#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_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
CDIP1	29965	genome.wustl.edu	37	16	4563854	4563854	+	Splice_Site	SNP	T	T	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr16:4563854T>A	ENST00000399599.3	-	3	634		c.e3-2		CDIP1_ENST00000567695.1_Splice_Site|CDIP1_ENST00000562334.1_Splice_Site|CDIP1_ENST00000564828.1_Splice_Site|CDIP1_ENST00000563507.1_Splice_Site|CDIP1_ENST00000563332.2_Splice_Site			Q9H305	CDIP1_HUMAN	cell death-inducing p53 target 1						apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	nucleus (GO:0005634)											AGGAACGGCCTGGACAGAGAG	0.642																																																0			16											19.0	23.0	21.0					16																	4563854		2035	4179	6214	4503855	SO:0001630	splice_region_variant	29965			AF131218	CCDS42114.1, CCDS58419.1, CCDS58420.1	16p13.3	2012-11-14	2012-11-14	2012-11-14	ENSG00000089486	ENSG00000089486			13234	protein-coding gene	gene with protein product	"""cell death involved p53-target"", ""lipopolysaccharide-induced TNF factor-like"""	610503	"""chromosome 16 open reading frame 5"""	C16orf5		10570909, 17599062	Standard	NM_013399		Approved	CDIP, LITAFL	uc002cww.3	Q9H305	OTTHUMG00000177172	ENST00000399599.3:c.86-2A>T	16.37:g.4563854T>A			4503855	A8K7M1|B4DFU1|B4DY75|D3DUD6|Q96ID8|Q9H0Q4|Q9P112	Splice_Site	SNP	-	e2-2	ENST00000399599.3	37	c.86-2	CCDS42114.1	16	.	.	.	.	.	.	.	.	.	.	T	16.89	3.247498	0.59103	.	.	ENSG00000089486	ENST00000399599	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2345	0.31618	0.0:0.0893:0.0:0.9107	.	.	.	.	.	-1	.	.	.	-	.	.	C16orf5	4503855	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	1.488000	0.35551	2.077000	0.62373	0.533000	0.62120	.	-	-		0.642	CDIP1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	C16orf5	protein_coding	OTTHUMT00000435718.2	T	NM_013399	Intron	4503855	-1	no_errors	NM_013399	genbank	human	validated	54_36p	splice_site	SNP	1.000	A
DCHS1	8642	genome.wustl.edu	37	11	6646929	6646929	+	Missense_Mutation	SNP	C	C	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr11:6646929C>A	ENST00000299441.3	-	18	7172	c.6761G>T	c.(6760-6762)aGc>aTc	p.S2254I		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2254	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAGGGCTGGGCTCCCTCTGTC	0.597																																																0			11											42.0	42.0	42.0					11																	6646929		2201	4296	6497	6603505	SO:0001583	missense	8642			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6761G>T	11.37:g.6646929C>A	ENSP00000299441:p.Ser2254Ile		6603505	O15098	Missense_Mutation	SNP	superfamily_Cadherin,HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1	p.S2254I	ENST00000299441.3	37	c.6761	CCDS7771.1	11	.	.	.	.	.	.	.	.	.	.	C	14.76	2.632091	0.46944	.	.	ENSG00000166341	ENST00000299441	T	0.54866	0.55	4.85	2.88	0.33553	Cadherin (4);Cadherin-like (1);	0.387690	0.22362	N	0.061080	T	0.46386	0.1390	L	0.39020	1.185	0.45250	D	0.998257	P	0.46784	0.884	P	0.49887	0.625	T	0.29458	-1.0011	10	0.32370	T	0.25	.	7.0346	0.24987	0.0:0.5806:0.3157:0.1037	.	2254	Q96JQ0	PCD16_HUMAN	I	2254	ENSP00000299441:S2254I	ENSP00000299441:S2254I	S	-	2	0	DCHS1	6603505	0.930000	0.31532	1.000000	0.80357	0.993000	0.82548	0.032000	0.13732	1.266000	0.44231	0.563000	0.77884	AGC	-	superfamily_Cadherin,HMMPfam_Cadherin,HMMSmart_CA		0.597	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCHS1	protein_coding	OTTHUMT00000257258.1	C	NM_003737		6603505	-1	no_errors	NM_003737	genbank	human	reviewed	54_36p	missense	SNP	0.992	A
ENO2	2026	genome.wustl.edu	37	12	7027206	7027206	+	Nonsense_Mutation	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr12:7027206C>T	ENST00000535366.1	+	6	1173	c.547C>T	c.(547-549)Cga>Tga	p.R183*	ENO2_ENST00000538763.1_Nonsense_Mutation_p.R140*|ENO2_ENST00000545045.2_Intron|ENO2_ENST00000541477.1_Nonsense_Mutation_p.R183*|ENO2_ENST00000229277.1_Nonsense_Mutation_p.R183*|ENO2_ENST00000544774.1_Nonsense_Mutation_p.R140*			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	183					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GGATGCCATGCGACTAGGTGC	0.542																																																0			12											104.0	95.0	98.0					12																	7027206		2203	4300	6503	6897467	SO:0001587	stop_gained	2026			M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.547C>T	12.37:g.7027206C>T	ENSP00000437402:p.Arg183*		6897467	B7Z2X9|Q96J33	Nonsense_Mutation	SNP	HMMPfam_Enolase_N,superfamily_Enolase N-terminal domain-like,superfamily_Enolase C-terminal domain-like,HMMPfam_Enolase_C,PatternScan_ENOLASE	p.R183*	ENST00000535366.1	37	c.547	CCDS8570.1	12	.	.	.	.	.	.	.	.	.	.	c	36	5.853274	0.97030	.	.	ENSG00000111674	ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000535366	.	.	.	4.91	0.293	0.15742	.	0.059493	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.2417	15.8482	0.78907	0.4677:0.5323:0.0:0.0	.	.	.	.	X	183;183;140;140;183	.	ENSP00000229277:R183X	R	+	1	2	ENO2	6897467	1.000000	0.71417	0.842000	0.33263	0.690000	0.40134	2.662000	0.46766	0.134000	0.18681	-2.095000	0.00367	CGA	-	superfamily_Enolase C-terminal domain-like,HMMPfam_Enolase_C		0.542	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ENO2	protein_coding	OTTHUMT00000401786.1	C			6897467	+1	no_errors	NM_001975	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	T
