#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	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_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ACE	1636	genome.wustl.edu	37	17	61570872	61570872	+	Silent	SNP	C	C	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr17:61570872C>T	ENST00000290866.4	+	20	3012	c.2988C>T	c.(2986-2988)ttC>ttT	p.F996F	ACE_ENST00000490216.2_Silent_p.F422F|ACE_ENST00000413513.3_Silent_p.F422F|ACE_ENST00000428043.1_Silent_p.F996F|ACE_ENST00000421982.2_Silent_p.F242F|ACE_ENST00000577647.1_Silent_p.F422F|ACE_ENST00000290863.6_Silent_p.F422F	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	996	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	TCCAGTATTTCATGCAGTACA	0.577																																						dbGAP											0													88.0	84.0	85.0					17																	61570872		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2988C>T	17.37:g.61570872C>T			B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	pfam_Peptidase_M2,prints_Peptidase_M2	p.F996	ENST00000290866.4	37	c.2988	CCDS11637.1	17																																																																																			ACE	-	pfam_Peptidase_M2,prints_Peptidase_M2	ENSG00000159640		0.577	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACE	HGNC	protein_coding	OTTHUMT00000337675.2	118	0.00	0	C			61570872	61570872	+1	no_errors	ENST00000290866	ensembl	human	known	69_37n	silent	79	28.83	32	SNP	1.000	T
ARCN1	372	genome.wustl.edu	37	11	118468587	118468587	+	Silent	SNP	A	A	G			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr11:118468587A>G	ENST00000264028.4	+	9	1502	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	ARCN1_ENST00000359415.4_Silent_p.Q510Q|ARCN1_ENST00000392859.3_Silent_p.Q381Q|ARCN1_ENST00000534182.2_Intron	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	469	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TCCCTGTTCAAGTTTCCTTTG	0.433																																						dbGAP											0													130.0	119.0	123.0					11																	118468587		2200	4295	6495	-	-	-	SO:0001819	synonymous_variant	0			X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"""coatomer protein complex, subunit delta"""	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.1407A>G	11.37:g.118468587A>G			B4E1X2|E9PEU4|Q52M80	Silent	SNP	pfam_Clathrin_mu_C,pfam_AP_mu_sigma_su,superfamily_Clathrin_mu_C,superfamily_Longin-like_dom,pfscan_Clathrin_mu_C	p.Q469	ENST00000264028.4	37	c.1407	CCDS8400.1	11																																																																																			ARCN1	-	pfam_Clathrin_mu_C,superfamily_Clathrin_mu_C,pfscan_Clathrin_mu_C	ENSG00000095139		0.433	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARCN1	HGNC	protein_coding	OTTHUMT00000389278.1	277	0.00	0	A			118468587	118468587	+1	no_errors	ENST00000264028	ensembl	human	known	69_37n	silent	94	51.55	100	SNP	1.000	G
ARNT	405	genome.wustl.edu	37	1	150807078	150807078	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr1:150807078C>A	ENST00000358595.5	-	8	939	c.739G>T	c.(739-741)Gaa>Taa	p.E247*	ARNT_ENST00000354396.2_Nonsense_Mutation_p.E247*|ARNT_ENST00000505755.1_Nonsense_Mutation_p.E232*|ARNT_ENST00000515192.1_Nonsense_Mutation_p.E238*|ARNT_ENST00000468970.1_5'UTR	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	247					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCTGACCTTCCTTTTTCACT	0.473			T	ETV6	AML																																	dbGAP		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	0													188.0	162.0	171.0					1																	150807078		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.739G>T	1.37:g.150807078C>A	ENSP00000351407:p.Glu247*		B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Nonsense_Mutation	SNP	pfam_PAS_fold_3,pfam_PAS_fold,pfam_HLH_DNA-bd,superfamily_HLH_DNA-bd,smart_HLH_DNA-bd,smart_PAS,smart_PAC,pfscan_PAS,pfscan_HLH_DNA-bd,prints_Nuc_translocat,tigrfam_PAS	p.E247*	ENST00000358595.5	37	c.739	CCDS970.1	1	.	.	.	.	.	.	.	.	.	.	C	39	7.759296	0.98474	.	.	ENSG00000143437	ENST00000358595;ENST00000368975;ENST00000354396;ENST00000515192;ENST00000394700;ENST00000505755	.	.	.	5.61	5.61	0.85477	.	0.146974	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.6376	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	X	247;247;247;238;231;232	.	ENSP00000346372:E247X	E	-	1	0	ARNT	149073702	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.461000	0.80834	2.643000	0.89663	0.467000	0.42956	GAA	ARNT	-	pfam_PAS_fold	ENSG00000143437		0.473	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ARNT	HGNC	protein_coding	OTTHUMT00000084741.2	322	0.00	0	C			150807078	150807078	-1	no_errors	ENST00000358595	ensembl	human	known	69_37n	nonsense	248	11.43	32	SNP	1.000	A
