#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_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_ORegAnno_bin	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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
AKR1C3	8644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	5144389	5144389	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr10:5144389C>T	ENST00000380554.3	+	6	1319	c.667C>T	c.(667-669)Cga>Tga	p.R223*	AKR1C3_ENST00000439082.2_Nonsense_Mutation_p.R104*|AKR1C3_ENST00000605149.1_Nonsense_Mutation_p.R200*	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	223					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	GGGATCTCAACGAGACAAACG	0.383																																																0													100.0	92.0	95.0					10																	5144389		2203	4300	6503	SO:0001587	stop_gained	8644			L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.667C>T	10.37:g.5144389C>T	ENSP00000369927:p.Arg223*		A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Nonsense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	C	38	6.678916	0.97755	.	.	ENSG00000196139	ENST00000439082;ENST00000380554	.	.	.	2.15	-4.3	0.03710	.	0.000000	0.51477	D	0.000085	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1433	0.42749	0.7631:0.2368:0.0:0.0	.	.	.	.	X	104;223	.	ENSP00000369927:R223X	R	+	1	2	AKR1C3	5134389	0.001000	0.12720	0.000000	0.03702	0.067000	0.16453	0.474000	0.22148	-0.766000	0.04639	0.491000	0.48974	CGA		0.383	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		18	61	18	61
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu	37	10	24825812	24825812	+	Missense_Mutation	SNP	A	A	T			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr10:24825812A>T	ENST00000376454.3	+	17	3554	c.3524A>T	c.(3523-3525)aAg>aTg	p.K1175M	KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000307544.6_Missense_Mutation_p.K858M|KIAA1217_ENST00000396445.1_Missense_Mutation_p.K858M|KIAA1217_ENST00000376451.2_Missense_Mutation_p.K858M|KIAA1217_ENST00000458595.1_Missense_Mutation_p.K1140M|KIAA1217_ENST00000376452.3_Missense_Mutation_p.K1139M|KIAA1217_ENST00000396446.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1175					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GTGCCACCCAAGGAGAAGAAG	0.507																																																0													88.0	72.0	77.0					10																	24825812		2203	4300	6503	SO:0001583	missense	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.3524A>T	10.37:g.24825812A>T	ENSP00000365637:p.Lys1175Met		A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	A	14.83	2.652395	0.47362	.	.	ENSG00000120549	ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451	T;T;T;T;T;T	0.60672	1.31;1.35;0.7;0.17;0.71;0.87	5.62	3.23	0.37069	.	0.112361	0.56097	D	0.000023	T	0.70979	0.3286	M	0.71581	2.175	0.48571	D	0.999678	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.979;0.996;0.998;0.999;0.998	T	0.69866	-0.5029	10	0.87932	D	0	.	8.3635	0.32372	0.7985:0.1329:0.0686:0.0	.	1140;1139;858;858;858;1175	Q5T5P2-7;A6NLF3;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2	.;.;.;.;.;SKT_HUMAN	M	1140;858;1175;1139;858;858;858;858	ENSP00000392625:K1140M;ENSP00000365637:K1175M;ENSP00000365635:K1139M;ENSP00000302343:K858M;ENSP00000379722:K858M;ENSP00000365634:K858M	ENSP00000302343:K858M	K	+	2	0	KIAA1217	24865818	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	6.548000	0.73896	0.392000	0.25172	-0.256000	0.11100	AAG		0.507	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		6	65	6	65
LRP1	4035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	57588464	57588464	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr12:57588464G>A	ENST00000243077.3	+	50	8639	c.8173G>A	c.(8173-8175)Gag>Aag	p.E2725K	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2725	LDL-receptor class A 15. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TGAACATGGCGAGGACGAGAC	0.597																																																0													71.0	63.0	66.0					12																	57588464		2203	4300	6503	SO:0001583	missense	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.8173G>A	12.37:g.57588464G>A	ENSP00000243077:p.Glu2725Lys		Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	g	15.37	2.813969	0.50527	.	.	ENSG00000123384	ENST00000243077	D	0.95622	-3.76	5.07	5.07	0.68467	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.163970	0.39210	N	0.001436	D	0.93255	0.7851	L	0.52364	1.645	0.80722	D	1	P	0.44380	0.834	B	0.38296	0.27	D	0.93942	0.7224	10	0.56958	D	0.05	.	17.2421	0.87016	0.0:0.0:1.0:0.0	.	2725	Q07954	LRP1_HUMAN	K	2725	ENSP00000243077:E2725K	ENSP00000243077:E2725K	E	+	1	0	LRP1	55874731	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	6.699000	0.74613	2.339000	0.79563	0.450000	0.29827	GAG		0.597	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		13	48	13	48
KLC1	3831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	104143843	104143843	+	Missense_Mutation	SNP	A	A	G	rs568689263		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr14:104143843A>G	ENST00000348520.6	+	12	1790	c.1471A>G	c.(1471-1473)Atg>Gtg	p.M491V	KLC1_ENST00000389744.4_Missense_Mutation_p.M491V|KLC1_ENST00000554280.1_Missense_Mutation_p.M491V|KLC1_ENST00000246489.7_Missense_Mutation_p.M491V|KLC1_ENST00000555836.1_Missense_Mutation_p.M491V|KLC1_ENST00000553286.1_Missense_Mutation_p.M491V|KLC1_ENST00000380038.3_Missense_Mutation_p.M491V|RP11-73M18.2_ENST00000472726.2_Missense_Mutation_p.M663V|KLC1_ENST00000452929.2_Missense_Mutation_p.M491V|KLC1_ENST00000445352.4_Missense_Mutation_p.M489V|KLC1_ENST00000557450.1_Missense_Mutation_p.M491V|KLC1_ENST00000334553.6_Missense_Mutation_p.M491V|KLC1_ENST00000557575.1_Missense_Mutation_p.M491V|KLC1_ENST00000347839.6_Missense_Mutation_p.M491V	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	491					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				AGAAGCTGCTATGAGGTCTCG	0.398																																																0													139.0	133.0	135.0					14																	104143843		2203	4300	6503	SO:0001583	missense	3831			AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"""Tetratricopeptide (TTC) repeat domain containing"""	6387	protein-coding gene	gene with protein product		600025	"""kinesin 2 60/70kDa"", ""kinesin 2"""	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1471A>G	14.37:g.104143843A>G	ENSP00000341154:p.Met491Val		A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Missense_Mutation	SNP	ENST00000348520.6	37	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.02|12.02	1.814117|1.814117	0.32053|0.32053	.