ATP2B2	491	genome.wustl.edu	37	3	10443904	10443904	+	Missense_Mutation	SNP	C	C	G			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr3:10443904C>G	ENST00000352432.4	-	3	595	c.526G>C	c.(526-528)Gag>Cag	p.E176Q	ATP2B2_ENST00000383800.4_Missense_Mutation_p.E176Q|ATP2B2_ENST00000360273.2_Missense_Mutation_p.E176Q|ATP2B2_ENST00000343816.4_Missense_Mutation_p.E176Q|ATP2B2_ENST00000397077.1_Missense_Mutation_p.E176Q			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	176					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						AACTGTTTCTCTTTGCTCCAG	0.587																																					Ovarian(125;1619 1709 15675 19819 38835)											0			3											131.0	141.0	138.0					3																	10443904		2203	4300	6503	10418904	SO:0001583	missense	491			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.526G>C	3.37:g.10443904C>G	ENSP00000324172:p.Glu176Gln		10418904	O00766|Q12994|Q16818	Missense_Mutation	SNP	HMMPfam_Cation_ATPase_N,superfamily_Calcium ATPase transmembrane domain M,HMMPfam_E1-E2_ATPase,superfamily_Calcium ATPase transduction domain A,HMMPfam_Hydrolase,superfamily_HAD-like,PatternScan_ATPASE_E1_E2,superfamily_Metal cation-transporting ATPase ATP-binding domain N,HMMPfam_Cation_ATPase_C	p.E176Q	ENST00000352432.4	37	c.526	CCDS33701.1	3	.	.	.	.	.	.	.	.	.	.	C	32	5.156244	0.94686	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79;-2.79;-2.79	5.43	5.43	0.79202	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.94892	0.8349	M	0.65975	2.015	0.80722	D	1	D;P;D	0.76494	0.999;0.932;0.994	D;P;D	0.83275	0.996;0.812;0.958	D	0.94681	0.7865	10	0.54805	T	0.06	-40.3579	19.2437	0.93893	0.0:1.0:0.0:0.0	.	176;188;176	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	Q	176;176;176;176;176;142;63;176	ENSP00000324172:E176Q;ENSP00000373311:E176Q;ENSP00000380267:E176Q;ENSP00000353414:E176Q;ENSP00000344677:E176Q;ENSP00000414854:E63Q	ENSP00000342954:E176Q	E	-	1	0	ATP2B2	10418904	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.527000	0.85204	0.563000	0.77884	GAG	-	superfamily_Calcium ATPase transmembrane domain M,HMMPfam_E1-E2_ATPase		0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	ATP2B2	protein_coding	OTTHUMT00000250576.2	C	NM_001683		10418904	-1	no_errors	NM_001001331	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
LDLR	3949	genome.wustl.edu	37	19	11231184	11231184	+	Missense_Mutation	SNP	G	G	C			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr19:11231184G>C	ENST00000558518.1	+	14	2313	c.2126G>C	c.(2125-2127)aGg>aCg	p.R709T	LDLR_ENST00000455727.2_Missense_Mutation_p.R541T|LDLR_ENST00000558013.1_Missense_Mutation_p.R709T|LDLR_ENST00000545707.1_Intron|LDLR_ENST00000535915.1_Missense_Mutation_p.R668T|LDLR_ENST00000557933.1_Missense_Mutation_p.R709T	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	709	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	AGGGACATGAGGAGCTGCCTC	0.627																																					GBM(18;201 575 7820 21545)											1	Unknown(1)	lung(1)	19											44.0	42.0	43.0					19																	11231184		2203	4300	6503	11092184	SO:0001583	missense	3949			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.2126G>C	19.37:g.11231184G>C	ENSP00000454071:p.Arg709Thr		11092184	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	superfamily_LDL receptor-like module,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,HMMSmart_SM00179,superfamily_EGF/Laminin,HMMSmart_SM00181,HMMPfam_EGF,PatternScan_ASX_HYDROXYL,PatternScan_EGF_2,PatternScan_EGF_CA,HMMPfam_EGF_CA,superfamily_YWTD domain,HMMSmart_SM00135,HMMPfam_Ldl_recept_b	p.R709T	ENST00000558518.1	37	c.2126	CCDS12254.1	19	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966791	0.74131	.	.	ENSG00000130164	ENST00000252444;ENST00000535915;ENST00000455727	D;D	0.97328	-4.34;-4.34	5.3	3.18	0.36537	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.000000	0.56097	D	0.000039	D	0.97990	0.9338	M	0.82132	2.575	0.54753	D	0.999985	D;D;P;D;D	0.89917	0.999;0.999;0.832;1.0;0.999	D;D;P;D;D	0.83275	0.993;0.994;0.672;0.996;0.985	D	0.97409	1.0001	10	0.54805	T	0.06	.	10.4662	0.44609	0.1598:0.0:0.8402:0.0	.	541;588;668;721;709	B4DR00;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;LDLR_HUMAN	T	709;668;541	ENSP00000440520:R668T;ENSP00000397829:R541T	ENSP00000252444:R709T	R	+	2	0	LDLR	11092184	1.000000	0.71417	0.992000	0.48379	0.700000	0.40528	4.334000	0.59291	0.635000	0.30488	0.655000	0.94253	AGG	-	superfamily_EGF/Laminin,HMMSmart_SM00181		0.627	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	LDLR	protein_coding	OTTHUMT00000415973.2	G			11092184	+1	no_errors	NM_000527	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
IGHV3OR15-7	28318	genome.wustl.edu	37	15	20192895	20192895	+	RNA	SNP	C	C	G			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr15:20192895C>G	ENST00000558565.2	-	0	359									immunoglobulin heavy variable 3/OR15-7 (pseudogene)																		TCACGCTGACCTCCCCTCACT	0.587																																																0			15																																								18452909			0			Z29597		15q11.2	2012-06-12	2011-04-15		ENSG00000259490	ENSG00000259490		"""Immunoglobulins / IGH orphons"""	5633	pseudogene	immunoglobulin pseudogene			"""immunoglobulin heavy variable 3/OR15-7"", ""immunoglobulin heavy variable 3/OR15-7 pseudogene"""				Standard			Approved	IGHV3/OR15-7			OTTHUMG00000171835		15.37:g.20192895C>G			18452909		Missense_Mutation	SNP	HMMPfam_V-set,superfamily_Immunoglobulin,HMMSmart_SM00409,HMMSmart_SM00406	p.G244R	ENST00000558565.2	37	c.730		15																																																																																			-	HMMSmart_SM00409		0.587	IGHV3OR15-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	LOC646057	IG_V_gene	OTTHUMT00000415305.2	C			18452909	-1	no_errors	XM_001716562	genbank	human	model	54_36p	missense	SNP	0.001	G