CCNG2	901	genome.wustl.edu	37	4	78082828	78082828	+	Silent	SNP	C	C	G			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr4:78082828C>G	ENST00000316355.5	+	6	989	c.633C>G	c.(631-633)ctC>ctG	p.L211L	CCNG2_ENST00000354403.5_Silent_p.L211L|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000502280.1_Silent_p.L211L|CCNG2_ENST00000509972.1_Silent_p.L211L|CCNG2_ENST00000395640.1_Silent_p.L211L	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	211					cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						TGTGCCTTCTCAATTTGGAAG	0.279																																						dbGAP											0													65.0	67.0	66.0					4																	78082828		2202	4298	6500	-	-	-	SO:0001819	synonymous_variant	0			BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.633C>G	4.37:g.78082828C>G			B4DF25|Q6FGA7|Q6FGC6	Silent	SNP	pfam_Cyclin_N,superfamily_Cyclin-like,smart_Cyclin-like	p.L211	ENST00000316355.5	37	c.633	CCDS3581.1	4																																																																																			CCNG2	-	NULL	ENSG00000138764		0.279	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCNG2	HGNC	protein_coding	OTTHUMT00000252404.3	280	0.36	1	C	NM_004354		78082828	78082828	+1	no_errors	ENST00000316355	ensembl	human	known	69_37n	silent	153	23.38	47	SNP	1.000	G
CNN2	1265	genome.wustl.edu	37	19	1032430	1032430	+	Missense_Mutation	SNP	C	C	G	rs568958979		TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr19:1032430C>G	ENST00000263097.4	+	3	588	c.225C>G	c.(223-225)atC>atG	p.I75M	CNN2_ENST00000562958.2_Missense_Mutation_p.I75M|CNN2_ENST00000348419.3_Missense_Mutation_p.I75M|CNN2_ENST00000565096.2_Missense_Mutation_p.I75M|CNN2_ENST00000606983.1_3'UTR	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	75	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCCCAAGATCAACCGCTCCA	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17968	0.001		0.0	False		,,,				2504	0.0					dbGAP											0													94.0	94.0	94.0					19																	1032430		2203	4300	6503	-	-	-	SO:0001583	missense	0			D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.225C>G	19.37:g.1032430C>G	ENSP00000263097:p.Ile75Met		A5D8U8|A6NFI4|D6W5X9|Q92578	Missense_Mutation	SNP	pfam_Calponin_repeat,pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain,pfscan_Calponin_repeat,prints_SM22_calponin,prints_Calponin	p.I75M	ENST00000263097.4	37	c.225	CCDS12053.1	19	.	.	.	.	.	.	.	.	.	.	C	15.37	2.813469	0.50527	.	.	ENSG00000064666	ENST00000263097;ENST00000348419;ENST00000442531	D;D	0.95918	-3.85;-3.85	4.05	2.72	0.32119	Calponin homology domain (5);	0.074727	0.53938	U	0.000057	D	0.97417	0.9155	M	0.92604	3.325	0.31154	N	0.705123	P;P;P;P;P	0.49090	0.866;0.919;0.919;0.9;0.919	D;D;D;P;D	0.66196	0.927;0.942;0.942;0.867;0.942	D	0.94600	0.7795	10	0.87932	D	0	.	5.8224	0.18534	0.0:0.6659:0.2038:0.1303	.	75;75;75;75;75	B4DUT8;B4DDF4;A6NFI4;Q99439;Q6FHE4	.;.;.;CNN2_HUMAN;.	M	75;75;54	ENSP00000263097:I75M;ENSP00000340129:I75M	ENSP00000263097:I75M	I	+	3	3	CNN2	983430	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.740000	0.38228	1.827000	0.53221	0.306000	0.20318	ATC	CNN2	-	pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain,prints_Calponin	ENSG00000064666		0.622	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNN2	HGNC	protein_coding	OTTHUMT00000420293.3	138	0.00	0	C	NM_004368		1032430	1032430	+1	no_errors	ENST00000263097	ensembl	human	known	69_37n	missense	97	32.17	46	SNP	1.000	G