|.	.|.	ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000126214;ENSG00000256500|ENSG00000126214	ENST00000348520;ENST00000443396;ENST00000380038;ENST00000389744;ENST00000557575;ENST00000553286;ENST00000347839;ENST00000555836;ENST00000334553;ENST00000246489;ENST00000557450;ENST00000554280;ENST00000452929;ENST00000445352;ENST00000472726|ENST00000537046	T;D;T;T;T;T;T;T;T;D;T;T;D;T|.	0.82255|.	-1.01;-1.58;-1.0;-0.98;-1.0;-0.99;-0.99;-1.01;-1.01;-1.59;-1.0;-1.02;-1.57;-0.26|.	5.52|5.52	4.35|4.35	0.52113|0.52113	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.211416|.	0.64402|.	D|.	0.000013|.	T|T	0.61073|0.61073	0.2318|0.2318	L|L	0.50333|0.50333	1.59|1.59	0.44352|0.44352	D|D	0.997244|0.997244	B;B;B;B;B;B;B|.	0.06786|.	0.0;0.0;0.0;0.0;0.0;0.001;0.0|.	B;B;B;B;B;B;B|.	0.11329|.	0.001;0.001;0.006;0.002;0.002;0.003;0.002|.	T|T	0.57579|0.57579	-0.7787|-0.7787	10|5	0.54805|.	T|.	0.06|.	-18.6761|-18.6761	13.1016|13.1016	0.59222|0.59222	0.8664:0.1336:0.0:0.0|0.8664:0.1336:0.0:0.0	.|.	491;491;663;491;491;491;489|.	F8VTM4;F8W6L3;E7EVH7;Q07866-4;Q07866-6;Q07866;G5E9S8|.	.;.;.;.;.;KLC1_HUMAN;.|.	V|C	491;491;491;491;491;491;491;491;491;491;491;491;491;489;663|96	ENSP00000341154:M491V;ENSP00000369377:M491V;ENSP00000374394:M491V;ENSP00000450617:M491V;ENSP00000452487:M491V;ENSP00000334618:M491V;ENSP00000452481:M491V;ENSP00000334523:M491V;ENSP00000246489:M491V;ENSP00000450648:M491V;ENSP00000451242:M491V;ENSP00000414982:M491V;ENSP00000412693:M489V;ENSP00000439065:M663V|.	ENSP00000246489:M491V|.	M|Y	+|+	1|2	0|0	KLC1;RP11-73M18.2|KLC1	103213596|103213596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.813000|0.813000	0.45954|0.45954	3.368000|3.368000	0.52357|0.52357	1.005000|1.005000	0.39183|0.39183	0.533000|0.533000	0.62120|0.62120	ATG|TAT		0.398	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552		23	48	23	48
MYO5A	4644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	52720613	52720613	+	Missense_Mutation	SNP	G	G	C			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr15:52720613G>C	ENST00000399231.3	-	3	535	c.292C>G	c.(292-294)Ctt>Gtt	p.L98V	MYO5A_ENST00000553916.1_Missense_Mutation_p.L98V|MYO5A_ENST00000399233.2_Missense_Mutation_p.L98V|MYO5A_ENST00000358212.6_Missense_Mutation_p.L98V|MYO5A_ENST00000356338.6_Missense_Mutation_p.L98V	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	98	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTATAAATAAGTTTGGAATCA	0.408																																																0													128.0	117.0	120.0					15																	52720613		1909	4124	6033	SO:0001583	missense	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.292C>G	15.37:g.52720613G>C	ENSP00000382177:p.Leu98Val		A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.280678	0.59758	.	.	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000553916	D;D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76;-3.76	5.76	5.76	0.90799	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.96824	0.8963	L	0.55017	1.72	0.80722	D	1	B;D	0.71674	0.238;0.998	B;D	0.83275	0.166;0.996	D	0.94670	0.7856	10	0.16420	T	0.52	.	19.9571	0.97224	0.0:0.0:1.0:0.0	.	98;98	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	V	98	ENSP00000382177:L98V;ENSP00000382179:L98V;ENSP00000348693:L98V;ENSP00000350945:L98V;ENSP00000451109:L98V	ENSP00000348693:L98V	L	-	1	0	MYO5A	50507905	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	8.030000	0.88816	2.721000	0.93114	0.655000	0.94253	CTT		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		42	92	42	92
CLCN7	1186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	1510460	1510460	+	Missense_Mutation	SNP	C	C	T	rs200960952		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr16:1510460C>T	ENST00000382745.4	-	6	1158	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	CLCN7_ENST00000448525.1_Missense_Mutation_p.A161T|CLCN7_ENST00000262318.8_Missense_Mutation_p.A161T	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	185					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				AGCACGAAGGCGGCGTTCAGC	0.597																																																0								C	THR/ALA,THR/ALA	0,4398		0,0,2199	149.0	117.0	128.0		481,553	4.8	0.4	16		128	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CLCN7	NM_001114331.1,NM_001287.4	58,58	0,3,6496	TT,TC,CC		0.0349,0.0,0.0231	benign,benign	161/782,185/806	1510460	3,12995	2199	4300	6499	SO:0001583	missense	1186			Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.553G>A	16.37:g.1510460C>T	ENSP00000372193:p.Ala185Thr		A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	37	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	C	9.386	1.074339	0.20227	0.0	3.49E-4	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.82344	-1.6;-1.6	4.8	4.8	0.61643	Chloride channel, core (2);	0.298040	0.35349	N	0.003277	T	0.70011	0.3175	N	0.19112	0.55	0.38606	D	0.950793	B;B	0.14012	0.003;0.009	B;B	0.16289	0.015;0.003	T	0.66500	-0.5908	10	0.25751	T	0.34	-33.9658	11.0794	0.48051	0.0:0.9085:0.0:0.0915	.	161;185	E9PDB9;P51798	.;CLCN7_HUMAN	T	161;138;185;127	ENSP00000410907:A161T;ENSP00000372193:A185T	ENSP00000262318:A138T	A	-	1	0	CLCN7	1450461	0.987000	0.35691	0.352000	0.25734	0.111000	0.19643	3.381000	0.52455	2.211000	0.71520	0.585000	0.79938	GCC		0.597	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		32	64	32	64
CDH15	1013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	89261356	89261356	+	Silent	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr16:89261356G>A	ENST00000289746.2	+	14	2303	c.2238G>A	c.(2236-2238)gcG>gcA	p.A746A		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	746					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		GCTCGGTGGCGGGGACGCTGA	0.632																																																0													27.0	25.0	26.0					16																	89261356		2179	4283	6462	SO:0001819	synonymous_variant	1013			D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2238G>A	16.37:g.89261356G>A				Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																				0.632	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		9	16	9	16
