENSP00000337651:E103Q	E	-	1	0	ANKLE2	131841667	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.408000	0.80041	2.549000	0.85964	0.644000	0.83932	GAG		0.458	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			
ARMC4	55130	hgsc.bcm.edu	37	10	28250531	28250532	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr10:28250531_28250532insA	ENST00000305242.5	-	10	1443_1444	c.1351_1352insT	c.(1351-1353)tatfs	p.Y451fs	ARMC4_ENST00000545014.1_5'UTR|ARMC4_ENST00000239715.3_Frame_Shift_Ins_p.Y308fs|ARMC4_ENST00000537576.1_Frame_Shift_Ins_p.Y143fs|ARMC4_ENST00000480504.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	451					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AATTTGCCAATATTCTGATGGC	0.376																																																	0																																										SO:0001589	frameshift_variant	55130			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1352dupT	10.37:g.28250532_28250532dupA	ENSP00000306410:p.Tyr451fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K906|B7Z7I1|Q9H0C0	Frame_Shift_Ins	INS	ENST00000305242.5	37	CCDS7157.1																																																																																				0.376	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1		NM_018076	
ATXN2L	11273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	28847661	28847661	+	3'UTR	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:28847661A>T	ENST00000336783.4	+	0	3470				ATXN2L_ENST00000382686.4_Intron|ATXN2L_ENST00000325215.6_Intron|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000570200.1_Intron|ATXN2L_ENST00000395547.2_Nonsense_Mutation_p.R1052*|ATXN2L_ENST00000564304.1_Intron|ATXN2L_ENST00000340394.8_Intron	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like						regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)	p.R1052*(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						TAGGGTGGGCAGAAGCCACAG	0.662																																																	1	Substitution - Nonsense(1)	kidney(1)											49.0	57.0	54.0					16																	28847661		2197	4300	6497	SO:0001624	3_prime_UTR_variant	11273				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.*75A>T	16.37:g.28847661A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Nonsense_Mutation	SNP	ENST00000336783.4	37	CCDS10641.1	.	.	.	.	.	.	.	.	.	.	.	40	8.382561	0.98786	.	.	ENSG00000168488	ENST00000395547	.	.	.	4.74	3.66	0.41972	.	0.000000	0.49305	D	0.000157	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-0.3552	6.5285	0.22314	0.8943:0.0:0.1057:0.0	.	.	.	.	X	1052	.	ENSP00000378917:R1052X	R	+	1	2	ATXN2L	28755162	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.314000	0.33597	2.137000	0.66172	0.450000	0.29827	AGA		0.662	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1		NM_007245	
BCKDHA	593	broad.mit.edu;hgsc.bcm.edu	37	19	41931921	41931921	+	IGR	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:41931921C>T	ENST00000269980.2	+	0	2103				CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000321702.2_Missense_Mutation_p.A255T|B3GNT8_ENST00000601379.1_5'Flank	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)	p.A255T(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GCCAGCAGGGCAGGGGTGTGT	0.657																																																	1	Substitution - Missense(1)	kidney(1)											41.0	44.0	43.0					19																	41931921		2203	4300	6503	SO:0001628	intergenic_variant	374907			J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41931921C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	6.301	0.423571	0.11928	.	.	ENSG00000177191	ENST00000321702	T	0.41065	1.01	4.09	3.05	0.35203	.	0.301812	0.28859	N	0.013903	T	0.30293	0.0760	L	0.39514	1.22	0.09310	N	0.999997	B	0.31989	0.35	B	0.35607	0.206	T	0.12553	-1.0543	10	0.18710	T	0.47	.	6.4623	0.21964	0.0:0.7809:0.0:0.2191	.	255	Q7Z7M8	B3GN8_HUMAN	T	255	ENSP00000312700:A255T	ENSP00000312700:A255T	A	-	1	0	B3GNT8	46623761	0.003000	0.15002	0.008000	0.14137	0.056000	0.15407	1.241000	0.32743	1.076000	0.40961	0.655000	0.94253	GCC		0.657	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3		NM_000709	
BEST1	7439	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	61727371	61727371	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:61727371T>C	ENST00000378043.4	+	9	1599	c.956T>C	c.(955-957)cTg>cCg	p.L319P	FTH1_ENST00000529631.1_Silent_p.T40T|FTH1_ENST00000529191.1_Missense_Mutation_p.Q48R|BEST1_ENST00000301774.9_Intron|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000378042.3_Missense_Mutation_p.L232P|BEST1_ENST00000435278.2_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.L259P|BEST1_ENST00000526988.1_Missense_Mutation_p.C281R	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	319					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.L319P(1)|p.L259P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						CAGGTGTCCCTGTTGGCTGTG	0.577																																																	2	Substitution - Missense(2)	kidney(2)											67.0	57.0	60.0					11																	61727371		2202	4299	6501	SO:0001583	missense	7439			AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.956T>C	11.37:g.61727371T>C	ENSP00000367282:p.Leu319Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	19.64|19.64|19.64	3.865313|3.865313|3.865313	0.71949|0.71949|0.71949	.|.|.	.|.|.	ENSG00000167995|ENSG00000167995|ENSG00000167996	ENST00000526988|ENST00000378043;ENST00000378042;ENST00000449131|ENST00000529191	D|D;D;D|D	0.99105|0.97772|0.86097	-5.43|-4.53;-4.21;-4.5|-2.07	4.74|4.74|4.74	4.74|4.74|4.74	0.60224|0.60224|0.60224	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000003|.	D|D|D	0.91068|0.91068|0.91068	0.7189|0.7189|0.7189	M|M|M	0.83774|0.83774|0.83774	2.66|2.66|2.66	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;P|D;D;D|.	0.49961|0.89917|.	0.93;0.93|1.0;1.0;1.0|.	P;B|D;D;D|.	0.48030|0.81914|.	0.564;0.289|0.995;0.988;0.995|.	D|D|D	0.91625|0.91625|0.91625	0.5314|0.5314|0.5314	9|10|6	0.87932|0.72032|.	D|D|.	0|0.01|.	-15.0855|-15.0855|-15.0855	14.2294|14.2294|14.2294	0.65882|0.65882|0.65882	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	281;327|232;319;259|.	B7Z1N8;B7Z336|O76090-4;O76090;O76090-3|.	.;.|.;BEST1_HUMAN;.|.	R|P|R	281|319;232;259|48	ENSP00000433195:C281R|ENSP00000367282:L319P;ENSP00000367281:L232P;ENSP00000399709:L259P|ENSP00000431659:Q48R	ENSP00000432681:C387R|ENSP00000367281:L232P|.	C|L|Q	+|+|-	1|2|2	0|0|0	BEST1|BEST1|FTH1	61483947|61483947|61483947	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.925000|0.925000|0.925000	0.36789|0.36789|0.36789	0.673000|0.673000|0.673000	0.39480|0.39480|0.39480	7.903000|7.903000|7.903000	0.87398|0.87398|0.87398	1.905000|1.905000|1.905000	0.55150|0.55150|0.55150	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	TGT|CTG|CAG		0.577	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1		NM_004183	
ACSM6	142827	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	96967148	96967148	+	Nonsense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr10:96967148G>A	ENST00000394005.3	+	3	596	c.587G>A	c.(586-588)tGg>tAg	p.W196*	C10orf129_ENST00000430183.1_Nonsense_Mutation_p.W41*|C10orf129_ENST00000341686.3_Nonsense_Mutation_p.W196*			Q6P461	ACSM6_HUMAN		196					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.W196*(1)|p.W41*(1)		breast(1)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TATGATGGGTGGTTGGATTTC	0.423																																																	2	Substitution - Nonsense(2)	kidney(2)											85.0	77.0	80.0					10																	96967148		2203	4300	6503	SO:0001587	stop_gained	142827																														ENST00000394005.3:c.587G>A	10.37:g.96967148G>A	ENSP00000377573:p.Trp196*	Somatic		WXS	Illumina HiSeq	Phase_I	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Nonsense_Mutation	SNP	ENST00000394005.3	37	CCDS7440.2	.	.	.	.	.	.	.	.	.	.	G	37	6.343099	0.97489	.	.	ENSG00000173124	ENST00000539707;ENST00000341686;ENST00000430183;ENST00000394005	.	.	.	1.2	0.26	0.15588	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8469	0.18671	0.1978:0.0:0.8022:0.0	.	.	.	.	X	222;196;41;196	.	ENSP00000340296:W196X	W	+	2	0	C10orf129	96957138	1.000000	0.71417	0.019000	0.16419	0.322000	0.28314	3.114000	0.50383	0.127000	0.18452	-0.261000	0.10672	TGG		0.423	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2			
RMI2	116028	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	11444604	11444604	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:11444604T>C	ENST00000312499.5	+	2	442	c.401T>C	c.(400-402)aTg>aCg	p.M134T	RMI2_ENST00000572173.1_Missense_Mutation_p.M71T|RMI2_ENST00000381820.2_Missense_Mutation_p.M71T|AC009121.1_ENST00000458885.1_RNA|RP11-485G7.6_ENST00000574681.1_RNA|RMI2_ENST00000576027.1_3'UTR	NM_152308.1	NP_689521.1	Q96E14	RMI2_HUMAN	RecQ mediated genome instability 2	134					DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.M134T(1)		endometrium(1)|kidney(1)|ovary(1)	3						CATGAAAGTATGTGGGAACTG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											108.0	102.0	104.0					16																	11444604		2197	4300	6497	SO:0001583	missense	0			AK123764	CCDS10548.1	16p13.13	2013-06-10	2013-06-10	2011-06-09	ENSG00000175643	ENSG00000175643			28349	protein-coding gene	gene with protein product		612426	"""chromosome 16 open reading frame 75"", ""RMI2, RecQ mediated genome instability 2, homolog (S. cerevisiae)"""	C16orf75		18923083, 20826341	Standard	NM_152308		Approved	MGC24665, BLAP18	uc002daw.1	Q96E14	OTTHUMG00000129793	ENST00000312499.5:c.401T>C	16.37:g.11444604T>C	ENSP00000310356:p.Met134Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B3KVZ6|Q49AE2|Q8TBL0	Missense_Mutation	SNP	ENST00000312499.5	37	CCDS10548.1	.	.	.	.	.	.	.	.	.	.	T	11.66	1.704357	0.30232	.	.	ENSG00000175643	ENST00000381820;ENST00000312499	.	.	.	5.92	5.92	0.95590	.	0.094876	0.64402	D	0.000001	T	0.67692	0.2920	M	0.75615	2.305	0.49915	D	0.99983	B	0.23249	0.082	B	0.20767	0.031	T	0.66799	-0.5832	9	0.59425	D	0.04	.	14.3168	0.66457	0.0:0.0:0.0:1.0	.	134	Q96E14	RMI2_HUMAN	T	71;134	.	ENSP00000310356:M134T	M	+	2	0	RMI2	11352105	1.000000	0.71417	0.992000	0.48379	0.415000	0.31203	2.968000	0.49224	2.263000	0.75096	0.533000	0.62120	ATG		0.443	RMI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252019.1		NM_152308	
C18orf8	29919	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	21084363	21084363	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr18:21084363C>T	ENST00000269221.3	+	2	241	c.131C>T	c.(130-132)aCt>aTt	p.T44I	C18orf8_ENST00000590868.1_Missense_Mutation_p.T44I	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	44						lysosomal membrane (GO:0005765)		p.T44I(1)		endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGTGGAGCTACTGGCGTGGTA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											218.0	192.0	201.0					18																	21084363		2203	4300	6503	SO:0001583	missense	29919			AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.131C>T	18.37:g.21084363C>T	ENSP00000269221:p.Thr44Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	37	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827634	0.90955	.	.	ENSG00000141452	ENST00000269221;ENST00000540942	T	0.11604	2.76	4.34	4.34	0.51931	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.981;0.992	T	0.32481	-0.9905	10	0.46703	T	0.11	-12.1412	17.2368	0.87001	0.0:1.0:0.0:0.0	.	44;44	Q96DM3;F5H2W0	MIC1_HUMAN;.	I	44	ENSP00000269221:T44I	ENSP00000269221:T44I	T	+	2	0	C18orf8	19338361	1.000000	0.71417	0.963000	0.40424	0.981000	0.71138	6.956000	0.76013	2.130000	0.65690	0.655000	0.94253	ACT		0.433	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1		NM_013326	
CCDC181	57821	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	169391258	169391258	+	Silent	SNP	A	A	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:169391258A>G	ENST00000367806.3	-	3	563	c.411T>C	c.(409-411)ctT>ctC	p.L137L	CCDC181_ENST00000545005.1_Silent_p.L137L|CCDC181_ENST00000367805.3_Silent_p.L137L|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	137						nucleus (GO:0005634)		p.L137L(1)									GATTCTGTAGAAGCTTGTTAG	0.398																																																	1	Substitution - coding silent(1)	kidney(1)											101.0	104.0	103.0					1																	169391258		2203	4300	6503	SO:0001819	synonymous_variant	57821			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.411T>C	1.37:g.169391258A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O60780|Q53FD5|Q5TID9|Q8TC48	Silent	SNP	ENST00000367806.3	37																																																																																					0.398	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1		NM_021179	
C1QTNF4	114900	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	47611595	47611595	+	Silent	SNP	G	G	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:47611595G>C	ENST00000302514.3	-	2	1284	c.768C>G	c.(766-768)gcC>gcG	p.A256A		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	256	C1q 2. {ECO:0000255|PROSITE- ProRule:PRU00368}.					extracellular space (GO:0005615)		p.A256A(1)		breast(2)|endometrium(1)|kidney(1)|lung(2)	6						CGTAAATCATGGCCTGCACCT	0.672																																																	1	Substitution - coding silent(1)	kidney(1)											34.0	41.0	39.0					11																	47611595		2197	4297	6494	SO:0001819	synonymous_variant	114900			AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"""complement-c1q tumor necrosis factor-related protein 4"""	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.768C>G	11.37:g.47611595G>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IV25	Silent	SNP	ENST00000302514.3	37	CCDS7942.1																																																																																				0.672	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1		NM_031909	
CBL	867	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	119168096	119168096	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:119168096C>T	ENST00000264033.4	+	14	2532	c.2156C>T	c.(2155-2157)gCa>gTa	p.A719V		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	719	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A719V(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TGGTTCAGAGCATGTGATTGC	0.398			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																															"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	1	Substitution - Missense(1)	kidney(1)											100.0	92.0	95.0					11																	119168096		2199	4295	6494	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2156C>T	11.37:g.119168096C>T	ENSP00000264033:p.Ala719Val	Somatic		WXS	Illumina HiSeq	Phase_I	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.619576	0.46736	.	.	ENSG00000110395	ENST00000264033	T	0.76060	-0.99	5.32	-0.291	0.12843	.	0.985567	0.08307	N	0.965970	T	0.50582	0.1624	N	0.08118	0	0.23174	N	0.99818	B	0.02656	0.0	B	0.01281	0.0	T	0.28267	-1.0049	10	0.12766	T	0.61	-22.0516	9.3311	0.38023	0.0:0.4767:0.0:0.5233	.	719	P22681	CBL_HUMAN	V	719	ENSP00000264033:A719V	ENSP00000264033:A719V	A	+	2	0	CBL	118673306	0.000000	0.05858	0.010000	0.14722	0.990000	0.78478	-0.462000	0.06704	-0.000000	0.14550	-0.157000	0.13467	GCA		0.398	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4		NM_005188	
CDK14	5218	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	90355879	90355879	+	Splice_Site	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:90355879A>T	ENST00000380050.3	+	3	254		c.e3-1		CDK14_ENST00000436577.2_Splice_Site|CDK14_ENST00000496279.1_Splice_Site|CDK14_ENST00000265741.3_Splice_Site|CDK14_ENST00000406263.1_Splice_Site			O94921	CDK14_HUMAN	cyclin-dependent kinase 14						cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.?(2)		breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						TTCTTTTCTCAGATATGTGTC	0.378																																					GBM(83;1228 1256 8311 16577 31299)												2	Unknown(2)	kidney(2)											60.0	57.0	58.0					7																	90355879		2203	4299	6502	SO:0001630	splice_region_variant	5218				CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"""Cyclin-dependent kinases"""	8883	protein-coding gene	gene with protein product		610679	"""PFTAIRE protein kinase 1"""	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.124-1A>T	7.37:g.90355879A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Splice_Site	SNP	ENST00000380050.3	37		.	.	.	.	.	.	.	.	.	.	A	15.94	2.982254	0.53827	.	.	ENSG00000058091	ENST00000380050;ENST00000265741	.	.	.	5.72	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7956	0.57558	0.8632:0.1368:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDK14	90193815	1.000000	0.71417	0.979000	0.43373	0.843000	0.47879	8.513000	0.90542	0.949000	0.37715	0.460000	0.39030	.		0.378	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5		NM_012395	Intron