CNTD2	79935	genome.wustl.edu	37	19	40729202	40729202	+	Missense_Mutation	SNP	T	T	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr19:40729202T>A	ENST00000430325.2	-	5	729	c.681A>T	c.(679-681)ttA>ttT	p.L227F	CNTD2_ENST00000513948.1_Missense_Mutation_p.L121F	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	227					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						AGGTGGCAAGTAACATCACCT	0.697																																						dbGAP											0													6.0	8.0	7.0					19																	40729202		686	1580	2266	-	-	-	SO:0001583	missense	0			AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.681A>T	19.37:g.40729202T>A	ENSP00000396755:p.Leu227Phe		B4DX65	Missense_Mutation	SNP	pfam_Cyclin_N,superfamily_Cyclin-like,smart_Cyclin-like,pirsf_Cyclin_A/B/D/E	p.L227F	ENST00000430325.2	37	c.681	CCDS12551.2	19	.	.	.	.	.	.	.	.	.	.	T	12.69	2.013442	0.35511	.	.	ENSG00000105219	ENST00000430325;ENST00000513948	T;T	0.31769	1.48;1.48	4.03	-8.07	0.01098	.	.	.	.	.	T	0.13628	0.0330	N	0.19112	0.55	0.09310	N	1	P	0.44877	0.845	B	0.38428	0.273	T	0.08806	-1.0704	9	0.08179	T	0.78	.	12.3216	0.54987	0.0:0.3891:0.5041:0.1068	.	227	B4DX65	.	F	227;121	ENSP00000396755:L227F;ENSP00000425529:L121F	ENSP00000396755:L227F	L	-	3	2	CNTD2	45421042	0.000000	0.05858	0.000000	0.03702	0.245000	0.25701	-4.215000	0.00272	-3.159000	0.00228	0.459000	0.35465	TTA	CNTD2	-	superfamily_Cyclin-like,pirsf_Cyclin_A/B/D/E	ENSG00000105219		0.697	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTD2	HGNC	protein_coding	OTTHUMT00000360785.1	10	0.00	0	T	NM_024877		40729202	40729202	-1	no_errors	ENST00000430325	ensembl	human	known	69_37n	missense	9	47.06	8	SNP	0.000	A
FAM212B	55924	genome.wustl.edu	37	1	112270149	112270149	+	Missense_Mutation	SNP	C	C	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr1:112270149C>A	ENST00000357260.5	-	2	516	c.335G>T	c.(334-336)tGt>tTt	p.C112F	FAM212B_ENST00000534365.1_Intron|FAM212B_ENST00000444059.2_Missense_Mutation_p.C97F	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	112										cervix(1)|endometrium(1)	2						ATCCCTTCCACAGACACTCCT	0.597																																						dbGAP											0													82.0	74.0	77.0					1																	112270149		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 183"""	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.335G>T	1.37:g.112270149C>A	ENSP00000349805:p.Cys112Phe		B3KP38|B4DF94|Q9NTI6	Missense_Mutation	SNP	NULL	p.C112F	ENST00000357260.5	37	c.335	CCDS841.1	1	.	.	.	.	.	.	.	.	.	.	C	0.308	-0.969816	0.02232	.	.	ENSG00000197852	ENST00000357260;ENST00000444059;ENST00000527621	.	.	.	4.66	2.69	0.31865	.	0.829674	0.11329	N	0.575224	T	0.19967	0.0480	L	0.57536	1.79	0.09310	N	1	B;B	0.34241	0.218;0.444	B;B	0.34652	0.116;0.187	T	0.08764	-1.0706	9	0.42905	T	0.14	-3.3611	4.743	0.13024	0.0:0.503:0.3111:0.1859	.	97;112	Q9NTI7-2;Q9NTI7	.;CA183_HUMAN	F	112;97;121	.	ENSP00000349805:C112F	C	-	2	0	C1orf183	112071672	0.000000	0.05858	0.193000	0.23327	0.238000	0.25445	0.315000	0.19451	2.401000	0.81631	0.484000	0.47621	TGT	FAM212B	-	NULL	ENSG00000197852		0.597	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	FAM212B	HGNC	protein_coding	OTTHUMT00000033060.2	51	0.00	0	C	NM_019099		112270149	112270149	-1	no_errors	ENST00000357260	ensembl	human	known	69_37n	missense	42	17.65	9	SNP	0.029	A
FRMPD4	9758	genome.wustl.edu	37	X	12736089	12736089	+	Missense_Mutation	SNP	A	A	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chrX:12736089A>T	ENST00000380682.1	+	16	3650	c.3144A>T	c.(3142-3144)aaA>aaT	p.K1048N		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1048					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CAGGAAAAAAACAGCAGGGGA	0.517																																						dbGAP											0													90.0	73.0	78.0					X																	12736089		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3144A>T	X.37:g.12736089A>T	ENSP00000370057:p.Lys1048Asn		A8K0X9|O15032	Missense_Mutation	SNP	pfam_FERM_central,pfam_PDZ,superfamily_FERM_central,superfamily_PDZ,smart_PDZ,smart_Band_41_domain,pfscan_FERM_domain,pfscan_PDZ,pfscan_WW_Rsp5_WWP	p.K1048N	ENST00000380682.1	37	c.3144	CCDS35201.1	X	.	.	.	.	.	.	.	.	.	.	A	12.13	1.844578	0.32606	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.08370	3.1	5.49	1.38	0.22167	.	0.098713	0.64402	D	0.000002	T	0.11965	0.0291	M	0.68317	2.08	0.32587	N	0.527669	P;B	0.44627	0.839;0.03	P;B	0.44394	0.448;0.007	T	0.11591	-1.0581	10	0.87932	D	0	-14.3917	8.5974	0.33723	0.576:0.0:0.424:0.0	.	1040;1048	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	N	1048;1039;1037	ENSP00000370057:K1048N	ENSP00000304583:K1037N	K	+	3	2	FRMPD4	12646010	0.969000	0.33509	0.996000	0.52242	0.807000	0.45602	0.072000	0.14617	0.246000	0.21394	0.486000	0.48141	AAA	FRMPD4	-	NULL	ENSG00000169933		0.517	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FRMPD4	HGNC	protein_coding	OTTHUMT00000055771.1	159	0.00	0	A	XM_045712		12736089	12736089	+1	no_errors	ENST00000380682	ensembl	human	known	69_37n	missense	106	25.87	37	SNP	0.998	T