CCR10	2826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	40832563	40832563	+	Missense_Mutation	SNP	T	T	C			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr17:40832563T>C	ENST00000332438.4	-	2	116	c.97A>G	c.(97-99)Aag>Gag	p.K33E	CTD-3193K9.4_ENST00000593139.1_RNA|CNTNAP1_ENST00000264638.4_5'Flank|CTD-3193K9.3_ENST00000592440.1_RNA|CCR10_ENST00000591765.1_5'UTR	NM_016602.2	NP_057686.2	P46092	CCR10_HUMAN	chemokine (C-C motif) receptor 10	33					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			lung(1)|ovary(1)|skin(1)	3		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ACATCGGCCTTGTAGCAAAGC	0.637																																																0													29.0	26.0	27.0					17																	40832563		2198	4283	6481	SO:0001583	missense	2826			AF215981	CCDS11435.1	17q21.1-q21.3	2012-08-08	2004-11-12	2004-11-12	ENSG00000184451	ENSG00000184451		"""GPCR / Class A : Chemokine receptors : C-C motif"""	4474	protein-coding gene	gene with protein product		600240	"""G protein-coupled receptor 2"""	GPR2		7851889	Standard	NM_016602		Approved		uc002iax.4	P46092	OTTHUMG00000132301	ENST00000332438.4:c.97A>G	17.37:g.40832563T>C	ENSP00000332504:p.Lys33Glu		Q4V749|Q6T7X2|Q9NZG2	Missense_Mutation	SNP	ENST00000332438.4	37	CCDS11435.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.983919	0.74474	.	.	ENSG00000184451	ENST00000332438	T	0.37058	1.22	4.38	4.38	0.52667	.	0.000000	0.44097	D	0.000493	T	0.31575	0.0801	L	0.49350	1.555	0.80722	D	1	B	0.29862	0.259	B	0.24848	0.056	T	0.19778	-1.0295	10	0.59425	D	0.04	.	11.218	0.48838	0.0:0.0:0.0:1.0	.	33	P46092	CCR10_HUMAN	E	33	ENSP00000332504:K33E	ENSP00000332504:K33E	K	-	1	0	CCR10	38086089	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.976000	0.56867	1.829000	0.53265	0.379000	0.24179	AAG		0.637	CCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255406.1	NM_016602		8	29	8	29
BRINP2	57795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	177247827	177247827	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr1:177247827G>A	ENST00000361539.4	+	7	1453	c.1141G>A	c.(1141-1143)Gtg>Atg	p.V381M	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	381					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.V381M(1)									TGGCTTGAAAGTGCTGTTCAA	0.607																																																1	Substitution - Missense(1)	breast(1)											109.0	113.0	111.0					1																	177247827		2203	4300	6503	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1141G>A	1.37:g.177247827G>A	ENSP00000354481:p.Val381Met		O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871409	0.33069	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.14391	2.51	5.39	-1.41	0.08941	.	0.697671	0.13934	N	0.352667	T	0.07818	0.0196	L	0.29908	0.895	0.19300	N	0.999978	B;B;B	0.18166	0.001;0.026;0.001	B;B;B	0.20767	0.003;0.031;0.003	T	0.29671	-1.0004	10	0.44086	T	0.13	-3.6204	2.6315	0.04946	0.3245:0.3691:0.2082:0.0982	.	131;276;381	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	M	131;381	ENSP00000354481:V381M	ENSP00000354481:V381M	V	+	1	0	FAM5B	175514450	0.071000	0.21146	0.532000	0.27989	0.948000	0.59901	0.152000	0.16302	-0.194000	0.10399	0.655000	0.94253	GTG		0.607	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		48	103	48	103
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	232607260	232607260	+	Silent	SNP	C	C	T	rs371442648		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr1:232607260C>T	ENST00000366630.1	-	7	2458	c.2100G>A	c.(2098-2100)agG>agA	p.R700R	SIPA1L2_ENST00000262861.4_Silent_p.R700R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	700	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TTCCTATGTGCCTTTTCCTCA	0.383																																																0													121.0	124.0	123.0					1																	232607260		2112	4272	6384	SO:0001819	synonymous_variant	57568			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2100G>A	1.37:g.232607260C>T			Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																				0.383	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		26	75	26	75
NCAPH2	29781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	50956005	50956005	+	Splice_Site	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr22:50956005G>A	ENST00000420993.2	+	4	388		c.e4-1		NCAPH2_ENST00000395698.3_Splice_Site|NCAPH2_ENST00000299821.11_Splice_Site|NCAPH2_ENST00000395701.3_Splice_Site	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2						chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		TTCTCTCTCAGGCGGGCCAAG	0.632																																																0													58.0	65.0	63.0					22																	50956005		2203	4300	6503	SO:0001630	splice_region_variant	29781			BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"""kleisin beta"", ""CAP-H2 subunit of the condensin II complex"""	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.267-1G>A	22.37:g.50956005G>A			B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Splice_Site	SNP	ENST00000420993.2	37	CCDS14094.2	.	.	.	.	.	.	.	.	.	.	G	18.63	3.664776	0.67700	.	.	ENSG00000025770	ENST00000420993;ENST00000395698;ENST00000395701;ENST00000523045;ENST00000299821;ENST00000496227	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3514	0.66705	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NCAPH2	49302871	0.997000	0.39634	1.000000	0.80357	0.871000	0.50021	4.392000	0.59659	2.413000	0.81919	0.561000	0.74099	.		0.632	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299	Intron	30	72	30	72