CHRM2	1129	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	136700642	136700642	+	Missense_Mutation	SNP	G	G	A	rs201165506		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:136700642G>A	ENST00000445907.2	+	3	1558	c.1030G>A	c.(1030-1032)Gtg>Atg	p.V344M	hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.V344M|CHRM2_ENST00000402486.3_Missense_Mutation_p.V344M|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.V344M|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.V344M|hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.V344M	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	344					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.V344M(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TAATACCACCGTGGAGGTAGT	0.463																																																	1	Substitution - Missense(1)	kidney(1)											85.0	86.0	86.0					7																	136700642		2203	4300	6503	SO:0001583	missense	1129				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1951	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 2"""	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.1030G>A	7.37:g.136700642G>A	ENSP00000399745:p.Val344Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.643421	0.47258	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05;0.05	5.4	5.4	0.78164	GPCR, rhodopsin-like superfamily (1);	0.254272	0.30911	N	0.008630	T	0.57975	0.2090	L	0.39085	1.19	0.80722	D	1	B	0.30193	0.272	B	0.33568	0.166	T	0.56098	-0.8035	10	0.41790	T	0.15	-9.5982	19.1729	0.93588	0.0:0.0:1.0:0.0	.	344	P08172	ACM2_HUMAN	M	344	ENSP00000399745:V344M;ENSP00000415386:V344M;ENSP00000319984:V344M;ENSP00000380733:V344M;ENSP00000384937:V344M;ENSP00000384401:V344M	ENSP00000319984:V344M	V	+	1	0	CHRM2	136351182	1.000000	0.71417	0.953000	0.39169	0.978000	0.69477	9.807000	0.99171	2.541000	0.85698	0.655000	0.94253	GTG		0.463	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			
CPSF3	51692	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	9588441	9588441	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:9588441G>A	ENST00000238112.3	+	11	1563	c.1357G>A	c.(1357-1359)Gca>Aca	p.A453T	CPSF3_ENST00000460593.1_Missense_Mutation_p.A416T	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	453					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.A453T(1)		NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GAATACAGAAGCAGTGACCTT	0.393																																					Colon(194;1259 2048 3845 5218 19985)												1	Substitution - Missense(1)	kidney(1)											80.0	78.0	79.0					2																	9588441		2203	4300	6503	SO:0001583	missense	51692			AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"""cleavage and polyadenylation specific factor 3, 73kD subunit"""			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.1357G>A	2.37:g.9588441G>A	ENSP00000238112:p.Ala453Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	37	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890042	0.52014	.	.	ENSG00000119203	ENST00000238112;ENST00000540142;ENST00000427001;ENST00000460593	T;T	0.37235	1.21;1.21	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.22437	0.0541	N	0.14661	0.345	0.80722	D	1	B;B	0.11235	0.002;0.004	B;B	0.09377	0.004;0.004	T	0.10291	-1.0636	10	0.05833	T	0.94	-18.3887	19.14	0.93444	0.0:0.0:1.0:0.0	.	404;453	E7ER23;Q9UKF6	.;CPSF3_HUMAN	T	453;175;404;416	ENSP00000238112:A453T;ENSP00000418957:A416T	ENSP00000238112:A453T	A	+	1	0	CPSF3	9505892	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.813000	0.99286	2.589000	0.87451	0.655000	0.94253	GCA		0.393	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1		NM_016207	
CRYGB	1419	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	209007477	209007477	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:209007477G>C	ENST00000260988.4	-	3	460	c.413C>G	c.(412-414)cCc>cGc	p.P138R		NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B	138	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)	p.P138R(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		CCTGTAGTTGGGCATCTCATA	0.547																																																	1	Substitution - Missense(1)	kidney(1)											104.0	103.0	103.0					2																	209007477		2203	4300	6503	SO:0001583	missense	1419				CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"""crystallin, gamma 1-2"""	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.413C>G	2.37:g.209007477G>C	ENSP00000260988:p.Pro138Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RB5|Q53ST2	Missense_Mutation	SNP	ENST00000260988.4	37	CCDS2380.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.364487	0.82463	.	.	ENSG00000182187	ENST00000260988	T	0.79454	-1.27	4.73	4.73	0.59995	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.050350	0.85682	D	0.000000	D	0.92296	0.7556	H	0.98682	4.3	0.80722	D	1	D	0.61080	0.989	D	0.66847	0.947	D	0.94916	0.8069	10	0.87932	D	0	.	15.5827	0.76459	0.0:0.0:1.0:0.0	.	138	P07316	CRGB_HUMAN	R	138	ENSP00000260988:P138R	ENSP00000260988:P138R	P	-	2	0	CRYGB	208715722	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.306000	0.65756	2.614000	0.88457	0.561000	0.74099	CCC		0.547	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256473.2		NM_005210	
CTDSP2	10106	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	58217389	58217389	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:58217389G>T	ENST00000398073.2	-	8	1115	c.812C>A	c.(811-813)cCt>cAt	p.P271H	CTDSP2_ENST00000547701.1_Missense_Mutation_p.P119H|CTDSP2_ENST00000548823.1_Missense_Mutation_p.P98H|MIR26A2_ENST00000385054.1_RNA	NM_005730.3	NP_005721.3	O14595	CTDS2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	271					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein dephosphorylation (GO:0006470)	nucleoplasm (GO:0005654)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)	p.P271H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)					GGCAGGCTAAGGGGCCCGCAG	0.582																																																	1	Substitution - Missense(1)	kidney(1)											27.0	33.0	31.0					12																	58217389		2103	4242	6345	SO:0001583	missense	10106			AF000152	CCDS41801.1	12q14.1	2012-06-14			ENSG00000175215	ENSG00000175215		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	17077	protein-coding gene	gene with protein product	"""conserved gene amplified in osteosarcoma"", ""nuclear LIM interactor-interacting factor 2"", ""NLI-interacting factor 2"", ""small CTD phosphatase 2"""	608711				9315096, 12721286	Standard	XM_005268556		Approved	OS4, SCP2, PSR2	uc001sqm.3	O14595	OTTHUMG00000170483	ENST00000398073.2:c.812C>A	12.37:g.58217389G>T	ENSP00000381148:p.Pro271His	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5H4|Q53ZR2|Q6NZY3|Q9UEX1	Missense_Mutation	SNP	ENST00000398073.2	37	CCDS41801.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763236	0.69763	.	.	ENSG00000175215	ENST00000398073;ENST00000548823;ENST00000549039;ENST00000547701	T;T	0.32023	2.19;1.47	5.26	4.35	0.52113	.	0.820040	0.11432	N	0.564691	T	0.39462	0.1079	N	0.22421	0.69	0.35708	D	0.816149	D;D;B	0.89917	1.0;1.0;0.001	D;D;B	0.91635	0.998;0.999;0.001	T	0.42464	-0.9450	10	0.87932	D	0	0.1882	8.441	0.32816	0.0817:0.0:0.7655:0.1528	.	145;98;271	B4DH48;F8W1I1;O14595	.;.;CTDS2_HUMAN	H	271;98;125;119	ENSP00000381148:P271H;ENSP00000448386:P125H	ENSP00000381148:P271H	P	-	2	0	CTDSP2	56503656	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.348000	0.44045	2.729000	0.93468	0.563000	0.77884	CCT		0.582	CTDSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409353.1		NM_005730	
DFNA5	1687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	24758693	24758693	+	Silent	SNP	G	G	A	rs367647197		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:24758693G>A	ENST00000342947.3	-	4	974	c.549C>T	c.(547-549)atC>atT	p.I183I	DFNA5_ENST00000409775.3_Silent_p.I183I|DFNA5_ENST00000419307.1_Silent_p.I19I|DFNA5_ENST00000545231.1_Silent_p.I19I|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409970.1_Silent_p.I19I	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	183					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)		p.I183I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GGATGCCCACGATGCCACCAC	0.577																																					GBM(78;184 1250 20134 20900 23600)												1	Substitution - coding silent(1)	kidney(1)						G	,,	0,4406		0,0,2203	235.0	185.0	202.0		549,57,549	0.0	1.0	7		202	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	183/497,19/333,183/497	24758693	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1687			AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.549C>T	7.37:g.24758693G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	G	2.157	-0.393120	0.04899	0.0	1.16E-4	ENSG00000105928	ENST00000446822	.	.	.	5.17	0.0276	0.14155	.	.	.	.	.	T	0.51381	0.1671	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37709	-0.9694	4	.	.	.	-5.0276	6.1498	0.20306	0.0:0.2849:0.4752:0.24	.	.	.	.	L	8	.	.	S	-	2	0	DFNA5	24725218	0.000000	0.05858	0.968000	0.41197	0.033000	0.12548	-0.102000	0.10956	-0.059000	0.13154	-0.147000	0.13772	TCG		0.577	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2		NM_004403	
DMGDH	29958	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	78359437	78359437	+	Splice_Site	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr5:78359437G>T	ENST00000255189.3	-	2	303	c.275C>A	c.(274-276)gCa>gAa	p.A92E	DMGDH_ENST00000520388.1_Intron|DMGDH_ENST00000380311.4_Splice_Site_p.R47R|DMGDH_ENST00000540686.1_Splice_Site_p.Q18K	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	92					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)	p.A92E(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TTTTCTTACTGCGTGCCAGGT	0.493																																																	1	Substitution - Missense(1)	kidney(1)											173.0	158.0	163.0					5																	78359437		2203	4300	6503	SO:0001630	splice_region_variant	29958			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.276+1C>A	5.37:g.78359437G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.1|20.1	3.935941|3.935941	0.73442|0.73442	.|.	.|.	ENSG00000132837|ENSG00000132837	ENST00000255189|ENST00000540686	D|T	0.82803|0.28666	-1.65|1.6	5.52|5.52	5.52|5.52	0.82312|0.82312	FAD dependent oxidoreductase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.47746|0.47746	0.1462|0.1462	M|M	0.90483|0.90483	3.12|3.12	0.33986|0.33986	D|D	0.648532|0.648532	D|B	0.76494|0.02656	0.999|0.0	D|B	0.77004|0.01281	0.989|0.0	T|T	0.59862|0.59862	-0.7374|-0.7374	10|9	0.87932|0.66056	D|D	0|0.02	.|.	19.7963|19.7963	0.96484|0.96484	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	92|18	Q9UI17|B4E1J9	M2GD_HUMAN|.	E|K	92|18	ENSP00000255189:A92E|ENSP00000439478:Q18K	ENSP00000255189:A92E|ENSP00000439478:Q18K	A|Q	-|-	2|1	0|0	DMGDH|DMGDH	78395193|78395193	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	9.662000|9.662000	0.98603|0.98603	2.756000|2.756000	0.94617|0.94617	0.561000|0.561000	0.74099|0.74099	GCA|CAA		0.493	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3		NM_013391	Missense_Mutation
DST	667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	56484745	56484745	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr6:56484745C>A	ENST00000370765.6	-	23	4194	c.4087G>T	c.(4087-4089)Gaa>Taa	p.E1363*	DST_ENST00000312431.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0				K -> E (in Ref. 3; AAL62061). {ECO:0000305}.	axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.E1363*(2)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TGTTTGAGTTCTTCTGCTTTC	0.453																																																	2	Substitution - Nonsense(2)	kidney(2)											187.0	173.0	178.0					6																	56484745		2203	4300	6503	SO:0001587	stop_gained	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.4087G>T	6.37:g.56484745C>A	ENSP00000359801:p.Glu1363*	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	38	6.762614	0.97821	.	.	ENSG00000151914	ENST00000370765	.	.	.	4.19	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	6.0914	0.19997	0.0:0.6765:0.1552:0.1684	.	.	.	.	X	1363	.	ENSP00000359801:E1363X	E	-	1	0	DST	56592704	0.677000	0.27577	0.013000	0.15412	0.472000	0.32918	1.771000	0.38542	0.410000	0.25675	-0.262000	0.10625	GAA		0.453	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2		NM_001723	
DOPEY1	23033	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	83838711	83838711	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr6:83838711C>G	ENST00000349129.2	+	16	2085	c.1825C>G	c.(1825-1827)Caa>Gaa	p.Q609E	DOPEY1_ENST00000237163.5_Missense_Mutation_p.Q590E|DOPEY1_ENST00000369739.3_Missense_Mutation_p.Q600E	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	609					protein transport (GO:0015031)			p.Q609E(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TATACAATATCAAGCAGACCG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											113.0	117.0	116.0					6																	83838711		2203	4300	6503	SO:0001583	missense	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.1825C>G	6.37:g.83838711C>G	ENSP00000195654:p.Gln609Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504021	0.44558	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.22743	1.96;1.94	5.66	5.66	0.87406	.	0.239734	0.34986	N	0.003526	T	0.19565	0.0470	L	0.59436	1.845	0.80722	D	1	P;P;P	0.45531	0.86;0.495;0.495	B;B;B	0.42851	0.4;0.106;0.106	T	0.01484	-1.1343	10	0.54805	T	0.06	.	19.7324	0.96188	0.0:1.0:0.0:0.0	.	500;600;609	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	E	609;590;590	ENSP00000195654:Q609E;ENSP00000237163:Q590E	ENSP00000237163:Q590E	Q	+	1	0	DOPEY1	83895430	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.294000	0.78760	2.663000	0.90544	0.655000	0.94253	CAA		0.443	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2		NM_015018	
EVX2	344191	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	176948341	176948341	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:176948341G>A	ENST00000308618.4	-	1	300	c.164C>T	c.(163-165)tCt>tTt	p.S55F		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	55					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.S55F(1)		kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		CAGGGGGGCAGACGGCAGGCG	0.602																																																	1	Substitution - Missense(1)	kidney(1)											38.0	44.0	42.0					2																	176948341		2203	4300	6503	SO:0001583	missense	344191				CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"""Homeoboxes / ANTP class : HOXL subclass"""	3507	protein-coding gene	gene with protein product		142991	"""eve, even-skipped homeobox homolog 2 (Drosophila)"""			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.164C>T	2.37:g.176948341G>A	ENSP00000312385:p.Ser55Phe	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000308618.4	37	CCDS33333.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835828	0.71373	.	.	ENSG00000174279	ENST00000308618	D	0.92299	-3.01	5.44	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.93022	0.7779	L	0.49126	1.545	0.58432	D	0.999993	D	0.67145	0.996	P	0.56700	0.804	D	0.93574	0.6906	10	0.72032	D	0.01	-25.3773	14.205	0.65728	0.0715:0.0:0.9285:0.0	.	55	Q03828	EVX2_HUMAN	F	55	ENSP00000312385:S55F	ENSP00000312385:S55F	S	-	2	0	EVX2	176656587	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.446000	0.80609	1.526000	0.49068	0.655000	0.94253	TCT		0.602	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1			
FAM182B	728882	broad.mit.edu	37	20	25848606	25848606	+	5'UTR	SNP	G	G	A	rs372155704		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr20:25848606G>A	ENST00000478164.1	-	0	180				FAM182B_ENST00000376404.2_5'UTR			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B											lung(1)	1						atcaccgtccgggcaggcctg	0.672																																																	0																																										SO:0001623	5_prime_UTR_variant	728882					20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170			34503	pseudogene	pseudogene							Standard	NR_027061		Approved			Q5T319	OTTHUMG00000032136	ENST00000478164.1:c.-812C>T	20.37:g.25848606G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q4G0Q1	RNA	SNP	ENST00000478164.1	37																																																																																					0.672	FAM182B-005	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000316665.1		NR_026714	