HDAC11	79885	genome.wustl.edu	37	3	13545616	13545616	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr3:13545616G>T	ENST00000295757.3	+	9	855	c.672G>T	c.(670-672)gaG>gaT	p.E224D	HDAC11_ENST00000404548.1_Missense_Mutation_p.S92I|HDAC11_ENST00000405025.1_Missense_Mutation_p.S64I|HDAC11_ENST00000402259.1_Missense_Mutation_p.E58D|HDAC11_ENST00000522202.1_Missense_Mutation_p.E173D|HDAC11_ENST00000446613.2_Missense_Mutation_p.E32D|HDAC11_ENST00000404040.1_Missense_Mutation_p.E124D|HDAC11_ENST00000433119.1_Missense_Mutation_p.S182I|HDAC11_ENST00000402271.1_Missense_Mutation_p.E145D|HDAC11_ENST00000437379.2_Missense_Mutation_p.E196D	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	224	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						GGAAGGTGGAGCTGGAGTGGG	0.542																																						dbGAP											0													81.0	76.0	78.0					3																	13545616		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.672G>T	3.37:g.13545616G>T	ENSP00000295757:p.Glu224Asp		B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Missense_Mutation	SNP	pfam_His_deacetylse_dom,prints_His_deacetylse	p.E224D	ENST00000295757.3	37	c.672	CCDS2615.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.017160|4.017160	0.75161|0.75161	.|.	.|.	ENSG00000163517|ENSG00000163517	ENST00000295757;ENST00000402259;ENST00000402271;ENST00000446613;ENST00000404040;ENST00000405478;ENST00000522202;ENST00000437379|ENST00000433119;ENST00000404548;ENST00000405025	T;T;T;T;T;T;T;T|.	0.78126|.	-0.52;-0.52;-0.52;-0.52;-0.52;-1.15;-0.52;-0.52|.	5.65|5.65	3.83|3.83	0.44106|0.44106	Histone deacetylase domain (2);|.	0.122386|.	0.64402|.	D|.	0.000013|.	T|T	0.64182|0.64182	0.2575|0.2575	M|M	0.75264|0.75264	2.295|2.295	0.47037|0.47037	D|D	0.999299|0.999299	P;P|D	0.42871|0.60160	0.567;0.792|0.987	B;P|P	0.46419|0.52267	0.366;0.516|0.694	T|T	0.67821|0.67821	-0.5571|-0.5571	10|8	0.87932|0.87932	D|D	0|0	-1.7016|-1.7016	8.1475|8.1475	0.31121|0.31121	0.181:0.0:0.819:0.0|0.181:0.0:0.819:0.0	.|.	173;224|182	B4DDK1;Q96DB2|Q658J9	.;HDA11_HUMAN|.	D|I	224;58;145;32;124;196;173;196|182;92;64	ENSP00000295757:E224D;ENSP00000384706:E58D;ENSP00000384123:E145D;ENSP00000401487:E32D;ENSP00000385475:E124D;ENSP00000385252:E196D;ENSP00000429794:E173D;ENSP00000395188:E196D|.	ENSP00000295757:E224D|ENSP00000385528:S92I	E|S	+|+	3|2	2|0	HDAC11|HDAC11	13520616|13520616	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.888000|0.888000	0.51559|0.51559	3.006000|3.006000	0.49529|0.49529	1.361000|1.361000	0.45981|0.45981	0.561000|0.561000	0.74099|0.74099	GAG|AGC	HDAC11	-	pfam_His_deacetylse_dom	ENSG00000163517		0.542	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDAC11	HGNC	protein_coding	OTTHUMT00000252028.5	249	0.00	0	G	NM_024827		13545616	13545616	+1	no_errors	ENST00000295757	ensembl	human	known	69_37n	missense	164	31.09	74	SNP	1.000	T
IFT122	55764	genome.wustl.edu	37	3	129207207	129207207	+	Silent	SNP	G	G	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr3:129207207G>A	ENST00000348417.2	+	16	2036	c.1959G>A	c.(1957-1959)gcG>gcA	p.A653A	IFT122_ENST00000504021.1_Silent_p.A547A|IFT122_ENST00000347300.2_Silent_p.A594A|IFT122_ENST00000296266.3_Silent_p.A704A|IFT122_ENST00000431818.2_Silent_p.A503A|IFT122_ENST00000349441.2_Silent_p.A542A|IFT122_ENST00000507564.1_Silent_p.A645A|IFT122_ENST00000440957.2_Silent_p.A444A	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	653					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						CCATGGAAGCGCTAGAAGGTT	0.498																																						dbGAP											0													82.0	77.0	79.0					3																	129207207		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.1959G>A	3.37:g.129207207G>A			B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.A704	ENST00000348417.2	37	c.2112	CCDS3061.1	3																																																																																			IFT122	-	NULL	ENSG00000163913		0.498	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	IFT122	HGNC	protein_coding	OTTHUMT00000355852.1	160	0.00	0	G	NM_018262		129207207	129207207	+1	no_errors	ENST00000296266	ensembl	human	known	69_37n	silent	140	18.13	31	SNP	0.517	A