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	73836722	73836722	+	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr2:73836722A>G	ENST00000264448.6	+	23	12598	c.12487A>G	c.(12487-12489)Aaa>Gaa	p.K4163E	ALMS1_ENST00000409009.1_Missense_Mutation_p.K4121E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4163	ALMS motif.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TCTGGGGAGAAAAGTTCCCTG	0.433																																																0													123.0	120.0	121.0					2																	73836722		1839	4075	5914	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12487A>G	2.37:g.73836722A>G	ENSP00000264448:p.Lys4163Glu		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896615	0.72639	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.09350	3.0;2.99	5.34	5.34	0.76211	.	0.064020	0.64402	D	0.000010	T	0.22589	0.0545	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.87578	0.949;0.998	T	0.00638	-1.1632	10	0.72032	D	0.01	.	11.6236	0.51132	1.0:0.0:0.0:0.0	.	4121;4163	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	E	4121;4163	ENSP00000386627:K4121E;ENSP00000264448:K4163E	ENSP00000264448:K4163E	K	+	1	0	ALMS1	73690230	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.806000	0.47947	2.242000	0.73789	0.482000	0.46254	AAA		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		14	81	14	81
MARCO	8685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	119739756	119739756	+	Missense_Mutation	SNP	C	C	T	rs369805550	byFrequency	TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr2:119739756C>T	ENST00000327097.4	+	11	1061	c.926C>T	c.(925-927)cCg>cTg	p.P309L	MARCO_ENST00000541757.1_Missense_Mutation_p.P231L	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	309	Collagen-like.				apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						CAGGGTGTTCCGGGCCCTCCT	0.642													C|||	2	0.000399361	0.0	0.0	5008	,	,		17624	0.0		0.0	False		,,,				2504	0.002				GBM(8;18 374 7467 11269 32796)											0								C	LEU/PRO	0,4406		0,0,2203	44.0	46.0	46.0		926	2.7	0.0	2		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	MARCO	NM_006770.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	309/521	119739756	1,13005	2203	4300	6503	SO:0001583	missense	8685			AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"""scavenger receptor class A, member 2"""	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.926C>T	2.37:g.119739756C>T	ENSP00000318916:p.Pro309Leu		B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.288449	0.23478	0.0	1.16E-4	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	D;D	0.92965	-3.14;-3.14	4.46	2.65	0.31530	.	0.376195	0.24952	N	0.034284	D	0.94023	0.8085	M	0.82193	2.58	0.09310	N	0.999998	D	0.71674	0.998	P	0.58077	0.832	D	0.87298	0.2303	9	.	.	.	.	7.2488	0.26138	0.1943:0.6182:0.1874:0.0	.	309	Q9UEW3	MARCO_HUMAN	L	309;309;231	ENSP00000318916:P309L;ENSP00000441769:P231L	.	P	+	2	0	MARCO	119456226	0.004000	0.15560	0.044000	0.18714	0.378000	0.30076	0.431000	0.21444	0.506000	0.28125	0.462000	0.41574	CCG		0.642	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		16	27	16	27
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			17	72	17	72
BBS7	55212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	122782768	122782768	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr4:122782768G>A	ENST00000264499.4	-	4	415	c.232C>T	c.(232-234)Cct>Tct	p.P78S	BBS7_ENST00000506636.1_Missense_Mutation_p.P78S	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	78					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						TTCTCCTGAGGTGTGTTGATA	0.418									Bardet-Biedl syndrome																																							0													88.0	88.0	88.0					4																	122782768		2203	4300	6503	SO:0001583	missense	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.232C>T	4.37:g.122782768G>A	ENSP00000264499:p.Pro78Ser		Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475834	0.44044	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.92048	-2.96;-2.96	5.47	5.47	0.80525	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89093	0.6617	L	0.50333	1.59	0.58432	D	0.999996	B;B	0.24132	0.045;0.098	B;B	0.20767	0.019;0.031	D	0.85326	0.1087	10	0.30854	T	0.27	-14.6749	14.8823	0.70542	0.0:0.1431:0.8569:0.0	.	78;78	Q8IWZ6-2;Q8IWZ6	.;BBS7_HUMAN	S	78	ENSP00000264499:P78S;ENSP00000423626:P78S	ENSP00000264499:P78S	P	-	1	0	BBS7	123002218	1.000000	0.71417	0.975000	0.42487	0.463000	0.32649	7.475000	0.81041	2.559000	0.86315	0.591000	0.81541	CCT		0.418	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			25	11	25	11
CAST	831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	96077000	96077000	+	Missense_Mutation	SNP	G	G	A	rs368744741		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr5:96077000G>A	ENST00000341926.3	+	12	862	c.700G>A	c.(700-702)Gcc>Acc	p.A234T	CAST_ENST00000359176.4_Missense_Mutation_p.A298T|CAST_ENST00000509903.1_Missense_Mutation_p.A199T|CAST_ENST00000395813.1_Missense_Mutation_p.A317T|CAST_ENST00000511049.1_Missense_Mutation_p.A220T|CTC-506B8.1_ENST00000502568.1_RNA|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000515663.1_5'Flank|CAST_ENST00000309190.5_Missense_Mutation_p.A212T|CAST_ENST00000325674.7_Missense_Mutation_p.A282T|CAST_ENST00000510756.1_Missense_Mutation_p.A295T|CAST_ENST00000508608.1_Missense_Mutation_p.A280T|CAST_ENST00000338252.3_Missense_Mutation_p.A221T|CAST_ENST00000395812.2_Missense_Mutation_p.A276T|CAST_ENST00000511782.1_Missense_Mutation_p.A220T|CAST_ENST00000504465.1_Missense_Mutation_p.A162T|CAST_ENST00000508579.1_5'Flank|CAST_ENST00000508830.1_Missense_Mutation_p.A317T			P20810	ICAL_HUMAN	calpastatin	234					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		TGCTATAGACGCCTTGTCATC	0.433																																																0													73.0	77.0	76.0					5																	96077000		2203	4300	6503	SO:0001583	missense	831			AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.700G>A	5.37:g.96077000G>A	ENSP00000339914:p.Ala234Thr		B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		.	.	.	.	.	.	.	.	.	.	G	15.19	2.759887	0.49468	.	.	ENSG00000153113	ENST00000338252;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000421689;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.54071	1.96;1.96;1.96;1.96;1.96;1.96;1.96;0.59;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96	6.17	1.97	0.26223	.	