OR4N5	390437	genome.wustl.edu	37	14	20612416	20612416	+	Silent	SNP	C	C	T	rs76001619	byFrequency	TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr14:20612416C>T	ENST00000333629.1	+	1	522	c.522C>T	c.(520-522)ctC>ctT	p.L174L	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L174L(1)		endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CAAACCAGCTCGATAACTTCT	0.507													C|||	15	0.00299521	0.0008	0.0	5008	,	,		20746	0.0129		0.001	False		,,,				2504	0.0															1	Substitution - coding silent(1)	lung(1)	14						C		2,4404	4.2+/-10.8	0,2,2201	122.0	113.0	116.0		522	-0.6	1.0	14	dbSNP_132	116	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	OR4N5	NM_001004724.1		0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615		174/309	20612416	8,12998	2203	4300	6503	19682256	SO:0001819	synonymous_variant	390437				CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"""GPCR / Class A : Olfactory receptors"""	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.522C>T	14.37:g.20612416C>T			19682256	Q6IF11	Silent	SNP	superfamily_SSF81321,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1	p.L174	ENST00000333629.1	37	c.522	CCDS32031.1	14																																																																																			-	superfamily_SSF81321,HMMPfam_7tm_1		0.507	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4N5	protein_coding	OTTHUMT00000410347.1	C			19682256	+1	no_errors	NM_001004724	genbank	human	provisional	54_36p	silent	SNP	0.103	T
CFAP61	26074	genome.wustl.edu	37	20	20177485	20177485	+	Intron	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr20:20177485G>A	ENST00000245957.5	+	16	1873				C20orf26_ENST00000389656.3_Intron|C20orf26_ENST00000377309.2_Intron	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN												NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GGTGTTGTACGCCGCATTCTA	0.418																																																0			20																																								20125485	SO:0001627	intron_variant	26074																														ENST00000245957.5:c.1797+65G>A	20.37:g.20177485G>A			20125485	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	superfamily_Acyl_CoA_acyltransferase	p.R557H	ENST00000245957.5	37	c.1670	CCDS33447.1	20																																																																																			-	NULL		0.418	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	C20orf26	protein_coding	OTTHUMT00000078228.3	G			20125485	+1	no_errors	ENST00000377303	ensembl	human	known	54_36p	missense	SNP	0.000	A
CYFIP1	23191	genome.wustl.edu	37	15	22991215	22991215	+	Silent	SNP	C	C	G			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr15:22991215C>G	ENST00000313077.7	+	25	3029	c.2904C>G	c.(2902-2904)ggC>ggG	p.G968G	CYFIP1_ENST00000435939.2_Silent_p.G537G|CYFIP1_ENST00000560848.1_Silent_p.G968G	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		ACGAGTACGGCTCTCCTGGTG	0.557																																																0			15											48.0	37.0	41.0					15																	22991215		2203	4300	6503	20542656	SO:0001819	synonymous_variant	23191			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2904C>G	15.37:g.22991215C>G			20542656		Silent	SNP	HMMPfam_FragX_IP	p.G968	ENST00000313077.7	37	c.2904	CCDS10009.1	15																																																																																			-	HMMPfam_FragX_IP		0.557	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYFIP1	protein_coding	OTTHUMT00000251136.2	C	NM_014608		20542656	+1	no_errors	NM_014608	genbank	human	validated	54_36p	silent	SNP	1.000	G
FANCF	2188	genome.wustl.edu	37	11	22647041	22647041	+	Missense_Mutation	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr11:22647041C>T	ENST00000327470.3	-	1	346	c.316G>A	c.(316-318)Gca>Aca	p.A106T	AC103801.2_ENST00000428556.2_5'UTR	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	106					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						TAACGAGCTGCATCCCCGAGG	0.677			"""N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										yes	Rec		Fanconi anaemia F	11	11p15	2188	"""Fanconi anemia, complementation group F"""		L	0			11											65.0	77.0	73.0					11																	22647041		2203	4300	6503	22603617	SO:0001583	missense	2188	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"""Fanconi anemia, complementation groups"""	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.316G>A	11.37:g.22647041C>T	ENSP00000330875:p.Ala106Thr	757	22603617	Q52LM0	Missense_Mutation	SNP	NULL	p.A106T	ENST00000327470.3	37	c.316	CCDS7857.1	11	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001844	0.54254	.	.	ENSG00000183161	ENST00000327470	T	0.34275	1.37	5.43	3.47	0.39725	.	0.278794	0.23720	U	0.045238	T	0.49643	0.1569	L	0.50333	1.59	0.26885	N	0.967464	D	0.76494	0.999	D	0.75020	0.985	T	0.31696	-0.9934	10	0.40728	T	0.16	-8.9758	11.052	0.47896	0.1225:0.6805:0.197:0.0	.	106	Q9NPI8	FANCF_HUMAN	T	106	ENSP00000330875:A106T	ENSP00000330875:A106T	A	-	1	0	FANCF	22603617	0.744000	0.28250	0.309000	0.25155	0.037000	0.13140	1.871000	0.39539	1.510000	0.48803	-0.181000	0.13052	GCA	-	NULL		0.677	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FANCF	protein_coding	OTTHUMT00000387712.2	C	NM_022725		22603617	-1	no_errors	NM_022725	genbank	human	reviewed	54_36p	missense	SNP	0.309	T