ITGB4	3691	genome.wustl.edu	37	17	73745040	73745040	+	Missense_Mutation	SNP	G	G	A	rs201487753		TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr17:73745040G>A	ENST00000200181.3	+	27	3417	c.3230G>A	c.(3229-3231)cGc>cAc	p.R1077H	ITGB4_ENST00000579662.1_Missense_Mutation_p.R1077H|ITGB4_ENST00000449880.2_Missense_Mutation_p.R1077H|ITGB4_ENST00000339591.3_Missense_Mutation_p.R1077H|ITGB4_ENST00000450894.3_Missense_Mutation_p.R1077H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1077	Calx-beta.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGCCAGGTCCGCCGTTTCCAC	0.642																																						dbGAP											0													31.0	35.0	33.0					17																	73745040		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3230G>A	17.37:g.73745040G>A	ENSP00000200181:p.Arg1077His		A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	pirsf_Integrin_bsu-4,pfam_Integrin_bsu_N,pfam_Fibronectin_type3,pfam_Calx_beta,pfam_Integrin_bsu_tail,pfam_EGF_extracell,superfamily_Fibronectin_type3,superfamily_Integrin_bsu_tail,superfamily_Plexin-like_fold,smart_Plexin-like,smart_Integrin_bsu_N,smart_Calx_beta,smart_Fibronectin_type3,pfscan_Fibronectin_type3,prints_Integrin_bsu	p.R1077H	ENST00000200181.3	37	c.3230	CCDS11727.1	17	.	.	.	.	.	.	.	.	.	.	G	9.203	1.029084	0.19512	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.28069	1.63;1.63;1.63	4.93	4.93	0.64822	Na-Ca exchanger/integrin-beta4 (2);	0.193469	0.36893	N	0.002360	T	0.44787	0.1310	L	0.56769	1.78	0.40101	D	0.976378	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.67548	0.92;0.952;0.952	T	0.47459	-0.9116	10	0.87932	D	0	.	5.8549	0.18714	0.2261:0.0:0.7739:0.0	.	1077;1077;1077	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	H	1077	ENSP00000200181:R1077H;ENSP00000344079:R1077H;ENSP00000400217:R1077H	ENSP00000200181:R1077H	R	+	2	0	ITGB4	71256635	1.000000	0.71417	0.998000	0.56505	0.117000	0.20001	4.624000	0.61254	2.568000	0.86640	0.650000	0.86243	CGC	ITGB4	-	pirsf_Integrin_bsu-4,pfam_Calx_beta,smart_Calx_beta	ENSG00000132470		0.642	ITGB4-001	KNOWN	basic|CCDS	protein_coding	ITGB4	HGNC	protein_coding	OTTHUMT00000448334.1	44	0.00	0	G			73745040	73745040	+1	no_errors	ENST00000200181	ensembl	human	known	69_37n	missense	55	28.21	22	SNP	1.000	A
KCNMA1	3778	genome.wustl.edu	37	10	79397263	79397264	+	In_Frame_Ins	INS	-	-	GAG	rs199671652|rs572827902	byFrequency	TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr10:79397263_79397264insGAG	ENST00000286628.8	-	1	136_137	c.137_138insCTC	c.(136-138)tct>tcCTCt	p.46_46S>SS	KCNMA1_ENST00000404857.1_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000406533.3_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000372440.1_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000404771.3_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000354353.5_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000372443.1_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000481070.1_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000480683.1_In_Frame_Ins_p.46_46S>SS|KCNMA1_ENST00000286627.5_In_Frame_Ins_p.46_46S>SS	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	46	Poly-Ser.				blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.S60delS(2)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	aagaagaggaagaggaggagga	0.619														42	0.00838658	0.0015	0.0043	5008	,	,		12119	0.0337		0.003	False		,,,				2504	0.0					dbGAP											2	Deletion - In frame(2)	large_intestine(2)																																								-	-	-	SO:0001652	inframe_insertion	0			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.135_137dupCTC	10.37:g.79397270_79397272dupGAG	ENSP00000286628:p.Ser60dup		F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	In_Frame_Ins	INS	pfam_K_chnl_Ca-activ_BK_asu,pfam_Ion_trans_dom,pfam_Ion_trans_2,pfam_RCK_N,prints_K_chnl_Ca-activ_BK_asu,prints_K_chnl	p.50in_frame_insS	ENST00000286628.8	37	c.138_137		10																																																																																			KCNMA1	-	NULL	ENSG00000156113		0.619	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	KCNMA1	HGNC	protein_coding	OTTHUMT00000048885.3	16	0.00	0	-	NM_002247		79397263	79397264	-1	no_errors	ENST00000406533	ensembl	human	known	69_37n	in_frame_ins	34	22.73	10	INS	0.506:0.437	GAG