0.739694	0.13862	N	0.357572	T	0.66799	0.2826	M	0.72118	2.19	0.09310	N	0.999992	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.997;0.992;1.0;1.0;0.999;1.0;1.0;0.999;1.0;0.998;0.999;1.0	D;P;P;D;D;D;D;D;D;D;P;D;D	0.85130	0.997;0.903;0.774;0.996;0.961;0.914;0.99;0.957;0.964;0.981;0.867;0.964;0.975	T	0.52268	-0.8598	10	0.44086	T	0.13	-7.1097	8.2986	0.32001	0.0751:0.0:0.5155:0.4093	.	162;82;280;199;212;193;234;282;276;298;295;317;221	E9PDE4;B7Z8S8;B7Z468;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2	.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.	T	221;317;282;317;298;282;276;298;295;280;234;220;212;234;162;199;220	ENSP00000343421:A221T;ENSP00000425721:A317T;ENSP00000422951:A282T;ENSP00000379158:A317T;ENSP00000352098:A298T;ENSP00000320319:A282T;ENSP00000379157:A276T;ENSP00000396558:A298T;ENSP00000422176:A295T;ENSP00000422677:A280T;ENSP00000339914:A234T;ENSP00000421130:A220T;ENSP00000312523:A212T;ENSP00000422325:A234T;ENSP00000425670:A162T;ENSP00000426946:A199T;ENSP00000423638:A220T	ENSP00000312523:A212T	A	+	1	0	CAST	96102756	0.351000	0.24887	0.678000	0.29963	0.223000	0.24884	1.316000	0.33620	0.880000	0.35969	-0.169000	0.13324	GCC		0.433	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		22	33	22	33
FUCA2	2519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	143823182	143823182	+	Silent	SNP	T	T	C			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr6:143823182T>C	ENST00000002165.6	-	5	1096	c.1041A>G	c.(1039-1041)gtA>gtG	p.V347V	RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|FUCA2_ENST00000438118.2_Missense_Mutation_p.S164G|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|FUCA2_ENST00000367585.1_5'UTR|RP1-20N2.6_ENST00000593045.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	347					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CCTCAAAAACTACAGAAATGG	0.408																																																0													78.0	76.0	77.0					6																	143823182		2203	4300	6503	SO:0001819	synonymous_variant	2519			BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1041A>G	6.37:g.143823182T>C			E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663260	0.47572	.	.	ENSG00000001036	ENST00000438118;ENST00000367585	T;T	0.73047	-0.71;-0.71	5.83	0.146	0.14833	.	.	.	.	.	T	0.55417	0.1919	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.55244	-0.8171	6	0.87932	D	0	-0.0125	9.266	0.37641	0.18:0.0:0.5202:0.2998	.	.	.	.	G	164	ENSP00000394151:S164G;ENSP00000356557:S164G	ENSP00000356557:S164G	S	-	1	0	FUCA2	143864875	0.339000	0.24784	0.179000	0.23059	0.902000	0.53008	0.025000	0.13577	0.083000	0.17047	0.528000	0.53228	AGT		0.408	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020		24	32	24	32
NRCAM	4897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	107808830	107808830	+	Missense_Mutation	SNP	T	T	C			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr7:107808830T>C	ENST00000425651.2	-	26	3204	c.3205A>G	c.(3205-3207)Agg>Ggg	p.R1069G	NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379028.3_Missense_Mutation_p.R1069G|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.R1069G	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1069	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TTGCTGATCCTGGGATTTACT	0.353																																																0													67.0	64.0	65.0					7																	107808830		1887	4121	6008	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3205A>G	7.37:g.107808830T>C	ENSP00000401244:p.Arg1069Gly		A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.681135	0.29872	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.59224	0.28;0.28;0.32	5.53	4.38	0.52667	Fibronectin, type III (3);	0.676470	0.15772	N	0.245361	T	0.44117	0.1278	N	0.22421	0.69	0.33242	D	0.557307	B	0.11235	0.004	B	0.25987	0.065	T	0.49380	-0.8946	10	0.22706	T	0.39	.	11.3227	0.49433	0.0:0.0716:0.0:0.9284	.	1069	Q92823	NRCAM_HUMAN	G	1069	ENSP00000368314:R1069G;ENSP00000401244:R1069G;ENSP00000368308:R1069G	ENSP00000368308:R1069G	R	-	1	2	NRCAM	107596066	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.289000	0.33307	0.922000	0.37019	0.528000	0.53228	AGG		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		6	32	6	32
RAB2A	5862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	61484623	61484623	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr8:61484623G>A	ENST00000262646.7	+	3	488	c.137G>A	c.(136-138)cGa>cAa	p.R46Q	RAB2A_ENST00000529579.1_Missense_Mutation_p.R46Q|RAB2A_ENST00000531289.1_Missense_Mutation_p.R22Q	NM_002865.2	NP_002856.1	P61019	RAB2A_HUMAN	RAB2A, member RAS oncogene family	46					ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(4)	6			BRCA - Breast invasive adenocarcinoma(89;0.0805)			TTCGGTGCTCGAATGATAACT	0.323																																																0													99.0	93.0	95.0					8																	61484623		2203	4300	6503	SO:0001583	missense	5862				CCDS6175.1, CCDS56537.1	8q12.1	2007-01-15	2007-01-15	2007-01-15	ENSG00000104388	ENSG00000104388		"""RAB, member RAS oncogene"""	9763	protein-coding gene	gene with protein product		179509	"""RAB2, member RAS oncogene family"""	RAB2			Standard	NM_002865		Approved		uc003xud.2	P61019	OTTHUMG00000134298	ENST00000262646.7:c.137G>A	8.37:g.61484623G>A	ENSP00000262646:p.Arg46Gln		B2R5W8|B4DMQ5|P08886	Missense_Mutation	SNP	ENST00000262646.7	37	CCDS6175.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.548492	0.86127	.	.	ENSG00000104388	ENST00000262646;ENST00000531289;ENST00000529579	T;T;T	0.76709	-1.04;-1.04;-1.04	5.75	3.94	0.45596	Small GTP-binding protein domain (1);	0.057015	0.64402	N	0.000002	T	0.65460	0.2693	L	0.37897	1.145	0.58432	D	0.999991	P;P	0.52170	0.951;0.802	B;B	0.39152	0.292;0.292	T	0.66372	-0.5940	10	0.87932	D	0	.	9.1584	0.37007	0.0786:0.1464:0.775:0.0	.	22;46	B4DMQ5;P61019	.;RAB2A_HUMAN	Q	46;22;46	ENSP00000262646:R46Q;ENSP00000431846:R22Q;ENSP00000431589:R46Q	ENSP00000262646:R46Q	R	+	2	0	RAB2A	61647177	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.656000	0.83736	0.752000	0.32923	0.561000	0.74099	CGA		0.323	RAB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259145.2			11	36	11	36