HIST1H2BD	3017	genome.wustl.edu	37	6	26158404	26158404	+	Missense_Mutation	SNP	G	G	C			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr6:26158404G>C	ENST00000289316.2	+	1	31	c.7G>C	c.(7-9)Gaa>Caa	p.E3Q	HIST1H2BD_ENST00000377777.4_Missense_Mutation_p.E3Q	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	3					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						TACGATGCCTGAACCTACCAA	0.507																																																0			6											89.0	90.0	90.0					6																	26158404		2203	4300	6503	26266383	SO:0001583	missense	3017			M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.7G>C	6.37:g.26158404G>C	ENSP00000289316:p.Glu3Gln		26266383		Missense_Mutation	SNP	superfamily_Histone-fold,HMMSmart_SM00427,HMMPfam_Histone,PatternScan_HISTONE_H2B	p.E3Q	ENST00000289316.2	37	c.7	CCDS4587.1	6	.	.	.	.	.	.	.	.	.	.	.	16.54	3.151004	0.57151	.	.	ENSG00000158373	ENST00000377777;ENST00000289316	T;T	0.18657	2.2;2.2	5.13	5.13	0.70059	.	0.325448	0.21773	N	0.069324	T	0.24812	0.0602	L	0.61387	1.9	0.47905	D	0.999546	B	0.33413	0.411	P	0.44772	0.46	T	0.02081	-1.1217	10	0.72032	D	0.01	.	16.1409	0.81522	0.0:0.0:1.0:0.0	.	3	P58876	H2B1D_HUMAN	Q	3	ENSP00000367008:E3Q;ENSP00000289316:E3Q	ENSP00000289316:E3Q	E	+	1	0	HIST1H2BD	26266383	1.000000	0.71417	0.751000	0.31187	0.029000	0.11900	6.327000	0.72910	2.769000	0.95229	0.650000	0.86243	GAA	-	NULL		0.507	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H2BD	protein_coding	OTTHUMT00000040088.1	G	NM_021063		26266383	+1	no_errors	NM_021063	genbank	human	reviewed	54_36p	missense	SNP	0.998	C
IGHV3OR16-12	28304	genome.wustl.edu	37	16	33605463	33605463	+	RNA	SNP	T	T	C			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr16:33605463T>C	ENST00000570121.2	+	0	132									immunoglobulin heavy variable 3/OR16-12 (non-functional)																		GTGCAGCCTCTGGATTCACCG	0.562																																																0			16																																								33512964			401847			Z29609		16p11.2	2013-10-18	2008-09-11		ENSG00000270467	ENSG00000270467		"""Immunoglobulins / IGH orphons"""	5636	other	immunoglobulin gene			"""immunoglobulin heavy variable 3/OR16-12"""				Standard			Approved	IGHV3/OR16-12			OTTHUMG00000176355		16.37:g.33605463T>C			33512964		Silent	SNP	superfamily_Alkaline phosphatase-like,HMMPfam_Phosphodiest,HMMPfam_V-set,superfamily_Immunoglobulin,HMMSmart_SM00406	p.S256	ENST00000570121.2	37	c.768		16																																																																																			-	HMMPfam_V-set,superfamily_Immunoglobulin,HMMSmart_SM00406		0.562	IGHV3OR16-12-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	LOC401847	IG_V_gene	OTTHUMT00000431813.2	T			33512964	+1	no_errors	XM_001718104	genbank	human	model	54_36p	silent	SNP	1.000	C
SLC32A1	140679	genome.wustl.edu	37	20	37353588	37353588	+	Missense_Mutation	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr20:37353588G>A	ENST00000217420.1	+	1	484	c.221G>A	c.(220-222)gGc>gAc	p.G74D		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	74					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	GGGGACGAGGGCGCTGAAGCG	0.672																																																0			20											20.0	26.0	24.0					20																	37353588		2195	4286	6481	36787002	SO:0001583	missense	140679			AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"""Solute carriers"""	11018	protein-coding gene	gene with protein product			"""vesicular inhibitory amino acid transporter"""	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.221G>A	20.37:g.37353588G>A	ENSP00000217420:p.Gly74Asp		36787002	Q8N489	Missense_Mutation	SNP	HMMPfam_Aa_trans	p.G74D	ENST00000217420.1	37	c.221	CCDS13307.1	20	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336327	0.24253	.	.	ENSG00000101438	ENST00000217420	T	0.08546	3.08	4.97	4.02	0.46733	.	0.054503	0.64402	D	0.000001	T	0.04407	0.0121	N	0.08118	0	0.47374	D	0.999403	B	0.02656	0.0	B	0.01281	0.0	T	0.43212	-0.9405	10	0.20046	T	0.44	-21.0723	11.1521	0.48464	0.0919:0.0:0.9081:0.0	.	74	Q9H598	VIAAT_HUMAN	D	74	ENSP00000217420:G74D	ENSP00000217420:G74D	G	+	2	0	SLC32A1	36787002	1.000000	0.71417	0.979000	0.43373	0.095000	0.18619	5.878000	0.69682	1.087000	0.41251	-0.258000	0.10820	GGC	-	NULL		0.672	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC32A1	protein_coding	OTTHUMT00000079206.1	G	NM_080552		36787002	+1	no_errors	NM_080552	genbank	human	reviewed	54_36p	missense	SNP	0.995	A