MAP2	4133	genome.wustl.edu	37	2	210557446	210557446	+	Missense_Mutation	SNP	G	G	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr2:210557446G>T	ENST00000360351.4	+	7	1058	c.552G>T	c.(550-552)aaG>aaT	p.K184N	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.K180N|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	184					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGTCAGAGAAGCAAAGTAAGC	0.458																																					Pancreas(27;423 979 28787 29963)	dbGAP											0													84.0	72.0	76.0					2																	210557446		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.552G>T	2.37:g.210557446G>T	ENSP00000353508:p.Lys184Asn		Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	pfam_MAP2_projctn,pfam_Tau/MAP_tubulin-bd_rpt	p.K184N	ENST00000360351.4	37	c.552	CCDS2384.1	2	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015215	0.35511	.	.	ENSG00000078018	ENST00000360351;ENST00000445941;ENST00000447185	T;T;T	0.21543	2.0;2.0;2.0	5.98	-5.9	0.02275	.	0.579118	0.16899	N	0.194962	T	0.15392	0.0371	L	0.46157	1.445	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.12578	-1.0542	10	0.66056	D	0.02	-0.0146	11.0109	0.47663	0.6248:0.0:0.2876:0.0876	.	180;184	P11137-3;P11137	.;MAP2_HUMAN	N	184;266;180	ENSP00000353508:K184N;ENSP00000409969:K266N;ENSP00000392164:K180N	ENSP00000353508:K184N	K	+	3	2	MAP2	210265691	0.315000	0.24571	0.001000	0.08648	0.983000	0.72400	-0.050000	0.11904	-1.237000	0.02539	-0.345000	0.07892	AAG	MAP2	-	NULL	ENSG00000078018		0.458	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MAP2	HGNC	protein_coding	OTTHUMT00000256521.2	89	0.00	0	G	NM_001039538		210557446	210557446	+1	no_errors	ENST00000360351	ensembl	human	known	69_37n	missense	47	35.14	26	SNP	0.000	T
MICAL3	57553	genome.wustl.edu	37	22	18300541	18300541	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr22:18300541G>A	ENST00000441493.2	-	26	5238	c.4886C>T	c.(4885-4887)gCc>gTc	p.A1629V	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1629					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GGGCCTGGGGGCGCCTGAGGC	0.716																																						dbGAP											0													10.0	13.0	12.0					22																	18300541		1981	4136	6117	-	-	-	SO:0001583	missense	0			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4886C>T	22.37:g.18300541G>A	ENSP00000416015:p.Ala1629Val		B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	pfam_DUF3585,pfam_CH-domain,pfam_CAMSAP_CH,pfam_Znf_LIM,pfam_mOase_FAD-bd,superfamily_CH-domain,smart_CH-domain,smart_Znf_LIM,pfscan_CH-domain,pfscan_Znf_LIM,prints_Rng_hydrolase-like	p.A1629V	ENST00000441493.2	37	c.4886	CCDS46659.1	22	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.08|12.08	1.831249|1.831249	0.32329|0.32329	.|.	.|.	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.64991|.	-0.13|.	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	0.301959|.	0.29198|.	N|.	0.012853|.	T|T	0.51058|0.51058	0.1652|0.1652	N|N	0.17082|0.17082	0.46|0.46	0.80722|0.80722	D|D	1|1	B|.	0.13594|.	0.008|.	B|.	0.08055|.	0.003|.	T|T	0.48222|0.48222	-0.9054|-0.9054	10|5	0.27785|.	T|.	0.31|.	.|.	17.7317|17.7317	0.88379|0.88379	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1629|.	Q7RTP6|.	MICA3_HUMAN|.	V|S	1629|611	ENSP00000416015:A1629V|.	ENSP00000416015:A1629V|.	A|P	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16680541|16680541	0.975000|0.975000	0.34042|0.34042	0.260000|0.260000	0.24451|0.24451	0.116000|0.116000	0.19942|0.19942	3.131000|3.131000	0.50515|0.50515	2.180000|2.180000	0.69256|0.69256	0.561000|0.561000	0.74099|0.74099	GCC|CCC	MICAL3	-	NULL	ENSG00000243156		0.716	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	MICAL3	HGNC	protein_coding	OTTHUMT00000447351.1	11	0.00	0	G			18300541	18300541	-1	no_errors	ENST00000441493	ensembl	human	known	69_37n	missense	2	81.82	9	SNP	0.949	A