SPANXD	64648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	140785767	140785767	+	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chrX:140785767A>G	ENST00000370515.3	-	2	482	c.149T>C	c.(148-150)aTa>aCa	p.I50T		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	50						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					AACCACTAGTATGGTCGAGGA	0.498																																																0													246.0	181.0	203.0					X																	140785767		2199	4273	6472	SO:0001583	missense	64648			AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.149T>C	X.37:g.140785767A>G	ENSP00000359546:p.Ile50Thr		Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	0.147	-1.095576	0.01858	.	.	ENSG00000196406	ENST00000370515	T	0.09255	3.0	.	.	.	.	.	.	.	.	T	0.07324	0.0185	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.35375	-0.9791	6	0.41790	T	0.15	.	.	.	.	.	50	Q9BXN6	SPNXD_HUMAN	T	50	ENSP00000359546:I50T	ENSP00000359546:I50T	I	-	2	0	SPANXD	140613433	0.009000	0.17119	0.002000	0.10522	0.008000	0.06430	0.072000	0.14617	0.358000	0.24211	0.058000	0.15282	ATA		0.498	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1			78	53	78	53
OR1A1	8383	broad.mit.edu;ucsc.edu	37	17	3119138	3119138	+	Missense_Mutation	SNP	C	C	T			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr17:3119138C>T	ENST00000304094.1	+	1	224	c.224C>T	c.(223-225)tCg>tTg	p.S75L		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						TTCTTCTCATCGGTAACCATC	0.483																																																0													228.0	189.0	202.0					17																	3119138		2203	4300	6503	SO:0001583	missense	8383			AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.224C>T	17.37:g.3119138C>T	ENSP00000305207:p.Ser75Leu		A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	37	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.483097	0.63962	.	.	ENSG00000172146	ENST00000304094	T	0.00406	7.55	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000109	T	0.00936	0.0031	M	0.61703	1.905	0.31845	N	0.622997	D	0.89917	1.0	D	0.83275	0.996	T	0.47995	-0.9073	10	0.87932	D	0	.	12.0758	0.53643	0.1721:0.8279:0.0:0.0	.	75	Q9P1Q5	OR1A1_HUMAN	L	75	ENSP00000305207:S75L	ENSP00000305207:S75L	S	+	2	0	OR1A1	3065888	0.000000	0.05858	1.000000	0.80357	0.588000	0.36517	1.336000	0.33850	2.584000	0.87258	0.436000	0.28706	TCG		0.483	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		50	134	50	134
HIST1H3C	8352	broad.mit.edu;ucsc.edu	37	6	26045799	26045799	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr6:26045799G>A	ENST00000540144.1	+	1	161	c.161G>A	c.(160-162)cGc>cAc	p.R54H	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	54					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						GAAATCCGTCGCTACCAGAAG	0.622																																																0													48.0	51.0	50.0					6																	26045799		2203	4300	6503	SO:0001583	missense	8352			X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.161G>A	6.37:g.26045799G>A	ENSP00000439493:p.Arg54His		A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000540144.1	37	CCDS4576.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.892503	0.33442	.	.	ENSG00000196532	ENST00000540144	T	0.46063	0.88	4.53	4.53	0.55603	.	.	.	.	.	T	0.52645	0.1747	.	.	.	0.49299	D	0.999774	.	.	.	.	.	.	T	0.56475	-0.7973	6	0.59425	D	0.04	.	17.1289	0.86722	0.0:0.0:1.0:0.0	.	.	.	.	H	54	ENSP00000439493:R54H	ENSP00000439493:R54H	R	+	2	0	HIST1H3C	26153778	1.000000	0.71417	0.999000	0.59377	0.017000	0.09413	9.684000	0.98659	2.460000	0.83146	0.491000	0.48974	CGC		0.622	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531		5	35	5	35
VNN3	55350	broad.mit.edu;ucsc.edu	37	6	133045776	133045776	+	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr6:133045776A>G	ENST00000207771.3	-	6	1241	c.1169T>C	c.(1168-1170)cTg>cCg	p.L390P	VNN3_ENST00000423615.2_3'UTR|VNN3_ENST00000275223.3_3'UTR|VNN3_ENST00000367927.5_3'UTR|VNN3_ENST00000392393.3_3'UTR|VNN3_ENST00000427187.2_3'UTR|VNN3_ENST00000417437.2_3'UTR|VNN3_ENST00000519686.2_3'UTR|VNN3_ENST00000414302.2_3'UTR|VNN3_ENST00000425515.2_3'UTR|VNN3_ENST00000509351.1_3'UTR			Q9NY84	VNN3_HUMAN	vanin 3	391					nitrogen compound metabolic process (GO:0006807)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)		TACTGTGTGCAGTCCATCAAA	0.388																																																0													26.0	25.0	25.0					6																	133045776		876	1991	2867	SO:0001583	missense	55350			AJ238982		6q23.2	2014-04-09	2010-11-15	2010-11-15	ENSG00000093134	ENSG00000093134	3.5.1.92	"""Vanins"""	16431	other	unknown		606592				10501839, 19932582, 19322213	Standard	NR_028290		Approved	HSA238982	uc010kfs.3	Q9NY84	OTTHUMG00000015589	ENST00000207771.3:c.1169T>C	6.37:g.133045776A>G	ENSP00000440594:p.Leu390Pro		B2DFY0|B2DFY1|B2DFY3|B2DFY5|B2DFY6|B2DFY7|B2DFY8|Q3SX90|Q9BQY2	Missense_Mutation	SNP	ENST00000207771.3	37		.	.	.	.	.	.	.	.	.	.	A	16.54	3.150736	0.57151	.	.	ENSG00000093134	ENST00000207771	D	0.96232	-3.95	5.14	2.67	0.31697	.	0.000000	0.53938	D	0.000048	D	0.90403	0.6996	.	.	.	0.80722	D	1	P	0.50819	0.939	B	0.42214	0.38	D	0.87090	0.2172	9	0.46703	T	0.11	-14.6474	7.441	0.27183	0.8025:0.0:0.0704:0.1271	.	391	Q9NY84	VNN3_HUMAN	P	390	ENSP00000440594:L390P	ENSP00000440594:L390P	L	-	2	0	VNN3	133087469	1.000000	0.71417	0.066000	0.19879	0.902000	0.53008	2.551000	0.45820	0.345000	0.23873	0.477000	0.44152	CTG		0.388	VNN3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NR_028290		6	13	6	13