RPAP1	26015	genome.wustl.edu	37	15	41816446	41816446	+	Silent	SNP	G	G	C	rs377353071		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr15:41816446G>C	ENST00000304330.4	-	16	2198	c.2082C>G	c.(2080-2082)ctC>ctG	p.L694L	RPAP1_ENST00000561603.1_Silent_p.L694L	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	694						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GCACTGGGTAGAGCTCCCTAG	0.577																																																0			15											49.0	45.0	46.0					15																	41816446		2203	4300	6503	39603738	SO:0001819	synonymous_variant	26015			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2082C>G	15.37:g.41816446G>C			39603738	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	HMMPfam_RPAP1_N,HMMPfam_RPAP1_C	p.L694	ENST00000304330.4	37	c.2082	CCDS10079.1	15																																																																																			-	NULL		0.577	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPAP1	protein_coding	OTTHUMT00000252694.2	G	NM_015540		39603738	-1	no_errors	NM_015540	genbank	human	reviewed	54_36p	silent	SNP	0.521	C
ZNF565	147929	genome.wustl.edu	37	19	36685968	36685968	+	Missense_Mutation	SNP	C	C	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr19:36685968C>A	ENST00000355114.5	-	3	946	c.220G>T	c.(220-222)Gtg>Ttg	p.V74L	ZNF565_ENST00000304116.5_Missense_Mutation_p.V34L|ZNF565_ENST00000392173.2_Missense_Mutation_p.V34L			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			TCCAGAGTCACCTCCCTGTAC	0.522																																																0			19											162.0	129.0	140.0					19																	36685968		2203	4300	6503	41377808	SO:0001583	missense	147929			AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"""Zinc fingers, C2H2-type"", ""-"""	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.220G>T	19.37:g.36685968C>A	ENSP00000347234:p.Val74Leu		41377808	B3KQ35|Q6NUS2	Missense_Mutation	SNP	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_SSF57667,HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2,PatternScan_ZINC_FINGER_C2H2_1	p.V34L	ENST00000355114.5	37	c.100		19	.	.	.	.	.	.	.	.	.	.	c	22.1	4.245256	0.80024	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.03801	3.8;3.8;3.8	4.33	4.33	0.51752	Krueppel-associated box (4);	0.000000	0.31123	N	0.008215	T	0.26268	0.0641	M	0.90870	3.155	0.25269	N	0.989532	D;B	0.76494	0.999;0.098	D;B	0.85130	0.997;0.08	T	0.10660	-1.0620	10	0.72032	D	0.01	.	12.1757	0.54184	0.0:1.0:0.0:0.0	.	74;34	B3KQ35;Q8N9K5	.;ZN565_HUMAN	L	34;34;74	ENSP00000376013:V34L;ENSP00000306869:V34L;ENSP00000347234:V74L	ENSP00000306869:V34L	V	-	1	0	ZNF565	41377808	0.915000	0.31059	0.975000	0.42487	0.931000	0.56810	1.638000	0.37165	2.223000	0.72356	0.561000	0.74099	GTG	-	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB		0.522	ZNF565-003	PUTATIVE	basic	protein_coding	ZNF565	protein_coding	OTTHUMT00000451697.1	C	NM_152477		41377808	-1	no_errors	NM_001042474	genbank	human	validated	54_36p	missense	SNP	0.969	A
MX2	4600	genome.wustl.edu	37	21	42767536	42767536	+	Silent	SNP	A	A	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr21:42767536A>T	ENST00000330714.3	+	7	1078	c.894A>T	c.(892-894)ctA>ctT	p.L298L	MX2_ENST00000543692.1_3'UTR|MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	298	Dynamin-type G.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				AACCAGATCTAATGGACAGGG	0.517																																																0			21											111.0	91.0	98.0					21																	42767536		2203	4300	6503	41689406	SO:0001819	synonymous_variant	4600				CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"""interferon-regulated resistance GTP-binding protein MXB"", ""second interferon-induced protein p78"""	147890	"""myxovirus (influenza) resistance 2, homolog of murine"", ""myxovirus (influenza virus) resistance 2 (mouse)"""			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.894A>T	21.37:g.42767536A>T			41689406	B7Z5D3|D3DSI7	Silent	SNP	HMMSmart_DYNc,superfamily_SSF52540,HMMPfam_Dynamin_N,PatternScan_DYNAMIN,HMMPfam_Dynamin_M,HMMPfam_GED,HMMSmart_GED	p.L298	ENST00000330714.3	37	c.894	CCDS13672.1	21																																																																																			-	HMMSmart_DYNc,superfamily_SSF52540		0.517	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MX2	protein_coding	OTTHUMT00000195147.1	A	NM_002463		41689406	+1	no_errors	NM_002463	genbank	human	reviewed	54_36p	silent	SNP	0.998	T
CATSPER2	117155	genome.wustl.edu	37	15	43924549	43924549	+	Nonsense_Mutation	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr15:43924549C>T	ENST00000321596.5	-	12	1608	c.1409G>A	c.(1408-1410)tGg>tAg	p.W470*	CATSPER2_ENST00000381761.1_Nonsense_Mutation_p.W474*|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000396879.1_Nonsense_Mutation_p.W468*|CATSPER2_ENST00000355438.2_Silent_p.L397L|CATSPER2_ENST00000354127.4_Nonsense_Mutation_p.W468*			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	470					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		AAGAGTCTCCCAGTCCAAACG	0.478																																																0			15											54.0	54.0	54.0					15																	43924549		2199	4297	6496	41711841	SO:0001587	stop_gained	117155			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.1409G>A	15.37:g.43924549C>T	ENSP00000321463:p.Trp470*		41711841	Q8NHT9|Q96P54|Q96P55	Nonsense_Mutation	SNP	superfamily_Voltage-gated potassium channels,HMMPfam_Ion_trans	p.W470*	ENST00000321596.5	37	c.1409	CCDS10099.1	15	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332331	0.81801	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127	.	.	.	4.19	4.19	0.49359	.	0.735641	0.09937	U	0.736493	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2601	0.54645	0.0:1.0:0.0:0.0	.	.	.	.	X	468;470;474;470;468	.	ENSP00000299989:W470X	W	-	2	0	CATSPER2	41711841	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	4.345000	0.59360	2.328000	0.79073	0.644000	0.83932	TGG	-	NULL		0.478	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CATSPER2	protein_coding	OTTHUMT00000133151.2	C	NM_054020		41711841	-1	no_errors	NM_172095	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	T