PCDH9	5101	genome.wustl.edu	37	13	67802338	67802338	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr13:67802338delA	ENST00000377865.2	-	1	369	c.235delT	c.(235-237)tccfs	p.S81fs	PCDH9_ENST00000328454.5_Frame_Shift_Del_p.S81fs|PCDH9_ENST00000544246.1_Frame_Shift_Del_p.S81fs|PCDH9_ENST00000456367.1_Frame_Shift_Del_p.S81fs|PCDH9_ENST00000377861.3_Frame_Shift_Del_p.S81fs			Q9HC56	PCDH9_HUMAN	protocadherin 9	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTGCTGCTGGAAACTTTCACC	0.483																																						dbGAP											0													60.0	57.0	58.0					13																	67802338		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.235delT	13.37:g.67802338delA	ENSP00000367096:p.Ser81fs		A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Frame_Shift_Del	DEL	pfam_Cadherin,pfam_Protocadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S79fs	ENST00000377865.2	37	c.235	CCDS9444.1	13																																																																																			PCDH9	-	pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000184226		0.483	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PCDH9	HGNC	protein_coding	OTTHUMT00000276387.1	140	0.00	0	A	NM_203487		67802338	67802338	-1	no_errors	ENST00000377865	ensembl	human	known	69_37n	frame_shift_del	82	17.17	17	DEL	1.000	-
PCDHA4	56144	genome.wustl.edu	37	5	140188734	140188734	+	Silent	SNP	C	C	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr5:140188734C>T	ENST00000530339.1	+	1	1962	c.1962C>T	c.(1960-1962)caC>caT	p.H654H	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.H654H|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.H654H|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAGGACCACGGCGAGCCCG	0.677																																						dbGAP											0													68.0	72.0	70.0					5																	140188734		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1962C>T	5.37:g.140188734C>T			O75285|Q2M253	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,prints_Cadherin,pfscan_Cadherin	p.H654	ENST00000530339.1	37	c.1962	CCDS54916.1	5																																																																																			PCDHA4	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000204967		0.677	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHA4	HGNC	protein_coding	OTTHUMT00000372864.2	37	0.00	0	C	NM_018907		140188734	140188734	+1	no_errors	ENST00000530339	ensembl	human	known	69_37n	silent	25	43.75	21	SNP	0.983	T
TIMELESS	8914	genome.wustl.edu	37	12	56817648	56817648	+	Silent	SNP	G	G	A			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr12:56817648G>A	ENST00000553532.1	-	16	2049	c.1899C>T	c.(1897-1899)ggC>ggT	p.G633G	TIMELESS_ENST00000229201.4_Silent_p.G632G|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TGTCTTGAGAGCCAAACACAT	0.468																																						dbGAP											0													114.0	109.0	111.0					12																	56817648		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1899C>T	12.37:g.56817648G>A				Silent	SNP	pfam_TIMELESS_C,pfam_Timeless	p.G633	ENST00000553532.1	37	c.1899	CCDS8918.1	12																																																																																			TIMELESS	-	NULL	ENSG00000111602		0.468	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TIMELESS	HGNC	protein_coding	OTTHUMT00000409771.1	308	0.00	0	G	NM_003920		56817648	56817648	-1	no_errors	ENST00000553532	ensembl	human	known	69_37n	silent	182	32.47	88	SNP	0.986	A
RFX4	5992	genome.wustl.edu	37	12	107141268	107141268	+	Missense_Mutation	SNP	G	G	T	rs550968854		TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr12:107141268G>T	ENST00000392842.1	+	16	2101	c.1687G>T	c.(1687-1689)Ggg>Tgg	p.G563W	RFX4_ENST00000229387.5_Missense_Mutation_p.G469W|RFX4_ENST00000357881.4_Missense_Mutation_p.G572W|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	563					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						GACGGCTGCTGGGTCCCCAGC	0.493																																						dbGAP											0													104.0	94.0	97.0					12																	107141268		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1687G>T	12.37:g.107141268G>T	ENSP00000376585:p.Gly563Trp		A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Missense_Mutation	SNP	pfam_DNA-bd_RFX	p.G572W	ENST00000392842.1	37	c.1714	CCDS9106.1	12	.	.	.	.	.	.	.	.	.	.	G	23.3	4.399119	0.83120	.	.	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000229387	T;T;T	0.67345	-0.26;-0.26;0.71	5.69	5.69	0.88448	.	0.202331	0.52532	D	0.000070	T	0.68805	0.3041	N	0.19112	0.55	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.998;0.997	D;D;P	0.71414	0.973;0.919;0.766	T	0.69796	-0.5048	10	0.46703	T	0.11	-22.7857	13.0787	0.59100	0.0731:0.0:0.9269:0.0	.	469;572;563	B2RDW4;Q33E94-2;Q33E94	.;.;RFX4_HUMAN	W	563;572;469	ENSP00000376585:G563W;ENSP00000350552:G572W;ENSP00000229387:G469W	ENSP00000229387:G469W	G	+	1	0	RFX4	105665398	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.168000	0.71908	2.678000	0.91216	0.655000	0.94253	GGG	RFX4	-	NULL	ENSG00000111783		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	RFX4	HGNC	protein_coding	OTTHUMT00000402707.1	73	0.00	0	G	NM_032491		107141268	107141268	+1	no_errors	ENST00000357881	ensembl	human	known	69_37n	missense	65	32.99	32	SNP	1.000	T