OBSCN	84033	broad.mit.edu;ucsc.edu	37	1	228529314	228529314	+	Splice_Site	SNP	G	G	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr1:228529314G>A	ENST00000422127.1	+	74	18077	c.18033G>A	c.(18031-18033)tgG>tgA	p.W6011*	OBSCN_ENST00000570156.2_Splice_Site_p.W6968*|OBSCN_ENST00000366709.4_Splice_Site_p.W3130*|OBSCN_ENST00000366707.4_Splice_Site_p.W3645*|OBSCN_ENST00000284548.11_Splice_Site_p.W6011*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6011					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGCCTGTGTGGCGTGAGTGTC	0.672																																																0													29.0	38.0	35.0					1																	228529314		2167	4246	6413	SO:0001630	splice_region_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18034+1G>A	1.37:g.228529314G>A			Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Splice_Site	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	64|64	82.940072|82.940072	0.99994|0.99994	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|.	.|.	.|.	5.07|5.07	5.07|5.07	0.68467|0.68467	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|.	0.52338|.	0.1728|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.45702|.	-0.9243|.	3|.	.|0.07813	.|T	.|0.8	.|.	18.442|18.442	0.90670|0.90670	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	T|X	628|6011;6011;3645;3130	.|.	.|ENSP00000284548:W6011X	A|W	+|+	1|3	0|0	OBSCN|OBSCN	226595937|226595937	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.792000|0.792000	0.44763|0.44763	7.473000|7.473000	0.81007|0.81007	2.342000|2.342000	0.79632|0.79632	0.563000|0.563000	0.77884|0.77884	GCG|TGG		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	Nonsense_Mutation	5	20	5	20
HCLS1	3059	broad.mit.edu;ucsc.edu	37	3	121351926	121351926	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr3:121351926C>A	ENST00000314583.3	-	11	1087	c.996G>T	c.(994-996)caG>caT	p.Q332H	HCLS1_ENST00000473883.1_5'UTR|HCLS1_ENST00000428394.2_Missense_Mutation_p.Q295H	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	332					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		CCGGGAGAGTCTGCCTAATGG	0.587																																																0													43.0	41.0	42.0					3																	121351926		2203	4300	6503	SO:0001583	missense	3059				CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.996G>T	3.37:g.121351926C>A	ENSP00000320176:p.Gln332His		B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	37	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	C	9.662	1.144405	0.21205	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.20598	2.06;2.06	5.14	2.22	0.28083	.	0.617893	0.17747	N	0.163369	T	0.13670	0.0331	L	0.29908	0.895	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.20571	-1.0271	10	0.66056	D	0.02	-3.1794	5.7028	0.17891	0.347:0.562:0.0:0.091	.	295;332	E7EVW7;P14317	.;HCLS1_HUMAN	H	332;295	ENSP00000320176:Q332H;ENSP00000387645:Q295H	ENSP00000320176:Q332H	Q	-	3	2	HCLS1	122834616	0.047000	0.20315	0.008000	0.14137	0.011000	0.07611	0.279000	0.18771	0.359000	0.24239	0.655000	0.94253	CAG		0.587	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335		6	21	6	21
CLK1	1195	broad.mit.edu;hgsc.bcm.edu	37	2	201726490	201726493	+	Frame_Shift_Del	DEL	CTTC	CTTC	-	rs532247548		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr2:201726490_201726493delCTTC	ENST00000321356.4	-	2	228_231	c.93_96delGAAG	c.(91-96)aggaagfs	p.RK31fs	Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000434813.2_Frame_Shift_Del_p.RK73fs|CLK1_ENST00000492793.1_Intron	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	31					cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						TATGTGATCTCTTCCTTCTTTTAT	0.397																																																0																																										SO:0001589	frameshift_variant	1195			L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.93_96delGAAG	2.37:g.201726494_201726497delCTTC	ENSP00000326830:p.Arg31fs		B4DFW7|Q0P694|Q8N5V8	Frame_Shift_Del	DEL	ENST00000321356.4	37	CCDS2331.1																																																																																				0.397	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			45	165	45	165
RBPJ	3516	broad.mit.edu;hgsc.bcm.edu	37	4	26426086	26426088	+	In_Frame_Del	DEL	TTT	TTT	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr4:26426086_26426088delTTT	ENST00000361572.6	+	6	852_854	c.658_660delTTT	c.(658-660)tttdel	p.F221del	RBPJ_ENST00000342295.1_In_Frame_Del_p.F221del|RBPJ_ENST00000342320.4_In_Frame_Del_p.F207del|RBPJ_ENST00000507561.1_In_Frame_Del_p.F186del|RBPJ_ENST00000348160.4_In_Frame_Del_p.F208del|RBPJ_ENST00000355476.3_In_Frame_Del_p.F207del|RBPJ_ENST00000345843.3_In_Frame_Del_p.F206del|RBPJ_ENST00000504907.1_In_Frame_Del_p.F207del			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	221					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|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)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				GTGGGGAGCCTTTTTTATTCATC	0.36																																																0																																										SO:0001651	inframe_deletion	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.658_660delTTT	4.37:g.26426089_26426091delTTT	ENSP00000354528:p.Phe221del		B4DY22|Q5XKH9|Q6P1N3	In_Frame_Del	DEL	ENST00000361572.6	37	CCDS3437.1																																																																																				0.360	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		28	78	28	78
ZFHX4	79776	broad.mit.edu;hgsc.bcm.edu	37	8	77776374	77776377	+	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs76951673		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr8:77776374_77776377delCAAT	ENST00000521891.2	+	11	10872_10875	c.10424_10427delCAAT	c.(10423-10428)acaatcfs	p.TI3475fs	ZFHX4_ENST00000518282.1_Frame_Shift_Del_p.TI3449fs|ZFHX4_ENST00000455469.2_Frame_Shift_Del_p.TI3430fs|ZFHX4_ENST00000050961.6_Frame_Shift_Del_p.TI3426fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3426	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAGAGAAAACAATCAAACAAGCA	0.456										HNSCC(33;0.089)																																						0																																										SO:0001589	frameshift_variant	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.10424_10427delCAAT	8.37:g.77776374_77776377delCAAT	ENSP00000430497:p.Thr3475fs		G3V138|Q18PS0|Q6ZN20	Frame_Shift_Del	DEL	ENST00000521891.2	37	CCDS47878.2																																																																																				0.456	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		22	44	22	44