Unknown	0	genome.wustl.edu	37	9	45376408	45376408	+	IGR	SNP	C	C	A	rs373765008		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr9:45376408C>A								RP11-449H15.2 (163907 upstream) : RP11-187C18.5 (17436 downstream)																							CGAACACTGCCTTAAGAACTT	0.493																																																0			9																																								45266404	SO:0001628	intergenic_variant	441420																															9.37:g.45376408C>A			45266404		RNA	SNP	-	NULL		37	NULL		9																																																																																			-	-	0	0.493					LOC441420			C			45266404	+1	pseudogene	XR_036959	genbank	human	model	54_36p	rna	SNP	1.000	A
PCDH15	65217	genome.wustl.edu	37	10	55755492	55755492	+	Nonsense_Mutation	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr10:55755492G>A	ENST00000320301.6	-	21	3179	c.2785C>T	c.(2785-2787)Cga>Tga	p.R929*	PCDH15_ENST00000373955.1_Nonsense_Mutation_p.R929*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.R929*|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.R929*|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.R936*|PCDH15_ENST00000437009.1_Nonsense_Mutation_p.R858*|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.R929*|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.R934*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.R936*|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.R892*|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Nonsense_Mutation_p.R540*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.R907*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	929	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs2135720). {ECO:0000269|PubMed:11487575, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTGTATATTCGTTTACTAAAG	0.408										HNSCC(58;0.16)																																						0			10	GRCh37	CM050735	PCDH15	M							123.0	110.0	114.0					10																	55755492		2203	4300	6503	55425498	SO:0001587	stop_gained	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2785C>T	10.37:g.55755492G>A	ENSP00000322604:p.Arg929*		55425498	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like,HMMPfam_Cadherin	p.R929*	ENST00000320301.6	37	c.2785	CCDS7248.1	10	.	.	.	.	.	.	.	.	.	.	G	39	7.843184	0.98519	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	.	.	.	5.93	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6611	0.45702	0.0:0.127:0.6103:0.2626	.	.	.	.	X	936;934;929;929;540;936;892;929;907;929;929;934;858;929	.	ENSP00000322604:R929X	R	-	1	2	PCDH15	55425498	0.008000	0.16893	0.987000	0.45799	0.137000	0.21094	1.293000	0.33353	1.500000	0.48636	-0.152000	0.13540	CGA	-	superfamily_Cadherin-like		0.408	PCDH15-001	KNOWN	basic|CCDS	protein_coding	PCDH15	protein_coding	OTTHUMT00000048121.2	G	NM_033056		55425498	-1	no_errors	NM_033056	genbank	human	reviewed	54_36p	nonsense	SNP	0.910	A
NLRP12	91662	genome.wustl.edu	37	19	54312882	54312882	+	Silent	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr19:54312882G>A	ENST00000324134.6	-	3	2199	c.2031C>T	c.(2029-2031)cgC>cgT	p.R677R	NLRP12_ENST00000351894.4_Silent_p.R677R|NLRP12_ENST00000391773.1_Silent_p.R677R|NLRP12_ENST00000391775.3_Silent_p.R677R|NLRP12_ENST00000535162.1_Silent_p.R677R|NLRP12_ENST00000345770.5_Silent_p.R677R|NLRP12_ENST00000391772.1_Silent_p.R677R|NLRP12_ENST00000354278.3_Silent_p.R677R	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	677					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		AGCACCTCGCGCGGTCTTCCC	0.587																																																0			19											30.0	28.0	29.0					19																	54312882		2203	4299	6502	59004694	SO:0001819	synonymous_variant	91662			AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2031C>T	19.37:g.54312882G>A			59004694	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	HMMPfam_PAAD_DAPIN,superfamily_DEATH domain,HMMPfam_NACHT,superfamily_RNI-like,HMMSmart_SM00368	p.R677	ENST00000324134.6	37	c.2031	CCDS12864.1	19																																																																																			-	superfamily_RNI-like		0.587	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NLRP12	protein_coding	OTTHUMT00000134340.1	G	NM_144687		59004694	-1	no_errors	NM_144687	genbank	human	reviewed	54_36p	silent	SNP	0.000	A