FBXO18	84893	hgsc.bcm.edu;ucsc.edu	37	10	5953065	5953070	+	In_Frame_Del	DEL	GGAGAA	GGAGAA	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	GGAGAA	GGAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr10:5953065_5953070delGGAGAA	ENST00000362091.4	+	6	1300_1305	c.1185_1190delGGAGAA	c.(1183-1191)agggagaag>agg	p.EK396del	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000379999.5_In_Frame_Del_p.EK447del	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	396					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						ACGCCATGAGGGAGAAGGGGATTAAC	0.592																																																	0																																										SO:0001651	inframe_deletion	84893			AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.1185_1190delGGAGAA	10.37:g.5953065_5953070delGGAGAA	ENSP00000355415:p.Glu396_Lys397del	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	In_Frame_Del	DEL	ENST00000362091.4	37	CCDS7072.1																																																																																				0.592	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1		NM_032807	
GDF15	9518	broad.mit.edu;hgsc.bcm.edu	37	19	18499472	18499472	+	Silent	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:18499472G>T	ENST00000252809.3	+	2	686	c.654G>T	c.(652-654)gcG>gcT	p.A218A	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	218					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)	p.A218A(1)		kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CGGTCCGCGCGTCGCTGGAAG	0.736											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											15.0	17.0	16.0					19																	18499472		2157	4251	6408	SO:0001819	synonymous_variant	9518			BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"""prostate differentiation factor"""	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.654G>T	19.37:g.18499472G>T		Somatic	726	WXS	Illumina HiSeq	Phase_I	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																				0.736	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2		NM_004864	
GJC2	57165	broad.mit.edu	37	1	228346349	228346349	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:228346349C>T	ENST00000366714.2	+	2	1065	c.890C>T	c.(889-891)gCg>gTg	p.A297V		NM_020435.3	NP_065168.2	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	297					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|response to toxic substance (GO:0009636)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)	gap junction channel activity (GO:0005243)	p.A297V(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Prostate(94;0.0405)				GCGCAGGACGCGGTGCGCGGC	0.761																																																	1	Substitution - Missense(1)	kidney(1)											26.0	28.0	27.0					1																	228346349		2201	4295	6496	SO:0001583	missense	57165			AF014643	CCDS1569.1	1q41-q42	2009-01-02	2007-12-14	2007-11-06	ENSG00000198835	ENSG00000198835		"""Ion channels / Gap junction proteins (connexins)"""	17494	protein-coding gene	gene with protein product	"""connexin 47"""	608803	"""gap junction protein, alpha 12, 47kDa"""	GJA12		19056803	Standard	NM_020435		Approved	CX47, CX46.6, SPG44	uc001hsk.3	Q5T442	OTTHUMG00000039771	ENST00000366714.2:c.890C>T	1.37:g.228346349C>T	ENSP00000355675:p.Ala297Val	Somatic		WXS	Illumina GAIIx	Phase_I	O43440|Q7Z7J2|Q8IWJ9	Missense_Mutation	SNP	ENST00000366714.2	37	CCDS1569.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.670487	0.47781	.	.	ENSG00000198835	ENST00000366714	D	0.98192	-4.78	3.8	3.8	0.43715	.	0.075445	0.52532	D	0.000062	D	0.94584	0.8255	L	0.32530	0.975	0.48288	D	0.999621	P	0.37914	0.611	B	0.24006	0.05	D	0.94524	0.7730	10	0.36615	T	0.2	.	15.8635	0.79043	0.0:1.0:0.0:0.0	.	297	Q5T442	CXG2_HUMAN	V	297	ENSP00000355675:A297V	ENSP00000355675:A297V	A	+	2	0	GJC2	226412972	0.736000	0.28164	0.929000	0.37066	0.636000	0.38137	1.867000	0.39499	1.966000	0.57179	0.484000	0.47621	GCG		0.761	GJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095985.1		NM_020435	
GNAO1	2775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	56309956	56309956	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:56309956G>A	ENST00000262493.6	+	3	1121	c.275G>A	c.(274-276)gGc>gAc	p.G92D	GNAO1_ENST00000262494.7_Missense_Mutation_p.G92D	NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O	92					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)	p.G92D(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				GACACTTTGGGCATCGAATAT	0.522																																																	2	Substitution - Missense(2)	kidney(2)											108.0	91.0	97.0					16																	56309956		2198	4300	6498	SO:0001583	missense	2775				CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258			4389	protein-coding gene	gene with protein product		139311				1899283, 11395521	Standard	NM_020988		Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.275G>A	16.37:g.56309956G>A	ENSP00000262493:p.Gly92Asp	Somatic		WXS	Illumina HiSeq	Phase_I	P29777|Q8TD72|Q9UMV4	Missense_Mutation	SNP	ENST00000262493.6	37	CCDS10756.1	.	.	.	.	.	.	.	.	.	.	G	13.68	2.309633	0.40895	.	.	ENSG00000087258	ENST00000262493;ENST00000262494	D;D	0.88046	-2.33;-2.33	5.39	4.44	0.53790	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.82430	0.5035	L	0.45228	1.405	0.80722	D	1	B;B	0.12013	0.004;0.005	B;B	0.15870	0.014;0.008	T	0.77877	-0.2424	10	0.41790	T	0.15	.	13.2236	0.59903	0.0759:0.0:0.9241:0.0	.	92;92	P09471;P09471-2	GNAO_HUMAN;.	D	92	ENSP00000262493:G92D;ENSP00000262494:G92D	ENSP00000262493:G92D	G	+	2	0	GNAO1	54867457	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	7.912000	0.87465	1.289000	0.44618	-0.140000	0.14226	GGC		0.522	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256981.2		NM_020988	
HIVEP3	59269	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	42045713	42045713	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:42045713C>T	ENST00000372583.1	-	4	5641	c.4756G>A	c.(4756-4758)Ggt>Agt	p.G1586S	HIVEP3_ENST00000247584.5_Missense_Mutation_p.G1586S|HIVEP3_ENST00000429157.2_Missense_Mutation_p.G1586S|HIVEP3_ENST00000372584.1_Missense_Mutation_p.G1586S|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1586					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G1586S(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GAGTCCGTACCTTCTTGTGAC	0.493																																																	1	Substitution - Missense(1)	kidney(1)											175.0	145.0	155.0					1																	42045713		2203	4300	6503	SO:0001583	missense	59269			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.4756G>A	1.37:g.42045713C>T	ENSP00000361664:p.Gly1586Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	7.891	0.732279	0.15507	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05996	3.38;3.36;3.36;3.38	5.55	5.55	0.83447	.	0.000000	0.56097	D	0.000036	T	0.10165	0.0249	L	0.57536	1.79	0.38404	D	0.945749	P;P	0.51537	0.946;0.911	B;B	0.43155	0.41;0.232	T	0.01330	-1.1383	10	0.59425	D	0.04	-12.3291	13.5611	0.61790	0.0:0.9253:0.0:0.0747	.	1586;1586	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	S	1586	ENSP00000361665:G1586S;ENSP00000361664:G1586S;ENSP00000247584:G1586S;ENSP00000410828:G1586S	ENSP00000247584:G1586S	G	-	1	0	HIVEP3	41818300	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.221000	0.42917	2.894000	0.99253	0.655000	0.94253	GGT		0.493	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1		NM_024503	
INSR	3643	broad.mit.edu;hgsc.bcm.edu	37	19	7152929	7152929	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:7152929A>G	ENST00000302850.5	-	10	2181	c.2039T>C	c.(2038-2040)cTg>cCg	p.L680P	INSR_ENST00000341500.5_Missense_Mutation_p.L680P	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	680	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.L680P(2)		breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CCTCGAGGGCAGCTTCAGCCC	0.547																																																	2	Substitution - Missense(2)	kidney(2)											66.0	60.0	62.0					19																	7152929		2203	4300	6503	SO:0001583	missense	3643			M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2039T>C	19.37:g.7152929A>G	ENSP00000303830:p.Leu680Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	a	18.96	3.733880	0.69189	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	T;T	0.72942	-0.7;-0.7	5.55	5.55	0.83447	Fibronectin, type III (3);	0.000000	0.36409	U	0.002602	T	0.79423	0.4443	M	0.75264	2.295	0.80722	D	1	P;P;B	0.45126	0.609;0.851;0.409	B;P;B	0.53035	0.443;0.716;0.343	T	0.80892	-0.1179	10	0.52906	T	0.07	.	13.6724	0.62434	1.0:0.0:0.0:0.0	.	671;680;680	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	P	680	ENSP00000303830:L680P;ENSP00000342838:L680P	ENSP00000303830:L680P	L	-	2	0	INSR	7103929	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	8.677000	0.91203	2.121000	0.65114	0.487000	0.48397	CTG		0.547	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			
KDM5A	5927	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	442697	442697	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:442697C>T	ENST00000399788.2	-	12	1971	c.1609G>A	c.(1609-1611)Gtt>Att	p.V537I	KDM5A_ENST00000382815.4_Missense_Mutation_p.V537I	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	537	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.V537I(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						ATGATGGTAACTAACTGATGC	0.463			T	NUP98	AML																																			Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	2	Substitution - Missense(2)	kidney(2)											128.0	130.0	130.0					12																	442697		1985	4171	6156	SO:0001583	missense	5927				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1609G>A	12.37:g.442697C>T	ENSP00000382688:p.Val537Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642963	0.87859	.	.	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.70749	-0.51;-0.51;-0.51	5.53	5.53	0.82687	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	T	0.80773	0.4687	M	0.76328	2.33	0.80722	D	1	B;B;B;B	0.27765	0.074;0.188;0.012;0.174	B;B;B;B	0.43508	0.047;0.422;0.073;0.149	T	0.80358	-0.1416	10	0.87932	D	0	-11.1856	19.4553	0.94884	0.0:1.0:0.0:0.0	.	156;537;537;537	B4DVX3;F5H1F7;P29375;P29375-2	.;.;KDM5A_HUMAN;.	I	156;496;537;537;156	ENSP00000382688:V537I;ENSP00000372265:V537I;ENSP00000440622:V156I	ENSP00000261253:V156I	V	-	1	0	KDM5A	312958	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	7.659000	0.83766	2.594000	0.87642	0.591000	0.81541	GTT		0.463	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1		NM_005056	
KDM5C	8242	broad.mit.edu;hgsc.bcm.edu	37	X	53227796	53227796	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chrX:53227796C>A	ENST00000375401.3	-	17	2924	c.2392G>T	c.(2392-2394)Gag>Tag	p.E798*	KDM5C_ENST00000375379.3_Nonsense_Mutation_p.E798*|KDM5C_ENST00000404049.3_Nonsense_Mutation_p.E797*|KDM5C_ENST00000465402.1_5'Flank|KDM5C_ENST00000452825.3_Nonsense_Mutation_p.E731*|KDM5C_ENST00000375383.3_Nonsense_Mutation_p.E757*	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	798					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.E798*(1)|p.E731*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GCTTCAGACTCTAGTGCCCTC	0.527			"""N, F, S"""		clear cell renal carcinoma																																			Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	2	Substitution - Nonsense(2)	kidney(2)											37.0	34.0	35.0					X																	53227796		2203	4300	6503	SO:0001587	stop_gained	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2392G>T	X.37:g.53227796C>A	ENSP00000364550:p.Glu798*	Somatic		WXS	Illumina HiSeq	Phase_I	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Nonsense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	C	45	11.319086	0.99546	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	.	.	.	5.03	5.03	0.67393	.	0.097907	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-15.8722	14.8392	0.70212	0.0:1.0:0.0:0.0	.	.	.	.	X	731;798;797;798;757	.	ENSP00000364528:E798X	E	-	1	0	KDM5C	53244521	0.157000	0.22836	0.994000	0.49952	0.944000	0.59088	1.956000	0.40382	2.086000	0.62901	0.523000	0.50628	GAG		0.527	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2		NM_004187	
KIAA1467	57613	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	13233561	13233561	+	Missense_Mutation	SNP	C	C	G	rs192853755	byFrequency	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:13233561C>G	ENST00000197268.8	+	13	1986	c.1866C>G	c.(1864-1866)atC>atG	p.I622M		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	622						integral component of membrane (GO:0016021)		p.I622M(1)		NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TTCCATAGATCTAATCTGATG	0.363													C|||	5	0.000998403	0.0	0.0	5008	,	,		20985	0.005		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											91.0	84.0	87.0					12																	13233561		2203	4300	6503	SO:0001583	missense	57613			AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.1866C>G	12.37:g.13233561C>G	ENSP00000197268:p.Ile622Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Missense_Mutation	SNP	ENST00000197268.8	37	CCDS31750.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	8.354	0.831578	0.16820	.	.	ENSG00000084444	ENST00000197268	.	.	.	4.91	-2.94	0.05581	.	1.900440	0.02151	N	0.058020	T	0.11410	0.0278	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11084	-1.0602	9	0.36615	T	0.2	-14.1461	4.3913	0.11341	0.123:0.2412:0.4819:0.1539	.	622	A2RU67	K1467_HUMAN	M	622	.	ENSP00000197268:I622M	I	+	3	3	KIAA1467	13124828	0.141000	0.22595	0.001000	0.08648	0.131000	0.20780	-1.131000	0.03238	-0.900000	0.03896	-0.266000	0.10368	ATC		0.363	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1		NM_020853	
KLHDC7B	113730	broad.mit.edu;hgsc.bcm.edu	37	22	50987493	50987493	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr22:50987493C>A	ENST00000395676.2	+	1	1032	c.898C>A	c.(898-900)Ccc>Acc	p.P300T	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	300								p.P201T(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCAGGGCTCCCCAGGGGCCC	0.741																																																	1	Substitution - Missense(1)	kidney(1)											17.0	21.0	19.0					22																	50987493		1588	3419	5007	SO:0001583	missense	113730			BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.898C>A	22.37:g.50987493C>A	ENSP00000379034:p.Pro300Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000395676.2	37	CCDS14097.2	.	.	.	.	.	.	.	.	.	.	C	5.998	0.368130	0.11352	.	.	ENSG00000130487	ENST00000395676	D	0.81579	-1.51	3.92	-7.84	0.01196	.	.	.	.	.	T	0.47637	0.1456	N	0.02142	-0.665	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47898	-0.9081	9	0.11794	T	0.64	.	8.4421	0.32820	0.2645:0.5563:0.1792:0.0	.	300	Q96G42	KLD7B_HUMAN	T	300	ENSP00000379034:P300T	ENSP00000379034:P300T	P	+	1	0	KLHDC7B	49334359	0.000000	0.05858	0.000000	0.03702	0.817000	0.46193	-0.991000	0.03728	-1.333000	0.02247	0.306000	0.20318	CCC		0.741	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2		NM_138433	
LAMC2	3918	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	183194784	183194784	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:183194784G>C	ENST00000264144.4	+	8	1060	c.995G>C	c.(994-996)aGt>aCt	p.S332T	LAMC2_ENST00000493293.1_Missense_Mutation_p.S332T	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	332	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.S332T(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						CCCCAGCTGAGTTACTTTGAG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											109.0	119.0	116.0					1																	183194784		2203	4300	6503	SO:0001583	missense	3918			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.995G>C	1.37:g.183194784G>C	ENSP00000264144:p.Ser332Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398930	0.42512	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.31769	1.48;1.48	5.06	5.06	0.68205	Laminin B type IV (2);Laminin B, subgroup (1);Growth factor, receptor (1);	0.062104	0.64402	D	0.000004	T	0.42108	0.1188	L	0.41079	1.255	0.52501	D	0.999951	D;D;D	0.69078	0.991;0.997;0.989	D;D;P	0.71870	0.926;0.975;0.879	T	0.08953	-1.0697	10	0.21540	T	0.41	.	12.3121	0.54933	0.0886:0.0:0.9114:0.0	.	332;332;332	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	T	332	ENSP00000432063:S332T;ENSP00000264144:S332T	ENSP00000264144:S332T	S	+	2	0	LAMC2	181461407	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.926000	0.56491	2.336000	0.79503	0.655000	0.94253	AGT		0.398	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1		NM_005562	