RBM12B	389677	broad.mit.edu;hgsc.bcm.edu	37	8	94745644	94745648	+	Frame_Shift_Del	DEL	TTAAC	TTAAC	-	rs375433313		TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr8:94745644_94745648delTTAAC	ENST00000399300.2	-	3	3204_3208	c.2991_2995delGTTAA	c.(2989-2997)aagttaactfs	p.KLT997fs	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Frame_Shift_Del_p.KLT877fs	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	997	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TACAGCAAAGTTAACTTAACTTTTC	0.332																																																0																																										SO:0001589	frameshift_variant	389677				CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2991_2995delGTTAA	8.37:g.94745649_94745653delTTAAC	ENSP00000382239:p.Lys997fs		A8MYB5	Frame_Shift_Del	DEL	ENST00000399300.2	37	CCDS43755.1																																																																																				0.332	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		19	47	19	47
C12orf65	91574	broad.mit.edu;hgsc.bcm.edu	37	12	123738357	123738359	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr12:123738357_123738359delAAG	ENST00000253233.1	+	2	780_782	c.136_138delAAG	c.(136-138)aagdel	p.K47del	C12orf65_ENST00000366329.2_In_Frame_Del_p.K47del|C12orf65_ENST00000429587.2_In_Frame_Del_p.K47del|RP11-282O18.3_ENST00000543217.2_RNA|RP11-282O18.3_ENST00000541002.3_RNA	NM_152269.4	NP_689482.1	Q9H3J6	CL065_HUMAN	chromosome 12 open reading frame 65	47					cell death (GO:0008219)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000595)|Epithelial(86;0.00199)		GATGGCAGGCAAGAAGGACTACC	0.557																																																0																																										SO:0001651	inframe_deletion	0			AK095982	CCDS9244.1	12q24.31	2013-01-07			ENSG00000130921	ENSG00000130921			26784	protein-coding gene	gene with protein product		613541				20598281, 22688947, 23188110	Standard	NM_152269		Approved	FLJ38663, SPG55	uc001uen.3	Q9H3J6	OTTHUMG00000168852	ENST00000253233.1:c.136_138delAAG	12.37:g.123738360_123738362delAAG	ENSP00000253233:p.Lys47del		Q8WUC6	In_Frame_Del	DEL	ENST00000253233.1	37	CCDS9244.1																																																																																				0.557	C12orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401375.1	NM_152269		10	51	10	51
UBL3	5412	broad.mit.edu;hgsc.bcm.edu	37	13	30341404	30341406	+	In_Frame_Del	DEL	ACA	ACA	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr13:30341404_30341406delACA	ENST00000380680.4	-	5	1485_1487	c.340_342delTGT	c.(340-342)tgtdel	p.C114del		NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	114						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		ACAGGATTACACAACAATTACTC	0.433																																																0																																										SO:0001651	inframe_deletion	5412			AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042			12504	protein-coding gene	gene with protein product		604711		PNSC1		10375635	Standard	NM_007106		Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.340_342delTGT	13.37:g.30341407_30341409delACA	ENSP00000370055:p.Cys114del		B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	In_Frame_Del	DEL	ENST00000380680.4	37	CCDS9334.1																																																																																				0.433	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044342.1	NM_007106		12	38	12	38
TINF2	26277	broad.mit.edu;hgsc.bcm.edu	37	14	24709491	24709493	+	In_Frame_Del	DEL	TAA	TAA	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr14:24709491_24709493delTAA	ENST00000267415.7	-	7	1446_1448	c.1105_1107delTTA	c.(1105-1107)ttadel	p.L369del	TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000540705.1_In_Frame_Del_p.L334del|TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000399423.4_3'UTR|TINF2_ENST00000538777.1_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	369					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		CCCTAGGAGGTAATAATGATAGT	0.498									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome																																							0																																										SO:0001651	inframe_deletion	26277	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.1105_1107delTTA	14.37:g.24709494_24709496delTAA	ENSP00000267415:p.Leu369del		B3W5Q7|Q9H904|Q9UHC2	In_Frame_Del	DEL	ENST00000267415.7	37	CCDS41936.1																																																																																				0.498	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2			19	80	19	80
MED29	55588	broad.mit.edu;hgsc.bcm.edu	37	19	39879756	39879758	+	5'Flank	DEL	TCT	TCT	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr19:39879756_39879758delTCT	ENST00000599213.2	+	0	0				MED29_ENST00000594368.1_5'Flank|MED29_ENST00000315588.5_5'Flank|PAF1_ENST00000221265.3_In_Frame_Del_p.K181del|PAF1_ENST00000595564.1_In_Frame_Del_p.K171del|PAF1_ENST00000221266.7_In_Frame_Del_p.K171del			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			TCCTCAAAAGTCTTCTCAATGGC	0.483																																																0																																										SO:0001631	upstream_gene_variant	54623			AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"""intersex-like (Drosophila)"""	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70			19.37:g.39879759_39879761delTCT	Exception_encountered		B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	In_Frame_Del	DEL	ENST00000599213.2	37																																																																																					0.483	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829		30	104	30	104
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42797980	42797981	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-FG-5964-01A-11D-1705-08	TCGA-FG-5964-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6888be2-4517-41e4-a801-9c915f24e737	96d57c40-fcc5-4dc4-857c-b2d334627206	g.chr19:42797980_42797981delTG	ENST00000575354.2	+	16	4072_4073	c.4032_4033delTG	c.(4030-4035)tctgtgfs	p.V1345fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.V1343fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.V2252fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1345					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCTTTGACTCTGTGGACAAGTG	0.693			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4032_4033delTG	19.37:g.42797982_42797983delTG	ENSP00000458663:p.Val1345fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.693	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			32	35	32	35