CACNG4	27092	genome.wustl.edu	37	17	65026913	65026913	+	Silent	SNP	G	G	A	rs375384748		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr17:65026913G>A	ENST00000262138.3	+	4	779	c.777G>A	c.(775-777)tcG>tcA	p.S259S	RP11-74H8.1_ENST00000579138.1_RNA|AC005544.1_ENST00000375684.1_5'Flank	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	259					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			GGGACGTGTCGCCCATGGGCC	0.652																																																0			17						G		2,4404	4.2+/-10.8	0,2,2201	47.0	46.0	46.0		777	-10.3	0.1	17		46	0,8600		0,0,4300	no	coding-synonymous	CACNG4	NM_014405.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		259/328	65026913	2,13004	2203	4300	6503	62457375	SO:0001819	synonymous_variant	27092			AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"""Calcium channel subunits"""	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.777G>A	17.37:g.65026913G>A			62457375	B2RCK0	Silent	SNP	HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN	p.S259	ENST00000262138.3	37	c.777	CCDS11667.1	17																																																																																			-	NULL		0.652	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CACNG4	protein_coding	OTTHUMT00000447036.1	G	NM_014405		62457375	+1	no_errors	NM_014405	genbank	human	reviewed	54_36p	silent	SNP	0.901	A
CDH11	1009	genome.wustl.edu	37	16	65016067	65016067	+	Missense_Mutation	SNP	C	C	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr16:65016067C>A	ENST00000268603.4	-	8	1752	c.1137G>T	c.(1135-1137)gaG>gaT	p.E379D	CDH11_ENST00000394156.3_Missense_Mutation_p.E379D|CDH11_ENST00000566827.1_Missense_Mutation_p.E253D	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	379	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		ACATAGGGGGCTCATCAGCAT	0.527			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																													Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	0			16											166.0	138.0	147.0					16																	65016067		2203	4300	6503	63573568	SO:0001583	missense	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1137G>T	16.37:g.65016067C>A	ENSP00000268603:p.Glu379Asp		63573568	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	superfamily_Cadherin-like,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_C	p.E379D	ENST00000268603.4	37	c.1137	CCDS10803.1	16	.	.	.	.	.	.	.	.	.	.	C	19.75	3.886397	0.72410	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.68181	-0.31;-0.31	5.76	2.76	0.32466	Cadherin (3);Cadherin-like (1);	0.044982	0.85682	D	0.000000	T	0.78349	0.4269	M	0.74546	2.27	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.72982	0.962;0.979	T	0.79434	-0.1805	10	0.87932	D	0	.	10.2969	0.43629	0.0:0.7868:0.0:0.2132	.	379;379	P55287-2;P55287	.;CAD11_HUMAN	D	379;379;362	ENSP00000268603:E379D;ENSP00000377711:E379D	ENSP00000268603:E379D	E	-	3	2	CDH11	63573568	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	0.889000	0.28282	0.909000	0.36697	-0.150000	0.13652	GAG	-	HMMSmart_SM00112,superfamily_Cadherin-like		0.527	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH11	protein_coding	OTTHUMT00000268755.1	C	NM_033664		63573568	-1	no_errors	NM_001797	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
ATXN7	6314	genome.wustl.edu	37	3	63981813	63981813	+	Missense_Mutation	SNP	A	A	G			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr3:63981813A>G	ENST00000295900.6	+	12	2865	c.2315A>G	c.(2314-2316)cAt>cGt	p.H772R	ATXN7_ENST00000487717.1_Missense_Mutation_p.H772R|ATXN7_ENST00000398590.3_Missense_Mutation_p.H772R|ATXN7_ENST00000484332.1_Missense_Mutation_p.H627R|ATXN7_ENST00000538065.1_Missense_Mutation_p.H772R	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	772	Ser-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		AACGTCCGGCATGACCAGTCA	0.562																																																0			3											53.0	54.0	54.0					3																	63981813		1931	4123	6054	63956853	SO:0001583	missense	6314			AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2315A>G	3.37:g.63981813A>G	ENSP00000295900:p.His772Arg		63956853	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	HMMPfam_SCA7	p.H772R	ENST00000295900.6	37	c.2315	CCDS43102.1	3	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323746	0.24080	.	.	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.5	4.94	4.94	0.65067	.	0.112603	0.64402	D	0.000009	T	0.15565	0.0375	L	0.56769	1.78	0.39530	D	0.968656	P;P;P	0.40578	0.722;0.617;0.483	B;B;B	0.37198	0.243;0.173;0.084	T	0.07462	-1.0771	10	0.27785	T	0.31	-9.7073	14.9585	0.71138	1.0:0.0:0.0:0.0	.	627;772;772	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	R	772;772;772;772;627	ENSP00000381590:H772R;ENSP00000295900:H772R;ENSP00000420234:H772R;ENSP00000439585:H772R;ENSP00000428277:H627R	ENSP00000295900:H772R	H	+	2	0	ATXN7	63956853	1.000000	0.71417	0.988000	0.46212	0.131000	0.20780	3.574000	0.53863	1.996000	0.58369	0.529000	0.55759	CAT	-	NULL		0.562	ATXN7-001	KNOWN	basic|CCDS	protein_coding	ATXN7	protein_coding	OTTHUMT00000352070.1	A	NM_000333		63956853	+1	no_errors	NM_000333	genbank	human	reviewed	54_36p	missense	SNP	0.998	G
MALAT1	378938	genome.wustl.edu	37	11	65270182	65270182	+	lincRNA	SNP	C	C	G			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr11:65270182C>G	ENST00000534336.1	+	0	4950					NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		GAAAACAGCTCCTTGGTGAAT	0.368																																																0			11											40.0	40.0	40.0					11																	65270182		874	1988	2862	65026758			378938			AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65270182C>G			65026758		RNA	SNP	-	NULL	ENST00000534336.1	37	NULL		11																																																																																			-	-		0.368	MALAT1-001	KNOWN	basic	lincRNA	MALAT1	lincRNA	OTTHUMT00000389143.1	C	NR_002819		65026758	+1	no_errors	NR_002819	genbank	human	provisional	54_36p	rna	SNP	1.000	G