LIN7A	8825	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	81239638	81239638	+	Silent	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:81239638A>T	ENST00000552864.1	-	4	556	c.354T>A	c.(352-354)ctT>ctA	p.L118L		NM_004664.2	NP_004655.1	O14910	LIN7A_HUMAN	lin-7 homolog A (C. elegans)	118	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				exocytosis (GO:0006887)|inner ear development (GO:0048839)|neurotransmitter secretion (GO:0007269)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|synaptic vesicle transport (GO:0048489)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	L27 domain binding (GO:0097016)	p.L118L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(2)	15						CATTAAAACCAAGGCCTTCAT	0.458																																																	1	Substitution - coding silent(1)	kidney(1)											66.0	63.0	64.0					12																	81239638		2203	4300	6503	SO:0001819	synonymous_variant	8825			AF028826	CCDS9021.1	12q21.31	2014-09-04			ENSG00000111052	ENSG00000111052			17787	protein-coding gene	gene with protein product	"""mammalian LIN-7 1"""	603380				10341223, 17237226	Standard	NM_004664		Approved	MALS-1, TIP-33, LIN-7A, VELI1	uc001szj.1	O14910	OTTHUMG00000170168	ENST00000552864.1:c.354T>A	12.37:g.81239638A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A4FTY3|Q147W1|Q6LES3|Q7LDS4	Silent	SNP	ENST00000552864.1	37	CCDS9021.1	.	.	.	.	.	.	.	.	.	.	A	0.517	-0.863998	0.02590	.	.	ENSG00000111052	ENST00000552093	.	.	.	5.27	0.0828	0.14430	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3019	10.1771	0.42946	0.4279:0.5045:0.0676:0.0	.	.	.	.	X	84	.	ENSP00000448891:L84X	L	-	2	0	LIN7A	79763769	0.999000	0.42202	1.000000	0.80357	0.034000	0.12701	0.773000	0.26661	0.054000	0.16065	-1.333000	0.01266	TTG		0.458	LIN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407760.1			
Unknown	0	broad.mit.edu	37	13	19415641	19415641	+	IGR	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr13:19415641A>T								LINC00418 (121772 upstream) : RP11-38M15.11 (18325 downstream)																							aaaaaaaaaaaaacccaaaca	0.418																																																	0																																										SO:0001628	intergenic_variant	0																															13.37:g.19415641A>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.418									
Unknown	0	broad.mit.edu	37	9	66500794	66500794	+	IGR	SNP	T	T	C	rs7866420		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr9:66500794T>C								RP11-262H14.1 (31484 upstream) : RP11-262H14.7 (16411 downstream)																							TTAAAGACTTTGGACCACCTA	0.647																																																	0																																										SO:0001628	intergenic_variant	0																															9.37:g.66500794T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.647									
LOXL3	84695	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	74763177	74763177	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:74763177A>C	ENST00000264094.3	-	7	1265	c.1194T>G	c.(1192-1194)caT>caG	p.H398Q	LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409986.1_Missense_Mutation_p.H253Q|LOXL3_ENST00000409549.1_Missense_Mutation_p.H398Q|LOXL3_ENST00000393937.2_Missense_Mutation_p.H253Q	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	398	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.H398Q(1)		endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CATCCTGGCTATGTGAACAAT	0.557																																																	1	Substitution - Missense(1)	kidney(1)											98.0	97.0	97.0					2																	74763177		2203	4300	6503	SO:0001583	missense	84695			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1194T>G	2.37:g.74763177A>C	ENSP00000264094:p.His398Gln	Somatic		WXS	Illumina HiSeq	Phase_I	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.74|17.74	3.463401|3.463401	0.63513|0.63513	.|.	.|.	ENSG00000115318|ENSG00000115318	ENST00000264094;ENST00000393937;ENST00000409549;ENST00000409986|ENST00000420535	T;T;T;T|.	0.33654|.	1.4;1.4;1.4;1.4|.	5.09|5.09	-5.76|-5.76	0.02376|0.02376	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.85852|.	0.5793|.	H|H	0.98256|0.98256	4.185|4.185	0.38839|0.38839	D|D	0.956029|0.956029	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.999|.	D;D;D;D|.	0.97110|.	0.999;1.0;0.998;0.997|.	D|.	0.88748|.	0.3248|.	10|.	0.87932|.	D|.	0|.	.|.	14.4136|14.4136	0.67135|0.67135	0.3863:0.0:0.6137:0.0|0.3863:0.0:0.6137:0.0	.|.	253;398;253;398|.	B9A025;E7END4;Q6IPL7;P58215|.	.;.;.;LOXL3_HUMAN|.	Q|E	398;253;398;253|125	ENSP00000264094:H398Q;ENSP00000377512:H253Q;ENSP00000386696:H398Q;ENSP00000386545:H253Q|.	ENSP00000264094:H398Q|.	H|X	-|-	3|1	2|0	LOXL3|LOXL3	74616685|74616685	0.008000|0.008000	0.16893|0.16893	0.883000|0.883000	0.34634|0.34634	0.829000|0.829000	0.46940|0.46940	0.053000|0.053000	0.14184|0.14184	-1.070000|-1.070000	0.03149|0.03149	0.450000|0.450000	0.29827|0.29827	CAT|TAG		0.557	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1		NM_032603	
MAFB	9935	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	39317054	39317054	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr20:39317054G>A	ENST00000373313.2	-	1	826	c.437C>T	c.(436-438)cCg>cTg	p.P146L	MAFB_ENST00000396967.1_Missense_Mutation_p.P146L	NM_005461.3	NP_005452.2	Q9Y5Q3	MAFB_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B	146					brain segmentation (GO:0035284)|inner ear morphogenesis (GO:0042472)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|respiratory gaseous exchange (GO:0007585)|rhombomere 5 development (GO:0021571)|rhombomere 6 development (GO:0021572)|segment specification (GO:0007379)|sensory organ development (GO:0007423)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P146L(1)		kidney(1)|large_intestine(1)	2		Myeloproliferative disorder(115;0.00878)				GCCGGCGCCCGGGTACGCgtg	0.716			T	IGH@	MM																																			Dom	yes		20	20q11.2-q13.1	9935	v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian)		L	1	Substitution - Missense(1)	kidney(1)											9.0	11.0	10.0					20																	39317054		2156	4239	6395	SO:0001583	missense	9935			AF134157	CCDS13311.1	20q11.1-q13.1	2013-07-09	2013-07-09	2001-11-30	ENSG00000204103	ENSG00000204103			6408	protein-coding gene	gene with protein product		608968	"""Kreisler (mouse) maf-related leucine zipper homolog"""	KRML		10444328	Standard	NM_005461		Approved		uc002xji.3	Q9Y5Q3	OTTHUMG00000033052	ENST00000373313.2:c.437C>T	20.37:g.39317054G>A	ENSP00000362410:p.Pro146Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KNE1|Q9H1F1	Missense_Mutation	SNP	ENST00000373313.2	37	CCDS13311.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.968956	0.34754	.	.	ENSG00000204103	ENST00000373313;ENST00000396967	D;D	0.97455	-4.39;-4.39	4.86	3.9	0.45041	.	1.291000	0.05356	U	0.532809	D	0.92580	0.7643	N	0.08118	0	0.80722	D	1	D	0.58268	0.982	B	0.41571	0.36	D	0.84232	0.0467	10	0.44086	T	0.13	-6.9199	11.5934	0.50959	0.0:0.0:0.678:0.322	.	146	Q9Y5Q3	MAFB_HUMAN	L	146	ENSP00000362410:P146L;ENSP00000380167:P146L	ENSP00000362410:P146L	P	-	2	0	MAFB	38750468	0.997000	0.39634	0.937000	0.37676	0.850000	0.48378	1.699000	0.37804	1.046000	0.40249	0.456000	0.33151	CCG		0.716	MAFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080375.2			
MEGF6	1953	hgsc.bcm.edu	37	1	3424401	3424402	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:3424401_3424402insG	ENST00000356575.4	-	14	1972_1973	c.1746_1747insC	c.(1744-1749)gcctgcfs	p.C583fs	MEGF6_ENST00000294599.4_Frame_Shift_Ins_p.C478fs	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	583	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GGGCAGCGGCAGGCCCCCGTGA	0.584																																					Ovarian(73;978 3658)												0																																										SO:0001589	frameshift_variant	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.1747dupC	1.37:g.3424403_3424403dupG	ENSP00000348982:p.Cys583fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q4AC86|Q5VV39	Frame_Shift_Ins	INS	ENST00000356575.4	37	CCDS41237.1																																																																																				0.584	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1		NM_001409	
MCOLN3	55283	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	85491737	85491737	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:85491737T>C	ENST00000370589.2	-	9	1032	c.980A>G	c.(979-981)aAg>aGg	p.K327R	MCOLN3_ENST00000474447.1_5'Flank|WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000341115.4_Missense_Mutation_p.K271R|MCOLN3_ENST00000370587.1_3'UTR	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	327					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K327R(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		AGAAACTTCCTTCTTATAATG	0.343																																																	1	Substitution - Missense(1)	kidney(1)											51.0	49.0	50.0					1																	85491737		2203	4299	6502	SO:0001583	missense	55283			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.980A>G	1.37:g.85491737T>C	ENSP00000359621:p.Lys327Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	T	6.622	0.483244	0.12581	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.75589	-0.95;-0.95	6.16	5.03	0.67393	.	0.041428	0.85682	D	0.000000	T	0.38348	0.1037	L	0.28458	0.855	0.41074	D	0.985471	B;B;B	0.30542	0.004;0.238;0.284	B;B;B	0.28139	0.003;0.086;0.055	T	0.31998	-0.9923	10	0.10377	T	0.69	0.0737	8.1296	0.31018	0.0:0.0665:0.1365:0.797	.	327;271;327	A8K841;Q8TDD5-2;Q8TDD5	.;.;MCLN3_HUMAN	R	327;327;271;271	ENSP00000359621:K327R;ENSP00000342698:K271R	ENSP00000304843:K327R	K	-	2	0	MCOLN3	85264325	1.000000	0.71417	0.997000	0.53966	0.917000	0.54804	3.979000	0.56888	1.124000	0.41980	0.528000	0.53228	AAG		0.343	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2		NM_018298	
MYL10	93408	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	101256829	101256829	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:101256829G>A	ENST00000223167.4	-	8	784	c.607C>T	c.(607-609)Ccc>Tcc	p.P203S		NM_138403.4	NP_612412.2	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	203	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)	p.P203S(1)		breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	12						ACATCTGGGGGAAATGCTGCA	0.557																																					Esophageal Squamous(24;575 709 17516 40384 51639)												1	Substitution - Missense(1)	kidney(1)											142.0	122.0	129.0					7																	101256829		2203	4300	6503	SO:0001583	missense	93408			BC002778	CCDS34713.1	7q22.1	2013-01-10			ENSG00000106436	ENSG00000106436		"""Myosins / Light chain"", ""EF-hand domain containing"""	29825	protein-coding gene	gene with protein product						1628631	Standard	NM_138403		Approved	MGC3479, MYLC2PL, PLRLC	uc003uyr.3	Q9BUA6	OTTHUMG00000157137	ENST00000223167.4:c.607C>T	7.37:g.101256829G>A	ENSP00000223167:p.Pro203Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000223167.4	37	CCDS34713.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.323596	0.60634	.	.	ENSG00000106436	ENST00000223167	T	0.78364	-1.17	4.84	4.84	0.62591	EF-hand-like domain (1);	0.000000	0.64402	D	0.000001	D	0.88097	0.6345	M	0.84082	2.675	0.80722	D	1	D	0.65815	0.995	D	0.68765	0.96	D	0.89708	0.3910	10	0.62326	D	0.03	.	15.5111	0.75782	0.0:0.0:1.0:0.0	.	203	Q9BUA6	MYL10_HUMAN	S	203	ENSP00000223167:P203S	ENSP00000223167:P203S	P	-	1	0	MYL10	101043549	1.000000	0.71417	0.972000	0.41901	0.218000	0.24690	8.740000	0.91579	2.242000	0.73789	0.650000	0.86243	CCC		0.557	MYL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347575.1		NM_138403	
NCLN	56926	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	3192504	3192504	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:3192504C>T	ENST00000246117.4	+	2	652	c.221C>T	c.(220-222)aCg>aTg	p.T74M	NCLN_ENST00000590671.1_5'UTR	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	74					regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.T74M(1)		kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCGCGCACGATGGCGGCG	0.706																																																	1	Substitution - Missense(1)	kidney(1)											14.0	16.0	15.0					19																	3192504		2172	4219	6391	SO:0001583	missense	56926			BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"""nicastrin-like protein"""	609156	"""nicalin homolog (zebrafish)"""			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.221C>T	19.37:g.3192504C>T	ENSP00000246117:p.Thr74Met	Somatic		WXS	Illumina HiSeq	Phase_I	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Missense_Mutation	SNP	ENST00000246117.4	37	CCDS32869.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481302	0.63849	.	.	ENSG00000125912	ENST00000246117	T	0.32515	1.45	4.38	4.38	0.52667	.	0.105496	0.64402	D	0.000005	T	0.51449	0.1675	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.53019	-0.8497	10	0.48119	T	0.1	-7.2067	15.5394	0.76031	0.0:1.0:0.0:0.0	.	74	Q969V3	NCLN_HUMAN	M	74	ENSP00000246117:T74M	ENSP00000246117:T74M	T	+	2	0	NCLN	3143504	1.000000	0.71417	0.896000	0.35187	0.289000	0.27227	7.333000	0.79214	1.992000	0.58205	0.555000	0.69702	ACG		0.706	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1		NM_020170	
NOTCH2	4853	broad.mit.edu;hgsc.bcm.edu	37	1	120464896	120464896	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:120464896G>A	ENST00000256646.2	-	28	5395	c.5176C>T	c.(5176-5178)Cgt>Tgt	p.R1726C	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1726					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|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)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.R1726C(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGCTCACGACGCTTGTGATTG	0.488			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																															Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Missense(1)	kidney(1)											87.0	84.0	85.0					1																	120464896		2203	4300	6503	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5176C>T	1.37:g.120464896G>A	ENSP00000256646:p.Arg1726Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532466	0.85812	.	.	ENSG00000134250	ENST00000256646	D	0.85088	-1.94	5.44	5.44	0.79542	.	0.196730	0.25135	U	0.032879	D	0.91280	0.7251	M	0.87827	2.91	0.80722	D	1	D	0.76494	0.999	P	0.57679	0.825	D	0.92348	0.5887	10	0.87932	D	0	.	18.6191	0.91315	0.0:0.0:1.0:0.0	.	1726	Q04721	NOTC2_HUMAN	C	1726	ENSP00000256646:R1726C	ENSP00000256646:R1726C	R	-	1	0	NOTCH2	120266419	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.356000	0.79445	2.715000	0.92844	0.655000	0.94253	CGT		0.488	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1		NM_024408	
NR1H3	10062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	47283271	47283271	+	Silent	SNP	G	G	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:47283271G>C	ENST00000467728.1	+	5	2120	c.882G>C	c.(880-882)gcG>gcC	p.A294A	NR1H3_ENST00000407404.1_Intron|NR1H3_ENST00000405853.3_Intron|NR1H3_ENST00000395397.3_Silent_p.A249A|NR1H3_ENST00000441012.2_Silent_p.A294A|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000405576.1_Intron|NR1H3_ENST00000481889.2_Silent_p.A249A|NR1H3_ENST00000527949.1_Intron			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	294	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A294A(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						AGACCTCTGCGATCGAGGTGG	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											50.0	49.0	49.0					11																	47283271		2201	4298	6499	SO:0001819	synonymous_variant	10062			U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.882G>C	11.37:g.47283271G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K3J9|D3DQR1|Q8IW13|Q96H87	Silent	SNP	ENST00000467728.1	37	CCDS7929.1																																																																																				0.577	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			