TSC1	7248	genome.wustl.edu	37	9	135798857	135798857	+	Missense_Mutation	SNP	A	A	T	rs397514852		TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr9:135798857A>T	ENST00000298552.3	-	6	607	c.386T>A	c.(385-387)cTc>cAc	p.L129H	TSC1_ENST00000403810.1_Missense_Mutation_p.L129H|TSC1_ENST00000475903.1_5'UTR|TSC1_ENST00000545250.1_Missense_Mutation_p.L78H|TSC1_ENST00000440111.2_Missense_Mutation_p.L129H	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	129					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)			NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GCCTGTTGTGAGGACAACGAC	0.478			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																													dbGAP	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	0													140.0	114.0	123.0					9																	135798857		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.386T>A	9.37:g.135798857A>T	ENSP00000298552:p.Leu129His		B7Z897|Q5VVN5	Missense_Mutation	SNP	pfam_Hamartin,superfamily_ARM-type_fold	p.L129H	ENST00000298552.3	37	c.386	CCDS6956.1	9	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482954	0.63962	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250;ENST00000537172;ENST00000424271;ENST00000403810	D;D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49;-3.49	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.97176	0.9077	M	0.83603	2.65	0.80722	D	1	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	0.97110	1.0;1.0;0.998;0.998;1.0;0.999	D	0.97871	1.0286	10	0.87932	D	0	-11.639	14.3559	0.66738	1.0:0.0:0.0:0.0	.	8;78;129;129;129;129	B7Z604;B7Z897;Q86WV8;Q59IT9;Q32NF0;Q92574	.;.;.;.;.;TSC1_HUMAN	H	129;129;78;8;8;129	ENSP00000298552:L129H;ENSP00000394524:L129H;ENSP00000444017:L78H;ENSP00000438099:L8H;ENSP00000386093:L129H	ENSP00000298552:L129H	L	-	2	0	TSC1	134788678	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	8.710000	0.91388	1.994000	0.58287	0.533000	0.62120	CTC	TSC1	-	pfam_Hamartin,superfamily_ARM-type_fold	ENSG00000165699		0.478	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TSC1	HGNC	protein_coding	OTTHUMT00000054799.1	154	0.00	0	A			135798857	135798857	-1	no_errors	ENST00000298552	ensembl	human	known	69_37n	missense	52	49.04	51	SNP	1.000	T
ZNF207	7756	genome.wustl.edu	37	17	30678929	30678929	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BH-A0AU-01A-11D-A12Q-09	TCGA-BH-A0AU-11A-11D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	d06209b8-8aba-44d8-b94a-990861c2324a	9b7a36f8-d6c8-49f5-bfaf-26661bac3be3	g.chr17:30678929C>T	ENST00000321233.6	+	2	320	c.166C>T	c.(166-168)Cag>Tag	p.Q56*	RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000341711.6_Intron|ZNF207_ENST00000394673.2_Nonsense_Mutation_p.Q56*|ZNF207_ENST00000342555.6_Nonsense_Mutation_p.Q59*|ZNF207_ENST00000577908.1_Nonsense_Mutation_p.Q56*|MIR632_ENST00000385193.1_RNA|ZNF207_ENST00000394670.4_Nonsense_Mutation_p.Q56*	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	56	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TCATTGCATGCAGGTAAGGAT	0.348																																						dbGAP											0													87.0	81.0	83.0					17																	30678929		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.166C>T	17.37:g.30678929C>T	ENSP00000322777:p.Gln56*		A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Nonsense_Mutation	SNP	smart_Znf_C2H2-like	p.Q56*	ENST00000321233.6	37	c.166	CCDS11271.1	17	.	.	.	.	.	.	.	.	.	.	C	39	7.300304	0.98196	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000342555	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.2925	0.90135	0.0:1.0:0.0:0.0	.	.	.	.	X	56;56;59;56;56	.	ENSP00000322777:Q56X	Q	+	1	0	ZNF207	27703042	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.391000	0.81399	0.655000	0.94253	CAG	ZNF207	-	smart_Znf_C2H2-like	ENSG00000010244		0.348	ZNF207-003	KNOWN	basic|CCDS	protein_coding	ZNF207	HGNC	protein_coding	OTTHUMT00000256251.2	254	0.00	0	C			30678929	30678929	+1	no_errors	ENST00000394670	ensembl	human	known	69_37n	nonsense	161	28.12	63	SNP	1.000	T