NR1I3	9970	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	161200669	161200669	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:161200669A>T	ENST00000367982.4	-	8	1018	c.863T>A	c.(862-864)cTg>cAg	p.L288Q	NR1I3_ENST00000508387.1_Missense_Mutation_p.C113S|NR1I3_ENST00000515621.1_Missense_Mutation_p.L209Q|NR1I3_ENST00000504010.1_Missense_Mutation_p.L216Q|NR1I3_ENST00000502985.1_Missense_Mutation_p.C142S|NR1I3_ENST00000511676.1_Missense_Mutation_p.L255Q|NR1I3_ENST00000437437.2_Missense_Mutation_p.L255Q|NR1I3_ENST00000511748.1_Missense_Mutation_p.C113S|NR1I3_ENST00000508740.1_Missense_Mutation_p.L260Q|NR1I3_ENST00000428574.2_Missense_Mutation_p.L289Q|NR1I3_ENST00000412844.2_Missense_Mutation_p.L264Q|NR1I3_ENST00000367981.3_Missense_Mutation_p.L260Q|NR1I3_ENST00000367985.3_Missense_Mutation_p.L250Q|NR1I3_ENST00000506209.1_Missense_Mutation_p.L255Q|NR1I3_ENST00000367984.4_Missense_Mutation_p.L245Q|NR1I3_ENST00000367979.2_Missense_Mutation_p.L293Q|NR1I3_ENST00000511944.1_Missense_Mutation_p.C142S|NR1I3_ENST00000442691.2_Missense_Mutation_p.L288Q|NR1I3_ENST00000367980.2_Missense_Mutation_p.L293Q|NR1I3_ENST00000505005.1_Missense_Mutation_p.L245Q|NR1I3_ENST00000367983.4_Missense_Mutation_p.L284Q|NR1I3_ENST00000479324.1_5'UTR|NR1I3_ENST00000512372.1_Missense_Mutation_p.L216Q			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	288					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.L284Q(1)|p.L289Q(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CTCCTCTTGCAGCTGATCAAT	0.602																																																	2	Substitution - Missense(2)	kidney(2)											95.0	84.0	88.0					1																	161200669		2203	4300	6503	SO:0001583	missense	9970			Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"""Nuclear hormone receptors"""	7969	protein-coding gene	gene with protein product	"""constitutive androstane receptor"""	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.863T>A	1.37:g.161200669A>T	ENSP00000356961:p.Leu288Gln	Somatic		WXS	Illumina HiSeq	Phase_I	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	37	CCDS41430.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.5|25.5	4.648361|4.648361	0.87958|0.87958	.|.	.|.	ENSG00000143257|ENSG00000143257	ENST00000508387;ENST00000502985;ENST00000511944;ENST00000511748|ENST00000512372;ENST00000367983;ENST00000367980;ENST00000437437;ENST00000442691;ENST00000412844;ENST00000428574;ENST00000505005;ENST00000508740;ENST00000367982;ENST00000504010;ENST00000511676;ENST00000367981;ENST00000515621;ENST00000367984;ENST00000367985;ENST00000367979;ENST00000506209	D;D;D;D|D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.92647|0.97256	-2.88;-3.08;-3.08;-2.88|-3.99;-4.31;-4.31;-4.31;-4.31;-4.31;-4.31;-3.99;-4.31;-4.31;-3.99;-4.31;-4.31;-4.31;-3.99;-3.99;-4.31;-4.31	5.38|5.38	5.38|5.38	0.77491|0.77491	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.325647	.|0.28332	.|N	.|0.015734	D|D	0.98052|0.98052	0.9358|0.9358	M|M	0.85777|0.85777	2.775|2.775	.|0.39206	.|D	.|0.963221	B;B|P;D;P;D;P;B;P;D;P;D;D;D;P;P;D;D;D	0.17038|0.76494	0.01;0.02|0.777;0.998;0.951;0.996;0.491;0.274;0.661;0.999;0.478;0.994;0.986;0.991;0.661;0.861;0.994;0.998;0.998	B;B|P;D;P;P;B;B;B;D;B;P;P;P;B;P;P;D;D	0.12156|0.66084	0.007;0.005|0.453;0.941;0.691;0.877;0.184;0.135;0.335;0.915;0.193;0.903;0.701;0.822;0.335;0.469;0.839;0.927;0.915	D|D	0.99671|0.99671	1.0996|1.0996	8|9	0.14656|0.87932	T|D	0.56|0	.|.	13.3527|13.3527	0.60611|0.60611	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	113;142|255;264;245;245;250;284;288;288;293;209;216;216;255;255;260;260;289	Q6GZ70;Q6GZ72|E9PCF2;E9PHN4;Q6GZ85;E9PHC8;Q0VAC9;F1D8Q1;Q14994;E9PC13;Q4U0F0;D6REZ7;Q6GZ87;E9PDU3;Q6GZ68;E9PH10;Q6GZ84;E9PGH6;E9PB75	.;.|.;.;.;.;.;.;NR1I3_HUMAN;.;.;.;.;.;.;.;.;.;.	S|Q	113;142;142;113|216;284;293;255;288;264;289;245;260;288;216;255;260;209;245;250;293;255	ENSP00000422982:C113S;ENSP00000421374:C142S;ENSP00000426292:C142S;ENSP00000427600:C113S|ENSP00000425417:L216Q;ENSP00000356962:L284Q;ENSP00000356959:L293Q;ENSP00000407446:L255Q;ENSP00000406493:L288Q;ENSP00000399361:L264Q;ENSP00000412672:L289Q;ENSP00000424934:L245Q;ENSP00000423666:L260Q;ENSP00000356961:L288Q;ENSP00000424345:L216Q;ENSP00000427175:L255Q;ENSP00000356960:L260Q;ENSP00000421588:L209Q;ENSP00000356963:L245Q;ENSP00000356965:L250Q;ENSP00000356958:L293Q;ENSP00000423089:L255Q	ENSP00000421374:C142S|ENSP00000356958:L293Q	C|L	-|-	1|2	0|0	NR1I3|NR1I3	159467293|159467293	0.974000|0.974000	0.33945|0.33945	0.989000|0.989000	0.46669|0.46669	0.992000|0.992000	0.81027|0.81027	4.695000|4.695000	0.61767|0.61767	2.033000|2.033000	0.60031|0.60031	0.459000|0.459000	0.35465|0.35465	TGC|CTG		0.602	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2			
NRIP1	8204	hgsc.bcm.edu	37	21	16338779	16338779	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr21:16338779A>T	ENST00000400202.1	-	3	2447	c.1735T>A	c.(1735-1737)Tcc>Acc	p.S579T	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Missense_Mutation_p.S579T|NRIP1_ENST00000400199.1_Missense_Mutation_p.S579T			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	579	Repression domain 2.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TATGGTGGGGAATTCCATTTG	0.443																																																	0													238.0	236.0	236.0					21																	16338779		2203	4300	6503	SO:0001583	missense	8204			X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.1735T>A	21.37:g.16338779A>T	ENSP00000383063:p.Ser579Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	.	.	.	.	.	.	.	.	.	.	A	12.09	1.834138	0.32421	.	.	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.21734	1.99;1.99;1.99	6.02	0.622	0.17648	.	0.324995	0.29424	N	0.012198	T	0.14570	0.0352	L	0.46157	1.445	0.32333	N	0.560809	B	0.06786	0.001	B	0.09377	0.004	T	0.06373	-1.0830	10	0.52906	T	0.07	-14.8948	3.1943	0.06628	0.6425:0.1185:0.1255:0.1135	.	579	P48552	NRIP1_HUMAN	T	579	ENSP00000383060:S579T;ENSP00000383063:S579T;ENSP00000327213:S579T	ENSP00000327213:S579T	S	-	1	0	NRIP1	15260650	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	2.023000	0.41040	0.145000	0.18977	0.533000	0.62120	TCC		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1		NM_003489	
ODF3	113746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	199997	199997	+	Silent	SNP	T	T	C	rs202158636		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:199997T>C	ENST00000325113.4	+	7	1046	c.729T>C	c.(727-729)tcT>tcC	p.S243S	BET1L_ENST00000410108.1_Intron|ODF3_ENST00000525282.1_Silent_p.S196S	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	243					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)		p.S243S(1)		biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAAACACTCTGATTACATGA	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											138.0	102.0	114.0					11																	199997		2203	4300	6503	SO:0001819	synonymous_variant	113746			AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"""cancer/testis antigen 135"""	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.729T>C	11.37:g.199997T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLT0|Q69YX0	Silent	SNP	ENST00000325113.4	37	CCDS7688.1																																																																																				0.607	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1			
OR52B4	143496	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	4389154	4389154	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:4389154G>C	ENST00000408920.2	-	1	462	c.372C>G	c.(370-372)caC>caG	p.H124Q		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	124					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H124Q(1)		NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCAATATAGTGGTCAAAGG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											99.0	100.0	100.0					11																	4389154		2085	4227	6312	SO:0001583	missense	143496			AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"""GPCR / Class A : Olfactory receptors"""	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.372C>G	11.37:g.4389154G>C	ENSP00000386160:p.His124Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A6NP68|Q6IFK6	Missense_Mutation	SNP	ENST00000408920.2	37	CCDS41609.1	.	.	.	.	.	.	.	.	.	.	G	6.524	0.464889	0.12402	.	.	ENSG00000221996	ENST00000408920	T	0.36340	1.26	5.28	1.25	0.21368	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000017	T	0.19644	0.0472	N	0.17345	0.48	0.19300	N	0.99997	B	0.16802	0.019	B	0.17098	0.017	T	0.17653	-1.0362	10	0.87932	D	0	.	6.0935	0.20007	0.2224:0.0:0.6454:0.1322	.	124	Q8NGK2	O52B4_HUMAN	Q	124	ENSP00000386160:H124Q	ENSP00000386160:H124Q	H	-	3	2	OR52B4	4345730	0.109000	0.22037	0.150000	0.22450	0.064000	0.16182	-0.368000	0.07543	0.372000	0.24591	0.650000	0.86243	CAC		0.458	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3		NM_001005161	
TENM4	26011	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	78380861	78380861	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:78380861C>G	ENST00000278550.7	-	32	6991	c.6529G>C	c.(6529-6531)Gtg>Ctg	p.V2177L		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2177					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.V2177L(2)									TCCTTCTTCACTACTCGCCCC	0.498																																																	2	Substitution - Missense(2)	kidney(2)											83.0	87.0	85.0					11																	78380861		2097	4227	6324	SO:0001583	missense	0			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6529G>C	11.37:g.78380861C>G	ENSP00000278550:p.Val2177Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.050294	0.75846	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.89875	-2.58;0.88	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.92319	0.7563	L	0.47716	1.5	0.80722	D	1	D	0.64830	0.994	D	0.70716	0.97	D	0.91093	0.4908	9	.	.	.	.	18.8078	0.92045	0.0:1.0:0.0:0.0	.	2177	Q6N022	TEN4_HUMAN	L	2177;641	ENSP00000278550:V2177L;ENSP00000431711:V641L	.	V	-	1	0	ODZ4	78058509	1.000000	0.71417	0.979000	0.43373	0.982000	0.71751	4.825000	0.62708	2.677000	0.91161	0.655000	0.94253	GTG		0.498	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			
PASK	23178	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	242063382	242063382	+	Silent	SNP	G	G	C	rs533568232		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:242063382G>C	ENST00000405260.1	-	11	3584	c.2886C>G	c.(2884-2886)acC>acG	p.T962T	PASK_ENST00000539818.1_Silent_p.T746T|PASK_ENST00000234040.4_Silent_p.T962T|PASK_ENST00000403638.3_Silent_p.T962T|PASK_ENST00000358649.4_Silent_p.T962T|PASK_ENST00000544142.1_Silent_p.T776T	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	962					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.T962T(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGCTGGGTCCGGTGAGCTCAG	0.587																																																	2	Substitution - coding silent(2)	kidney(2)											52.0	54.0	53.0					2																	242063382		2203	4300	6503	SO:0001819	synonymous_variant	23178			U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2886C>G	2.37:g.242063382G>C		Somatic		WXS	Illumina HiSeq	Phase_I	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																				0.587	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1		NM_015148	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52588877	52588877	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr3:52588877delG	ENST00000296302.7	-	27	4473	c.4472delC	c.(4471-4473)ccgfs	p.P1492fs	PBRM1_ENST00000356770.4_Frame_Shift_Del_p.P1405fs|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.P1437fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.P1385fs|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000337303.4_Intron|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.P1412fs|PBRM1_ENST00000409114.3_Intron			Q86U86	PB1_HUMAN	polybromo 1	1492	Pro-rich.				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)			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)		AAGGCCTGGCGGATAGCCACC	0.537			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													53.0	53.0	53.0					3																	52588877		2203	4300	6503	SO:0001589	frameshift_variant	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.4472delC	3.37:g.52588877delG	ENSP00000296302:p.Pro1492fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.537	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PKHD1L1	93035	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	110502193	110502193	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr8:110502193T>G	ENST00000378402.5	+	60	9997	c.9893T>G	c.(9892-9894)aTa>aGa	p.I3298R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3298					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.I3300R(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AATGCAAGAATAAGTAATGTG	0.333										HNSCC(38;0.096)																																							1	Substitution - Missense(1)	kidney(1)											89.0	84.0	85.0					8																	110502193		1808	4079	5887	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9893T>G	8.37:g.110502193T>G	ENSP00000367655:p.Ile3298Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901382	0.72754	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85088	-1.94;-1.94	4.84	4.84	0.62591	Pectin lyase fold/virulence factor (1);	0.122741	0.52532	D	0.000065	D	0.88028	0.6327	M	0.90425	3.115	0.50467	D	0.999876	B	0.22211	0.066	B	0.27715	0.082	D	0.87613	0.2505	10	0.87932	D	0	.	12.6536	0.56776	0.0:0.0:0.0:1.0	.	3298	Q86WI1	PKHL1_HUMAN	R	3298;226	ENSP00000367655:I3298R;ENSP00000437376:I226R	ENSP00000367655:I3298R	I	+	2	0	PKHD1L1	110571369	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.276000	0.72601	1.940000	0.56252	0.383000	0.25322	ATA		0.333	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1		NM_177531	
PRKCQ	5588	hgsc.bcm.edu;ucsc.edu	37	10	6553149	6553149	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr10:6553149delC	ENST00000263125.5	-	3	225	c.126delG	c.(124-126)gggfs	p.G42fs	PRKCQ_ENST00000397176.2_Frame_Shift_Del_p.G42fs|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	42	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TATACATCTGCCCGTTCTCTA	0.458																																					Ovarian(50;572 1126 10530 25349 30594)												0													128.0	114.0	119.0					10																	6553149		2203	4300	6503	SO:0001589	frameshift_variant	5588			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.126delG	10.37:g.6553149delC	ENSP00000263125:p.Gly42fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Frame_Shift_Del	DEL	ENST00000263125.5	37	CCDS7079.1																																																																																				0.458	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1		NM_006257	
PRX	57716	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	40900919	40900919	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr19:40900919C>A	ENST00000324001.7	-	7	3610	c.3340G>T	c.(3340-3342)Ggg>Tgg	p.G1114W	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	1114	Glu-rich (acidic).				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G1114W(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCACAGCCCCCTCTGCCCTC	0.672																																																	1	Substitution - Missense(1)	kidney(1)											55.0	54.0	54.0					19																	40900919		2203	4300	6503	SO:0001583	missense	57716			AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.3340G>T	19.37:g.40900919C>A	ENSP00000326018:p.Gly1114Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	4.847	0.157440	0.09236	.	.	ENSG00000105227	ENST00000324001	T	0.01538	4.79	3.82	1.6	0.23607	.	0.281293	0.25427	N	0.030758	T	0.05273	0.0140	L	0.58810	1.83	0.20638	N	0.999879	D	0.65815	0.995	P	0.61477	0.889	T	0.13019	-1.0525	10	0.87932	D	0	-22.4553	7.4557	0.27266	0.0:0.7794:0.0:0.2206	.	1114	Q9BXM0	PRAX_HUMAN	W	1114	ENSP00000326018:G1114W	ENSP00000326018:G1114W	G	-	1	0	PRX	45592759	0.000000	0.05858	0.032000	0.17829	0.006000	0.05464	-0.539000	0.06113	0.829000	0.34733	-0.339000	0.08088	GGG		0.672	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1		NM_020956	
PTCHD2	57540	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	11594491	11594491	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:11594491G>T	ENST00000294484.6	+	18	3567	c.3429G>T	c.(3427-3429)tgG>tgT	p.W1143C	PTCHD2_ENST00000304391.6_Nonsense_Mutation_p.G30*|PTCHD2_ENST00000389575.3_Missense_Mutation_p.W1143C	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1143					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)	p.W1360C(1)		NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		ACCTGCGCTGGGAGAGCTTCC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											77.0	84.0	82.0					1																	11594491		2042	4196	6238	SO:0001583	missense	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.3429G>T	1.37:g.11594491G>T	ENSP00000294484:p.Trp1143Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.800567|6.800567	0.97849|0.97849	.|.	.|.	ENSG00000204624|ENSG00000204624	ENST00000304391|ENST00000294484;ENST00000389575	.|D;D	.|0.90788	.|-2.72;-2.73	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.92573	.|0.7641	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|D	.|0.92526	.|0.6029	.|10	0.87932|0.44086	D|T	0|0.13	-15.7862|-15.7862	17.6498|17.6498	0.88159|0.88159	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1143	.|Q9P2K9	.|PTHD2_HUMAN	X|C	30|1143	.|ENSP00000294484:W1143C;ENSP00000374226:W1143C	ENSP00000303400:G30X|ENSP00000294484:W1143C	G|W	+|+	1|3	0|0	PTCHD2|PTCHD2	11517078|11517078	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	9.578000|9.578000	0.98200|0.98200	2.430000|2.430000	0.82344|0.82344	0.561000|0.561000	0.74099|0.74099	GGA|TGG		0.607	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2		XM_052561	
RAB3GAP1	22930	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	135926185	135926185	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:135926185C>A	ENST00000264158.8	+	24	2823	c.2780C>A	c.(2779-2781)tCc>tAc	p.S927Y	RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.S883Y|ZRANB3_ENST00000412849.1_Intron|RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.S934Y	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	927					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.S927Y(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		AGGCAGAACTCCGTGTCAGAC	0.542																																																	1	Substitution - Missense(1)	kidney(1)											85.0	82.0	83.0					2																	135926185		2203	4300	6503	SO:0001583	missense	22930			D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.2780C>A	2.37:g.135926185C>A	ENSP00000264158:p.Ser927Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	C	9.635	1.137516	0.21123	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.48522	0.82;0.81;0.84	5.92	2.07	0.26955	.	0.875793	0.10341	N	0.686255	T	0.43612	0.1255	L	0.58101	1.795	0.09310	N	1	B;B	0.32128	0.357;0.303	B;B	0.33890	0.13;0.172	T	0.37384	-0.9708	10	0.59425	D	0.04	3.9413	6.9154	0.24357	0.0:0.6188:0.1166:0.2646	.	934;927	C9J837;Q15042	.;RB3GP_HUMAN	Y	927;883;934	ENSP00000264158:S927Y;ENSP00000444306:S883Y;ENSP00000411418:S934Y	ENSP00000264158:S927Y	S	+	2	0	RAB3GAP1	135642655	0.000000	0.05858	0.002000	0.10522	0.652000	0.38707	0.126000	0.15769	0.097000	0.17492	-0.150000	0.13652	TCC		0.542	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2		NM_012233	
RALGAPA1	253959	broad.mit.edu;hgsc.bcm.edu	37	14	36104763	36104763	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr14:36104763C>G	ENST00000389698.3	-	31	4590	c.4200G>C	c.(4198-4200)atG>atC	p.M1400I	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.M1447I|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.M1413I|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.M1400I	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1400	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.M1400I(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GAGGTAAGGCCATGATCCAGT	0.343																																																	2	Substitution - Missense(2)	kidney(2)											50.0	46.0	47.0					14																	36104763		2203	4298	6501	SO:0001583	missense	253959			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4200G>C	14.37:g.36104763C>G	ENSP00000374348:p.Met1400Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738247	0.89573	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;1.52;-0.16;-0.16	5.27	5.27	0.74061	.	0.038027	0.85682	D	0.000000	T	0.79534	0.4462	M	0.75615	2.305	0.58432	D	0.999999	D;P;P;D	0.59767	0.986;0.589;0.811;0.974	D;B;B;P	0.71656	0.974;0.298;0.425;0.841	T	0.80350	-0.1419	10	0.54805	T	0.06	-14.6817	19.2611	0.93968	0.0:1.0:0.0:0.0	.	1447;1413;1400;1400	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	I	1400;1400;1400;1447;38;1413;1447	ENSP00000374348:M1400I;ENSP00000302647:M1400I;ENSP00000258840:M1447I;ENSP00000451133:M38I;ENSP00000371803:M1413I;ENSP00000451877:M1447I	ENSP00000258840:M1447I	M	-	3	0	RALGAPA1	35174514	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.089000	0.76909	2.604000	0.88044	0.563000	0.77884	ATG		0.343	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1		XM_210022	
RALYL	138046	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	85774642	85774642	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr8:85774642G>A	ENST00000521268.1	+	6	1630	c.525G>A	c.(523-525)atG>atA	p.M175I	RALYL_ENST00000521695.1_Missense_Mutation_p.M175I|RALYL_ENST00000517638.1_Missense_Mutation_p.M188I|RALYL_ENST00000523850.1_Missense_Mutation_p.M102I|RALYL_ENST00000522455.1_Missense_Mutation_p.M175I|RALYL_ENST00000518566.1_Missense_Mutation_p.M164I|RALYL_ENST00000521376.1_Missense_Mutation_p.M86I	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	175							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M175I(2)		endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						TCTTTTCCATGAAAGGTGGAT	0.488																																																	2	Substitution - Missense(2)	kidney(2)											69.0	74.0	72.0					8																	85774642		1927	4139	6066	SO:0001583	missense	138046				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"""RNA binding motif (RRM) containing"""	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.525G>A	8.37:g.85774642G>A	ENSP00000430367:p.Met175Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	37	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247933	0.22880	.	.	ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850;ENST00000521376	T;T;T;T;T;T;T	0.16743	2.97;2.97;2.97;2.98;2.96;2.56;2.32	5.1	5.1	0.69264	.	0.355901	0.35179	N	0.003394	T	0.10208	0.0250	N	0.19112	0.55	0.29506	N	0.854598	B;B;B;B;B	0.09022	0.0;0.001;0.002;0.001;0.001	B;B;B;B;B	0.11329	0.002;0.002;0.004;0.006;0.002	T	0.16158	-1.0412	10	0.07990	T	0.79	-10.8077	12.2815	0.54767	0.0784:0.0:0.9216:0.0	.	164;175;102;188;175	B3KT61;B3KSX3;Q86SE5-2;G3V129;Q86SE5	.;.;.;.;RALYL_HUMAN	I	175;175;175;164;188;102;86	ENSP00000430394:M175I;ENSP00000428667:M175I;ENSP00000430367:M175I;ENSP00000430065:M164I;ENSP00000430128:M188I;ENSP00000428807:M102I;ENSP00000428310:M86I	ENSP00000430128:M188I	M	+	3	0	RALYL	85937197	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.195000	0.58400	2.511000	0.84671	0.551000	0.68910	ATG		0.488	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			
RASA1	5921	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	86674302	86674302	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr5:86674302C>T	ENST00000274376.6	+	18	2998	c.2434C>T	c.(2434-2436)Cat>Tat	p.H812Y	RASA1_ENST00000512763.1_Missense_Mutation_p.H645Y|RASA1_ENST00000506290.1_Missense_Mutation_p.H646Y|RASA1_ENST00000456692.2_Missense_Mutation_p.H635Y|CTC-428H11.2_ENST00000607486.1_RNA	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	812	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.H635Y(1)|p.H812Y(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GTTTGTTCATCATGCTTTGAA	0.348																																																	2	Substitution - Missense(2)	kidney(2)											92.0	85.0	87.0					5																	86674302		2203	4300	6503	SO:0001583	missense	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2434C>T	5.37:g.86674302C>T	ENSP00000274376:p.His812Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818330	0.71028	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.13	5.13	0.70059	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	T	0.27832	0.0685	N	0.25890	0.77	0.80722	D	1	D;D;D;D;D	0.67145	0.996;0.996;0.996;0.995;0.996	P;P;P;P;P	0.61070	0.883;0.823;0.883;0.814;0.77	T	0.01697	-1.1293	10	0.42905	T	0.14	.	18.9448	0.92618	0.0:1.0:0.0:0.0	.	646;645;646;635;812	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	Y	812;845;635;645;646	ENSP00000274376:H812Y;ENSP00000411221:H635Y;ENSP00000422008:H645Y;ENSP00000420905:H646Y	ENSP00000274376:H812Y	H	+	1	0	RASA1	86710058	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.009000	0.70745	2.545000	0.85829	0.561000	0.74099	CAT		0.348	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1		NM_002890	
RFC1	5981	hgsc.bcm.edu;ucsc.edu	37	4	39328257	39328258	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr4:39328257_39328258delAA	ENST00000381897.1	-	6	700_701	c.567_568delTT	c.(565-570)ctttcafs	p.S190fs	RFC1_ENST00000349703.2_Frame_Shift_Del_p.S190fs|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	190					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GTATTTTGTGAAAGCTATATTT	0.347																																					Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)												0																																										SO:0001589	frameshift_variant	5981			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.567_568delTT	4.37:g.39328257_39328258delAA	ENSP00000371321:p.Ser190fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Frame_Shift_Del	DEL	ENST00000381897.1	37	CCDS56329.1																																																																																				0.347	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1		NM_002913	
RFPL3	10738	hgsc.bcm.edu	37	22	32754354	32754355	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr22:32754354_32754355insG	ENST00000249007.4	+	1	501_502	c.296_297insG	c.(295-300)ctggttfs	p.V100fs	RFPL3_ENST00000397468.1_Frame_Shift_Ins_p.V71fs|RFPL3_ENST00000382088.3_Frame_Shift_Ins_p.V71fs|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	100							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						CTAGAGAGGCTGGTTTCCCACA	0.525																																																	0																																										SO:0001589	frameshift_variant	10738			AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.298dupG	22.37:g.32754356_32754356dupG	ENSP00000249007:p.Val100fs	Somatic		WXS	Illumina HiSeq	Phase_I	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Frame_Shift_Ins	INS	ENST00000249007.4	37	CCDS43011.1																																																																																				0.525	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3		NM_006604	
RIMKLB	57494	broad.mit.edu;hgsc.bcm.edu	37	12	8902521	8902521	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:8902521C>T	ENST00000538135.1	+	3	1064	c.239C>T	c.(238-240)aCc>aTc	p.T80I	RIMKLB_ENST00000535829.1_Missense_Mutation_p.T80I|RIMKLB_ENST00000357529.3_Missense_Mutation_p.T80I|RIMKLB_ENST00000299673.5_3'UTR			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	80					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.T80I(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGAGTACCAACCCCTTGGGTG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											47.0	48.0	48.0					12																	8902521		1890	4097	5987	SO:0001583	missense	57494			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"""N-acetylaspartyl-glutamate synthetase"""	614054	"""family with sequence similarity 80, member B"""	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.239C>T	12.37:g.8902521C>T	ENSP00000440943:p.Thr80Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	37	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.823977	0.90873	.	.	ENSG00000166532	ENST00000541044;ENST00000539923;ENST00000537189;ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	U	0.000000	T	0.72748	0.3499	L	0.55481	1.735	0.80722	D	1	D;D	0.65815	0.995;0.99	P;P	0.57960	0.83;0.81	T	0.75388	-0.3335	9	0.87932	D	0	.	17.8968	0.88891	0.0:1.0:0.0:0.0	.	80;80	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	I	80;80;141;80;80;80	.	ENSP00000350136:T80I	T	+	2	0	RIMKLB	8793788	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.392000	0.79840	2.571000	0.86741	0.591000	0.81541	ACC		0.463	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1		NM_020734	
RNASEL	6041	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	182551344	182551344	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:182551344A>G	ENST00000367559.3	-	4	1869	c.1616T>C	c.(1615-1617)tTt>tCt	p.F539S	RNASEL_ENST00000444138.1_Missense_Mutation_p.F539S|RNASEL_ENST00000539397.1_Missense_Mutation_p.F539S	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	539	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.F539S(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CAGATCCTCAAATGAGATGCT	0.433																																																	1	Substitution - Missense(1)	kidney(1)											167.0	155.0	159.0					1																	182551344		2203	4300	6503	SO:0001583	missense	6041			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1616T>C	1.37:g.182551344A>G	ENSP00000356530:p.Phe539Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q5W0L2|Q6AI46	Missense_Mutation	SNP	ENST00000367559.3	37	CCDS1347.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456291	0.63401	.	.	ENSG00000135828	ENST00000367559;ENST00000444138;ENST00000539397	T;T;T	0.27402	1.67;1.67;1.67	5.1	3.93	0.45458	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.321960	0.27000	N	0.021431	T	0.63331	0.2502	H	0.94771	3.58	0.29047	N	0.884745	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.65471	-0.6160	10	0.66056	D	0.02	-12.9723	9.9535	0.41653	0.8291:0.1709:0.0:0.0	.	539;539	Q6AI46;Q05823	.;RN5A_HUMAN	S	539	ENSP00000356530:F539S;ENSP00000411147:F539S;ENSP00000440844:F539S	ENSP00000356530:F539S	F	-	2	0	RNASEL	180817967	1.000000	0.71417	0.786000	0.31890	0.034000	0.12701	4.626000	0.61269	0.842000	0.35045	0.528000	0.53228	TTT		0.433	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1		NM_021133	
RUFY3	22902	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	71634345	71634345	+	Missense_Mutation	SNP	T	T	G	rs372261834		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr4:71634345T>G	ENST00000226328.4	+	5	1226	c.663T>G	c.(661-663)aaT>aaG	p.N221K	RUFY3_ENST00000502653.1_Missense_Mutation_p.N168K|RUFY3_ENST00000381006.3_Missense_Mutation_p.N221K|RUFY3_ENST00000417478.2_Missense_Mutation_p.N281K|RUFY3_ENST00000536664.1_Missense_Mutation_p.N205K	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	221	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)		p.N221K(2)		endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TTGATGCCAATTTCTGTATGA	0.443																																																	2	Substitution - Missense(2)	kidney(2)											207.0	195.0	199.0					4																	71634345		2203	4300	6503	SO:0001583	missense	22902			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.663T>G	4.37:g.71634345T>G	ENSP00000226328:p.Asn221Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992379	0.74703	.	.	ENSG00000018189	ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65;2.65	5.63	1.56	0.23342	RUN (3);	0.000000	0.85682	D	0.000000	T	0.34279	0.0892	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.975;0.99	D;D;P;P	0.64410	0.914;0.925;0.712;0.773	T	0.05007	-1.0912	9	.	.	.	-18.5015	9.4323	0.38617	0.0:0.3217:0.0:0.6783	.	205;221;221;281	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	K	281;221;221;205;157;168	ENSP00000399771:N281K;ENSP00000370394:N221K;ENSP00000226328:N221K;ENSP00000443652:N205K;ENSP00000425574:N157K;ENSP00000425400:N168K	.	N	+	3	2	RUFY3	71853209	0.935000	0.31712	0.999000	0.59377	0.994000	0.84299	0.013000	0.13310	0.050000	0.15949	0.455000	0.32223	AAT		0.443	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2		NM_014961	
SALL1	6299	hgsc.bcm.edu	37	16	51175664	51175664	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:51175664T>C	ENST00000251020.4	-	2	502	c.469A>G	c.(469-471)Agc>Ggc	p.S157G	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.S60G|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	157	Poly-Ser.				adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S157G(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ccgctgctgctgctgctgctg	0.642																																					GBM(103;1352 1446 1855 4775 8890)												1	Substitution - Missense(1)	large_intestine(1)																																								SO:0001583	missense	6299			X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.469A>G	16.37:g.51175664T>C	ENSP00000251020:p.Ser157Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.452578	0.00012	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.06294	3.32;3.32	0.225	-0.451	0.12214	.	0.410124	0.18238	N	0.147338	T	0.02610	0.0079	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39165	-0.9627	9	0.41790	T	0.15	.	.	.	.	.	157	Q9NSC2	SALL1_HUMAN	G	157;60;121	ENSP00000251020:S157G;ENSP00000407914:S60G	ENSP00000251020:S157G	S	-	1	0	SALL1	49733165	0.000000	0.05858	0.015000	0.15790	0.003000	0.03518	-1.472000	0.02341	-0.850000	0.04152	-0.879000	0.02964	AGC		0.642	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2		NM_002968	
SCNN1A	6337	broad.mit.edu;hgsc.bcm.edu	37	12	6463640	6463640	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr12:6463640C>T	ENST00000228916.2	-	8	1422	c.1324G>A	c.(1324-1326)Gtg>Atg	p.V442M	SCNN1A_ENST00000538979.1_5'UTR|SCNN1A_ENST00000540037.1_Missense_Mutation_p.V142M|SCNN1A_ENST00000358945.3_Missense_Mutation_p.V442M|SCNN1A_ENST00000360168.3_Missense_Mutation_p.V501M|SCNN1A_ENST00000543768.1_Missense_Mutation_p.V465M|SCNN1A_ENST00000396966.2_Missense_Mutation_p.V442M	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	442					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)	p.V442M(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	CAGTACTCCACGTTCTGGGGC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											69.0	67.0	67.0					12																	6463640		2203	4300	6503	SO:0001583	missense	6337			Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1324G>A	12.37:g.6463640C>T	ENSP00000228916:p.Val442Met	Somatic		WXS	Illumina HiSeq	Phase_I	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.880035	0.33162	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	4.95	4.06	0.47325	.	0.459943	0.19995	N	0.101470	T	0.50103	0.1596	L	0.51422	1.61	0.09310	N	1	B;P;B	0.46277	0.432;0.875;0.108	B;B;B	0.34301	0.117;0.179;0.027	T	0.44345	-0.9334	10	0.40728	T	0.16	-11.9469	11.3617	0.49646	0.0:0.9102:0.0:0.0898	.	465;442;501	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	M	501;442;142;442;442;465	ENSP00000353292:V501M;ENSP00000351825:V442M;ENSP00000440876:V142M;ENSP00000228916:V442M;ENSP00000380166:V442M;ENSP00000438739:V465M	ENSP00000228916:V442M	V	-	1	0	SCNN1A	6333901	0.189000	0.23263	0.021000	0.16686	0.107000	0.19398	2.429000	0.44758	1.102000	0.41551	-0.327000	0.08410	GTG		0.577	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			
SERTAD4	56256	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	210412917	210412917	+	Silent	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:210412917G>A	ENST00000367012.3	+	3	485	c.255G>A	c.(253-255)gaG>gaA	p.E85E	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	85						nucleus (GO:0005634)		p.E85E(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TGGAAGAAGAGGATTTTCACC	0.328																																																	1	Substitution - coding silent(1)	kidney(1)											94.0	101.0	99.0					1																	210412917		2203	4300	6503	SO:0001819	synonymous_variant	56256			BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.255G>A	1.37:g.210412917G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RD32	Silent	SNP	ENST00000367012.3	37	CCDS1494.1																																																																																				0.328	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1		NM_019605	
SLC25A13	10165	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	95776002	95776002	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:95776002C>T	ENST00000265631.5	-	14	1454	c.1318G>A	c.(1318-1320)Ggc>Agc	p.G440S	SLC25A13_ENST00000416240.2_Missense_Mutation_p.G441S|SLC25A13_ENST00000542654.1_Missense_Mutation_p.G332S			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	440					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)	p.G440S(1)		breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	ACCTGGGAGCCTCCAGCCTAA	0.408																																																	1	Substitution - Missense(1)	kidney(1)											87.0	100.0	96.0					7																	95776002		2203	4300	6503	SO:0001583	missense	10165			AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1318G>A	7.37:g.95776002C>T	ENSP00000265631:p.Gly440Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	C	31	5.074194	0.94000	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.78707	-1.2;-1.2;-1.2	4.53	3.65	0.41850	Mitochondrial carrier domain (2);	0.061967	0.64402	D	0.000006	D	0.83381	0.5242	L	0.60845	1.875	0.58432	D	0.999998	P;D;P	0.56746	0.907;0.977;0.925	P;P;P	0.62560	0.767;0.904;0.85	D	0.84946	0.0868	10	0.72032	D	0.01	-10.8487	12.8623	0.57920	0.0:0.9212:0.0:0.0788	.	332;441;440	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	S	440;441;332	ENSP00000265631:G440S;ENSP00000400101:G441S;ENSP00000440484:G332S	ENSP00000265631:G440S	G	-	1	0	SLC25A13	95613938	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.651000	0.83577	1.282000	0.44496	0.655000	0.94253	GGC		0.408	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2		NM_014251	
SLC34A3	142680	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	140129157	140129157	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr9:140129157G>A	ENST00000538474.1	+	12	1533	c.1309G>A	c.(1309-1311)Gca>Aca	p.A437T	SLC34A3_ENST00000361134.2_Missense_Mutation_p.A437T	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	437					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)	p.A437T(1)		kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGCCAGCCCCGCAGACAGGAT	0.662																																																	1	Substitution - Missense(1)	kidney(1)											47.0	40.0	42.0					9																	140129157		2201	4294	6495	SO:0001583	missense	142680			AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.1309G>A	9.37:g.140129157G>A	ENSP00000442397:p.Ala437Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	37	CCDS7038.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692300	0.68271	.	.	ENSG00000198569	ENST00000538474;ENST00000361134	T;T	0.31247	1.5;1.5	3.33	-3.47	0.04753	.	0.273016	0.23870	N	0.043745	T	0.18299	0.0439	N	0.13327	0.33	0.09310	N	1	P	0.51351	0.944	P	0.46208	0.507	T	0.30504	-0.9976	10	0.31617	T	0.26	0.0865	12.4817	0.55847	0.0:0.0:0.335:0.665	.	437	Q8N130	NPT2C_HUMAN	T	437	ENSP00000442397:A437T;ENSP00000355353:A437T	ENSP00000355353:A437T	A	+	1	0	SLC34A3	139248978	0.001000	0.12720	0.000000	0.03702	0.725000	0.41563	0.365000	0.20348	-0.902000	0.03886	0.448000	0.29417	GCA		0.662	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1		NM_080877	
SPRR3	6707	hgsc.bcm.edu	37	1	152975659	152975682	+	In_Frame_Del	DEL	GAGCCAGGCTGTACCAAGGTCCCT	GAGCCAGGCTGTACCAAGGTCCCT	-	rs568163793|rs553429466|rs74134624	byFrequency	TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	GAGCCAGGCTGTACCAAGGTCCCT	GAGCCAGGCTGTACCAAGGTCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:152975659_152975682delGAGCCAGGCTGTACCAAGGTCCCT	ENST00000295367.4	+	2	205_228	c.163_186delGAGCCAGGCTGTACCAAGGTCCCT	c.(163-186)gagccaggctgtaccaaggtccctdel	p.EPGCTKVP95del	SPRR3_ENST00000542696.1_In_Frame_Del_p.EPGCTKVP87del|SPRR3_ENST00000331860.3_In_Frame_Del_p.EPGCTKVP95del	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	95	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AAAGATTCCAGAGCCAGGCTGTACCAAGGTCCCTGAGCCAGGCT	0.562																																																	0									,	2036,1952		740,556,698					,	-1.4	0.0		dbSNP_130	70	3135,4775		852,1431,1672	no	coding,coding	SPRR3	NM_005416.2,NM_001097589.1	,	1592,1987,2370	A1A1,A1R,RR		39.6334,48.9468,43.4611	,	,		5171,6727				SO:0001651	inframe_deletion	6707			AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.163_186delGAGCCAGGCTGTACCAAGGTCCCT	1.37:g.152975659_152975682delGAGCCAGGCTGTACCAAGGTCCCT	ENSP00000295367:p.Glu95_Pro102del	Somatic		WXS	Illumina HiSeq	Phase_I	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	In_Frame_Del	DEL	ENST00000295367.4	37	CCDS1033.1																																																																																				0.562	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1		NM_005416	
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	RNA	DEL	AGAGCTCC	AGAGCTCC	-	rs367732188		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	AGAGCTCC	AGAGCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr7:74300557_74300564delAGAGCTCC	ENST00000423186.1	-	0	573_580							P0CL84	ST3L2_HUMAN	stromal antigen 3-like 2 (pseudogene)							nucleus (GO:0005634)		p.E82fs*32(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|pancreas(1)	5						CGGCCAGTGAAGAGCTCCAGGCGTGCGG	0.572																																																	2	Deletion - Frameshift(2)	large_intestine(1)|central_nervous_system(1)								96,356		38,20,168							0.0			1	208,1036		88,32,502	no	frameshift	STAG3L2	NM_001025202.2		126,52,670	A1A1,A1R,RR		16.7203,21.2389,17.9245				304,1392						442582					7q11.23	2013-06-26	2013-06-26			ENSG00000277072			33886	pseudogene	pseudogene			"""stromal antigen 3-like 2"""				Standard	NR_040584		Approved	MGC131759, STAG3L2P	uc011kfj.2	P0CL84	OTTHUMG00000156216		7.37:g.74300557_74300564delAGAGCTCC		Somatic		WXS	Illumina GAIIx	Phase_I	A6NMT8|A8K0A1|Q32NE4|Q6NXR2|Q7L5M5|Q7Z5K6	Frame_Shift_Del	DEL	ENST00000423186.1	37																																																																																					0.572	STAG3L2-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000343523.2		NM_001025202	
SYNE2	23224	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	64568741	64568741	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr14:64568741C>T	ENST00000344113.4	+	64	12685	c.12473C>T	c.(12472-12474)tCc>tTc	p.S4158F	SYNE2_ENST00000358025.3_Missense_Mutation_p.S4158F|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000357395.3_Missense_Mutation_p.S543F|SYNE2_ENST00000554584.1_Missense_Mutation_p.S4173F|SYNE2_ENST00000394768.2_Missense_Mutation_p.S543F|SYNE2_ENST00000555002.1_Missense_Mutation_p.S792F	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4158				S -> F (in Ref. 2; AAL33802 and 3). {ECO:0000305}.	centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.S4158F(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTTCCTCATCCTCTGGAACA	0.517																																																	1	Substitution - Missense(1)	kidney(1)											106.0	87.0	93.0					14																	64568741		2203	4300	6503	SO:0001583	missense	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.12473C>T	14.37:g.64568741C>T	ENSP00000341781:p.Ser4158Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.671035	0.47781	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000553308	T;T;T;T;T;T	0.58797	0.67;3.97;0.67;0.31;4.02;3.97	4.41	4.41	0.53225	.	0.000000	0.48767	D	0.000177	T	0.63988	0.2558	L	0.32530	0.975	0.80722	D	1	D;D;D	0.69078	0.958;0.997;0.997	P;D;D	0.66497	0.66;0.936;0.944	T	0.66488	-0.5911	10	0.54805	T	0.06	.	14.0951	0.65016	0.0:1.0:0.0:0.0	.	543;4158;4158	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	F	4158;543;4158;4173;4173;792;543;50	ENSP00000350719:S4158F;ENSP00000349969:S543F;ENSP00000341781:S4158F;ENSP00000452570:S4173F;ENSP00000450831:S792F;ENSP00000378249:S543F	ENSP00000261678:S4173F	S	+	2	0	SYNE2	63638494	0.993000	0.37304	0.887000	0.34795	0.875000	0.50365	3.565000	0.53798	2.162000	0.67917	0.462000	0.41574	TCC		0.517	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2		NM_182914	
SYT7	9066	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	61295625	61295625	+	Silent	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:61295625G>A	ENST00000263846.4	-	5	711	c.384C>T	c.(382-384)caC>caT	p.H128H	SYT7_ENST00000540831.1_5'UTR|SYT7_ENST00000540677.1_Silent_p.H203H|SYT7_ENST00000535826.1_Silent_p.H247H|SYT7_ENST00000542670.1_Silent_p.H336H|SYT7_ENST00000539008.1_Silent_p.H411H|SYT7_ENST00000542836.1_Silent_p.H172H	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	128					exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)	p.H128H(1)		kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGCAACCCTCGTGGGCCTCAT	0.652																																																	1	Substitution - coding silent(1)	kidney(1)											44.0	51.0	49.0					11																	61295625		2201	4299	6500	SO:0001819	synonymous_variant	9066			AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"""Synaptotagmins"""	11514	protein-coding gene	gene with protein product		604146	"""prostate cancer associated protein 7"""	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.384C>T	11.37:g.61295625G>A		Somatic		WXS	Illumina HiSeq	Phase_I	F5GZU9|Q08AH6	Silent	SNP	ENST00000263846.4	37	CCDS31577.1																																																																																				0.652	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1		NM_004200	
HIRIP3	8479	hgsc.bcm.edu	37	16	30002435	30002436	+	IGR	INS	-	-	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:30002435_30002436insG	ENST00000279392.3	-	0	3385				TAOK2_ENST00000279394.3_Frame_Shift_Ins_p.A900fs	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3						chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						CTTGAGCGGCAGGCCCGTGAGA	0.649																																																	0																																										SO:0001628	intergenic_variant	9344			AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118		16.37:g.30002437_30002437dupG		Somatic		WXS	Illumina HiSeq	Phase_I	H3BSR3|O75707|O75708	Frame_Shift_Ins	INS	ENST00000279392.3	37	CCDS10664.1																																																																																				0.649	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2		NM_003609	
TELO2	9894	broad.mit.edu	37	16	1557648	1557648	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:1557648A>C	ENST00000262319.6	+	20	2617	c.2338A>C	c.(2338-2340)Agc>Cgc	p.S780R		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	780					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)	p.S780R(1)		NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				CGTCCTGCTCAGCCTGCCTGC	0.697																																																	1	Substitution - Missense(1)	kidney(1)											45.0	39.0	41.0					16																	1557648		2197	4298	6495	SO:0001583	missense	9894			AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.2338A>C	16.37:g.1557648A>C	ENSP00000262319:p.Ser780Arg	Somatic		WXS	Illumina GAIIx	Phase_I	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.510465	0.64522	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.32515	1.45	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.55829	-0.8079	10	0.40728	T	0.16	-15.879	14.6226	0.68597	1.0:0.0:0.0:0.0	.	780	Q9Y4R8	TELO2_HUMAN	R	303;780	ENSP00000262319:S780R	ENSP00000262319:S780R	S	+	1	0	TELO2	1497649	1.000000	0.71417	0.975000	0.42487	0.215000	0.24574	5.445000	0.66594	1.962000	0.57031	0.379000	0.24179	AGC		0.697	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2		NM_016111	
THBS2	7058	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	169634969	169634969	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr6:169634969G>A	ENST00000366787.3	-	11	1760	c.1511C>T	c.(1510-1512)tCg>tTg	p.S504L	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	504	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.S504L(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AGTGCAGGCCGACCACGGGGA	0.682																																					Esophageal Squamous(91;219 1934 18562 44706)												1	Substitution - Missense(1)	kidney(1)											35.0	39.0	37.0					6																	169634969		2202	4299	6501	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1511C>T	6.37:g.169634969G>A	ENSP00000355751:p.Ser504Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.552634	0.65425	.	.	ENSG00000186340	ENST00000366787	T	0.64085	-0.08	4.38	3.47	0.39725	.	0.000000	0.37857	U	0.001920	T	0.62925	0.2468	H	0.96430	3.82	0.36815	D	0.886111	P	0.43826	0.818	B	0.39379	0.298	T	0.73170	-0.4067	10	0.46703	T	0.11	-15.7638	13.5042	0.61476	0.0:0.0:0.8423:0.1577	.	504	P35442	TSP2_HUMAN	L	504	ENSP00000355751:S504L	ENSP00000355751:S504L	S	-	2	0	THBS2	169376894	1.000000	0.71417	0.645000	0.29479	0.668000	0.39293	5.066000	0.64351	0.907000	0.36646	0.590000	0.80494	TCG		0.682	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1		NM_003247	
TLR6	10333	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	38830418	38830418	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr4:38830418G>T	ENST00000381950.1	-	1	742	c.677C>A	c.(676-678)aCt>aAt	p.T226N	TLR6_ENST00000436693.2_Missense_Mutation_p.T226N			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	226					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.T226N(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTTAATATTAGTCAGTTGTAA	0.333																																																	1	Substitution - Missense(1)	kidney(1)											46.0	52.0	50.0					4																	38830418		2199	4300	6499	SO:0001583	missense	10333				CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.677C>A	4.37:g.38830418G>T	ENSP00000371376:p.Thr226Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.759756	0.31137	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.08458	3.09;3.09	5.6	2.81	0.32909	.	0.444384	0.22932	N	0.053884	T	0.13670	0.0331	M	0.72894	2.215	0.21604	N	0.999623	B	0.29716	0.255	B	0.29598	0.104	T	0.09079	-1.0691	10	0.72032	D	0.01	.	16.3266	0.82986	0.0:0.36:0.64:0.0	.	226	Q9Y2C9	TLR6_HUMAN	N	226	ENSP00000389600:T226N;ENSP00000371376:T226N	ENSP00000371376:T226N	T	-	2	0	TLR6	38506813	0.937000	0.31787	0.999000	0.59377	0.905000	0.53344	1.189000	0.32114	0.257000	0.21650	0.491000	0.48974	ACT		0.333	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			
TTN	7273	broad.mit.edu;hgsc.bcm.edu	37	2	179441300	179441300	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr2:179441300G>A	ENST00000591111.1	-	275	64972	c.64748C>T	c.(64747-64749)cCa>cTa	p.P21583L	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P14284L|TTN-AS1_ENST00000591332.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P14351L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P23224L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P14159L|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P20656L			Q8WZ42	TITIN_HUMAN	titin	21583	Fibronectin type-III 56. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P20656L(1)|p.P20654L(1)|p.P14284L(1)|p.P14159L(1)|p.P14351L(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCACTGGGTGGACCAATTCC	0.428																																																	5	Substitution - Missense(5)	kidney(5)											154.0	151.0	152.0					2																	179441300		1943	4137	6080	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.64748C>T	2.37:g.179441300G>A	ENSP00000465570:p.Pro21583Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	10.92	1.487207	0.26686	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59772	0.24;0.24;0.24;0.24	5.72	3.91	0.45181	Fibronectin, type III (3);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.44644	0.1303	N	0.25485	0.75	0.51233	D	0.999918	B;B;B;B	0.15141	0.012;0.012;0.012;0.007	B;B;B;B	0.14578	0.011;0.011;0.011;0.007	T	0.37478	-0.9704	9	0.87932	D	0	.	11.3934	0.49827	0.0657:0.0:0.8077:0.1266	.	14159;14284;14351;21583	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	20656;14159;14351;14284;14157	ENSP00000343764:P20656L;ENSP00000434586:P14159L;ENSP00000340554:P14351L;ENSP00000352154:P14284L	ENSP00000340554:P14351L	P	-	2	0	TTN	179149546	1.000000	0.71417	0.155000	0.22561	0.917000	0.54804	6.053000	0.71089	0.867000	0.35654	0.655000	0.94253	CCA		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
TUBBP5	643224	broad.mit.edu	37	9	141071110	141071110	+	RNA	SNP	A	A	G			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr9:141071110A>G	ENST00000503395.1	+	0	1735									tubulin, beta pseudogene 5									p.P243P(7)									TGCGCTTCCCAGGCCAGCTGA	0.597																																																	7	Substitution - coding silent(7)	kidney(3)|prostate(2)|endometrium(2)																																										643224			AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141071110A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000503395.1	37																																																																																					0.597	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1		NR_027156	
UBR4	23352	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	19482023	19482023	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:19482023T>C	ENST00000375254.3	-	43	6239	c.6212A>G	c.(6211-6213)tAt>tGt	p.Y2071C	UBR4_ENST00000375267.2_Missense_Mutation_p.Y2071C|UBR4_ENST00000375217.2_Missense_Mutation_p.Y2071C|UBR4_ENST00000375226.2_Missense_Mutation_p.Y2071C	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2071					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Y2071C(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGCTGAGTATAGATGTACCC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											98.0	89.0	92.0					1																	19482023		2203	4300	6503	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6212A>G	1.37:g.19482023T>C	ENSP00000364403:p.Tyr2071Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.335018	0.81801	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;3.2	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.48732	0.1516	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.984	T	0.59005	-0.7535	10	0.87932	D	0	.	14.9281	0.70896	0.0:0.0:0.0:1.0	.	2071;2071	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	C	2071;2071;2071;2071;781;1287	ENSP00000364403:Y2071C;ENSP00000364416:Y2071C;ENSP00000364365:Y2071C;ENSP00000364374:Y2071C;ENSP00000404897:Y781C	ENSP00000364365:Y2071C	Y	-	2	0	UBR4	19354610	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.330000	0.79181	2.112000	0.64535	0.528000	0.53228	TAT		0.433	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1		NM_020765	
IGHV3OR16-9	28307	broad.mit.edu	37	16	32077407	32077407	+	RNA	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr16:32077407G>A	ENST00000354689.6	+	0	22				RP11-1166P10.6_ENST00000566806.1_RNA					immunoglobulin heavy variable 3/OR16-9 (non-functional)																		GGTGGAGTCTGGAGGAGGCTT	0.562																																																	0																																												0			Z29606		16p11.2	2013-12-06	2008-09-11		ENSG00000270472	ENSG00000270472		"""Immunoglobulins / IGH orphons"""	5644	other	immunoglobulin gene			"""immunoglobulin heavy variable 3/OR16-9"""				Standard			Approved	IGHV3/OR16-9			OTTHUMG00000184753		16.37:g.32077407G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000354689.6	37		.	.	.	.	.	.	.	.	.	.	G	2.248	-0.372146	0.05034	.	.	ENSG00000198229	ENST00000354689	.	.	.	.	.	.	.	.	.	.	.	T	0.48390	0.1497	.	.	.	.	.	.	.	.	.	.	.	.	T	0.58719	-0.7587	2	0.87932	D	0	.	.	.	.	.	.	.	.	R	8	.	ENSP00000346720:G8R	G	+	1	0	AC142381.1	31984908	1.000000	0.71417	0.149000	0.22428	0.151000	0.21798	4.205000	0.58466	0.107000	0.17824	0.109000	0.15622	GGA		0.562	IGHV3OR16-9-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000432530.2			
USH2A	7399	broad.mit.edu;hgsc.bcm.edu	37	1	216595423	216595423	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr1:216595423G>T	ENST00000307340.3	-	2	642	c.256C>A	c.(256-258)Cag>Aag	p.Q86K	USH2A_ENST00000366942.3_Missense_Mutation_p.Q86K|USH2A_ENST00000366943.2_Missense_Mutation_p.Q86K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	86					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.Q86K(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGGCAATCCTGAATACAAAAC	0.493										HNSCC(13;0.011)																																							1	Substitution - Missense(1)	kidney(1)											115.0	108.0	111.0					1																	216595423		2203	4300	6503	SO:0001583	missense	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.256C>A	1.37:g.216595423G>T	ENSP00000305941:p.Gln86Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	35	5.504454	0.96371	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.19532	2.56;2.55;2.14	5.27	5.27	0.74061	.	0.000000	0.40554	U	0.001072	T	0.49372	0.1553	M	0.74258	2.255	0.54753	D	0.999989	D;D	0.76494	0.999;0.997	D;D	0.77004	0.96;0.989	T	0.52660	-0.8546	10	0.87932	D	0	.	18.8833	0.92365	0.0:0.0:1.0:0.0	.	86;86	O75445-2;O75445	.;USH2A_HUMAN	K	86	ENSP00000305941:Q86K;ENSP00000355910:Q86K;ENSP00000355909:Q86K	ENSP00000305941:Q86K	Q	-	1	0	USH2A	214662046	1.000000	0.71417	0.946000	0.38457	0.661000	0.39034	7.703000	0.84585	2.463000	0.83235	0.591000	0.81541	CAG		0.493	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1		NM_007123	
VPS13B	157680	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	100515083	100515083	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr8:100515083A>T	ENST00000358544.2	+	27	4173	c.4062A>T	c.(4060-4062)gaA>gaT	p.E1354D	VPS13B_ENST00000357162.2_Missense_Mutation_p.E1354D|VPS13B_ENST00000395996.1_Missense_Mutation_p.E1354D	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1354					protein transport (GO:0015031)			p.E1354D(2)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TGGTCAGTGAACTAGAAGATC	0.318																																					Colon(161;2205 2542 7338 31318)												2	Substitution - Missense(2)	kidney(2)											198.0	217.0	210.0					8																	100515083		2203	4300	6503	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.4062A>T	8.37:g.100515083A>T	ENSP00000351346:p.Glu1354Asp	Somatic		WXS	Illumina HiSeq	Phase_I	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.791478	0.70452	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.47528	0.84;0.84;0.84	5.49	4.34	0.51931	.	0.119673	0.53938	D	0.000047	T	0.58609	0.2134	L	0.59436	1.845	0.34694	D	0.726024	D;P;D;B	0.76494	0.999;0.783;0.997;0.427	D;B;D;B	0.81914	0.995;0.385;0.978;0.082	T	0.64071	-0.6493	10	0.20046	T	0.44	.	8.7686	0.34717	0.8463:0.0:0.1537:0.0	.	1353;1354;1354;1354	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	D	1354	ENSP00000349685:E1354D;ENSP00000351346:E1354D;ENSP00000379318:E1354D	ENSP00000349685:E1354D	E	+	3	2	VPS13B	100584259	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.050000	0.49877	0.929000	0.37192	0.383000	0.25322	GAA		0.318	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1		NM_184042	
VPS18	57617	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	41194909	41194909	+	Silent	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr15:41194909G>T	ENST00000220509.5	+	5	2631	c.2292G>T	c.(2290-2292)gtG>gtT	p.V764V	VPS18_ENST00000558474.1_3'UTR	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	764					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)	p.V764V(1)		autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GGCACGTGGTGCAGGAAGAGG	0.562																																																	1	Substitution - coding silent(1)	kidney(1)											148.0	132.0	137.0					15																	41194909		2203	4300	6503	SO:0001819	synonymous_variant	57617			AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.2292G>T	15.37:g.41194909G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	37	CCDS10069.1																																																																																				0.562	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			
WASH3P	374666	broad.mit.edu	37	15	102516424	102516424	+	RNA	SNP	G	G	T	rs201105823		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr15:102516424G>T	ENST00000557932.1	+	0	1372				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.P449P(4)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						TGCCGCCACCGCAGCAGCCAC	0.647																																																	4	Substitution - coding silent(4)	endometrium(3)|kidney(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.102516424G>T		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000557932.1	37																																																																																					0.647	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1		NM_199163	
XKR4	114786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	56436707	56436707	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr8:56436707G>A	ENST00000327381.6	+	3	1974	c.1874G>A	c.(1873-1875)tGt>tAt	p.C625Y		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	625						integral component of membrane (GO:0016021)		p.C625Y(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCTTTTGAATGTTCCCCATCT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											116.0	107.0	110.0					8																	56436707		2203	4300	6503	SO:0001583	missense	114786			AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1874G>A	8.37:g.56436707G>A	ENSP00000328326:p.Cys625Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	37	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511550	0.44660	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	D	0.82167	-1.58	5.55	4.68	0.58851	.	0.193931	0.56097	N	0.000025	T	0.74891	0.3776	N	0.25647	0.755	0.40316	D	0.97877	B	0.06786	0.001	B	0.04013	0.001	T	0.71965	-0.4433	10	0.72032	D	0.01	-12.3404	14.7196	0.69297	0.0701:0.0:0.9299:0.0	.	625	Q5GH76	XKR4_HUMAN	Y	625	ENSP00000328326:C625Y	ENSP00000328326:C625Y	C	+	2	0	XKR4	56599261	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	4.148000	0.58085	1.353000	0.45828	0.655000	0.94253	TGT		0.448	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2		NM_052898	
ZBBX	79740	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	166958709	166958709	+	Splice_Site	SNP	T	T	A			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr3:166958709T>A	ENST00000392766.2	-	21	2617		c.e21-2		ZBBX_ENST00000455345.2_Splice_Site|ZBBX_ENST00000307529.5_Splice_Site|ZBBX_ENST00000392767.2_Splice_Site|ZBBX_ENST00000392764.1_Splice_Site	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.?(2)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CCAGAACAGCTGAAAATACAT	0.383																																																	2	Unknown(2)	kidney(2)											110.0	99.0	102.0					3																	166958709		1880	4121	6001	SO:0001630	splice_region_variant	79740			AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.2277-2A>T	3.37:g.166958709T>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Splice_Site	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	11.11	1.540998	0.27563	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	.	.	.	5.21	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2606	0.31781	0.1764:0.0:0.0:0.8236	.	.	.	.	.	-1	.	.	.	-	.	.	ZBBX	168441403	0.999000	0.42202	1.000000	0.80357	0.331000	0.28603	1.911000	0.39937	1.050000	0.40346	0.455000	0.32223	.		0.383	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3		NM_024687	Intron
ZNFX1	57169	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	47886935	47886935	+	Missense_Mutation	SNP	T	T	C	rs377494376		TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr20:47886935T>C	ENST00000396105.1	-	3	1660	c.1414A>G	c.(1414-1416)Agg>Ggg	p.R472G	ZNFX1_ENST00000371752.1_Missense_Mutation_p.R472G|ZNFX1_ENST00000371754.4_Missense_Mutation_p.R472G	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	472							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R472G(2)|p.R276G(1)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TCCTGCTCCCTGTTAGATACG	0.488																																																	3	Substitution - Missense(3)	kidney(3)											110.0	108.0	109.0					20																	47886935		2203	4300	6503	SO:0001583	missense	57169			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.1414A>G	20.37:g.47886935T>C	ENSP00000379412:p.Arg472Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.276981	0.59758	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744;ENST00000455070	D;D;D;T;D	0.90004	-2.46;-2.6;-2.6;-1.45;-2.1	5.72	3.72	0.42706	.	0.000000	0.85682	D	0.000000	D	0.94608	0.8262	M	0.88310	2.945	0.58432	D	0.999997	D	0.76494	0.999	D	0.68353	0.957	D	0.94659	0.7846	10	0.62326	D	0.03	-24.1664	13.8706	0.63617	0.0:0.0:0.7178:0.2822	.	472	Q9P2E3	ZNFX1_HUMAN	G	472;472;472;472;472;276	ENSP00000360819:R472G;ENSP00000360817:R472G;ENSP00000379412:R472G;ENSP00000360809:R472G;ENSP00000413800:R276G	ENSP00000360809:R472G	R	-	1	2	ZNFX1	47320342	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.598000	0.67585	0.730000	0.32425	-0.286000	0.09958	AGG		0.488	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2		NM_021035	
TECTA	7007	broad.mit.edu	37	11	121016494	121016494	+	Silent	SNP	G	G	T			TCGA-B0-5094-01A-01D-1421-08	TCGA-B0-5094-11A-01D-1421-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	8b910c03-86a9-488d-80b4-1f8c214c2941	b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47	g.chr11:121016494G>T	ENST00000392793.1	+	12	4045	c.3774G>T	c.(3772-3774)ctG>ctT	p.L1258L	TECTA_ENST00000264037.2_Silent_p.L1258L|TECTA_ENST00000478058.1_3'UTR			O75443	TECTA_HUMAN	tectorin alpha	1258	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.L1258L(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CCATGGGTCTGCTTGCATCGA	0.592																																						.											1	Substitution - coding silent(1)	kidney(1)											152.0	128.0	136.0					11																	121016494		2203	4299	6502	SO:0001819	synonymous_variant	7007			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.3774G>T	11.37:g.121016494G>T		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																				0.592	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1		NM_005422	