CDX4	1046	genome.wustl.edu	37	X	72667227	72667227	+	Silent	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chrX:72667227G>A	ENST00000373514.2	+	1	138	c.138G>A	c.(136-138)gcG>gcA	p.A46A		NM_005193.1	NP_005184.1	O14627	CDX4_HUMAN	caudal type homeobox 4	46					anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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)			endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|skin(1)	18	Renal(35;0.156)					ATTTCGCTGCGGCACCGGCTT	0.652																																																0			X											42.0	38.0	39.0					X																	72667227		2203	4300	6503	72583952	SO:0001819	synonymous_variant	1046			AF029879	CCDS14424.1	Xq13.2	2012-03-09	2007-07-09		ENSG00000131264	ENSG00000131264		"""Homeoboxes / ANTP class : HOXL subclass"""	1808	protein-coding gene	gene with protein product		300025	"""caudal type homeo box transcription factor 4"""			7655457	Standard	NM_005193		Approved		uc011mqk.2	O14627	OTTHUMG00000021831	ENST00000373514.2:c.138G>A	X.37:g.72667227G>A			72583952	A1A513|Q5JS20	Silent	SNP	HMMPfam_Caudal_act,PatternScan_HMG_COA_REDUCTASE_2,superfamily_Homeodomain-like,HMMSmart_SM00389,HMMPfam_Homeobox,PatternScan_HOMEOBOX_1	p.A46	ENST00000373514.2	37	c.138	CCDS14424.1	X																																																																																			-	HMMPfam_Caudal_act		0.652	CDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDX4	protein_coding	OTTHUMT00000057229.2	G	NM_005193		72583952	+1	no_errors	NM_005193	genbank	human	provisional	54_36p	silent	SNP	0.097	A
CLEC3A	10143	genome.wustl.edu	37	16	78062005	78062005	+	Splice_Site	SNP	C	C	A	rs199500922		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr16:78062005C>A	ENST00000575655.1	+	2	198	c.117C>A	c.(115-117)gaC>gaA	p.D39E	CLEC3A_ENST00000299642.4_Splice_Site_p.D48E|RP11-281J9.2_ENST00000563114.1_RNA	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	39					skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						TTTCCCCAGACAAGGATGGAG	0.433																																																0			16						C	GLU/ASP	0,4396		0,0,2198	87.0	85.0	85.0		117	-3.2	1.0	16		85	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	CLEC3A	NM_005752.4	45	0,1,6497	AA,AC,CC		0.0116,0.0,0.0077	benign	39/198	78062005	1,12995	2198	4300	6498	76619506	SO:0001630	splice_region_variant	10143			AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.116-1C>A	16.37:g.78062005C>A			76619506	B2R8C4|Q3SX91|Q6UXF5	Missense_Mutation	SNP	superfamily_C-type_lectin_fold,HMMSmart_CLECT,HMMPfam_Lectin_C,PatternScan_C_TYPE_LECTIN_1	p.D39E	ENST00000575655.1	37	c.117		16	.	.	.	.	.	.	.	.	.	.	C	0.078	-1.188127	0.01607	0.0	1.16E-4	ENSG00000166509	ENST00000299642	.	.	.	5.19	-3.17	0.05202	.	0.298940	0.34603	N	0.003822	T	0.08088	0.0202	N	0.01352	-0.895	0.29030	N	0.885766	B	0.02656	0.0	B	0.01281	0.0	T	0.36601	-0.9741	9	0.02654	T	1	.	7.0449	0.25040	0.4374:0.1358:0.4268:0.0	.	39	O75596	CLC3A_HUMAN	E	39	.	ENSP00000299642:D39E	D	+	3	2	CLEC3A	76619506	0.998000	0.40836	0.972000	0.41901	0.283000	0.27025	0.422000	0.21296	-0.533000	0.06323	-0.410000	0.06199	GAC	-	NULL		0.433	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	CLEC3A	protein_coding		C	NM_005752	Missense_Mutation	76619506	+1	no_errors	NM_005752	genbank	human	validated	54_36p	missense	SNP	0.025	A
PGGT1BP2	100132402	genome.wustl.edu	37	10	81652856	81652856	+	IGR	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr10:81652856C>T								NUTM2E (42224 upstream) : MBL1P (27077 downstream)																							AAAAATCGCACGTGCAGATCC	0.582																																																0			10																																								81642836	SO:0001628	intergenic_variant	0																															10.37:g.81652856C>T			81642836		RNA	SNP	-	NULL		37	NULL		10																																																																																			-	-	0	0.582					LOC100132402			C			81642836	-1	pseudogene	XR_037723	genbank	human	model	54_36p	rna	SNP	0.993	T
IGKV1D-17	28900	genome.wustl.edu	37	2	90122077	90122077	+	RNA	SNP	A	A	T	rs367584593		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr2:90122077A>T	ENST00000483379.1	+	0	476									immunoglobulin kappa variable 1D-17																		CACAATCAGCAGCCTGCAGCC	0.488																																																0			2											76.0	73.0	74.0					2																	90122077		1808	4045	5853	89759382			0			X63392		2p11.2	2012-02-08			ENSG00000242766	ENSG00000242766		"""Immunoglobulins / IGK locus"""	5749	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000151610		2.37:g.90122077A>T			89759382		Missense_Mutation	SNP	HMMPfam_V-set,superfamily_SSF48726,HMMSmart_IGv	p.S99C	ENST00000483379.1	37	c.295		2																																																																																			-	HMMPfam_V-set,superfamily_SSF48726,HMMSmart_IGv		0.488	IGKV1D-17-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	ENSG00000211627	IG_V_gene	OTTHUMT00000323282.1	A	NG_000833		89759382	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000390272	ensembl	human	known	54_36p	missense	SNP	1.000	T
PNISR	25957	genome.wustl.edu	37	6	99852478	99852478	+	Splice_Site	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr6:99852478C>T	ENST00000369239.5	-	9	1307		c.e9+1		PNISR_ENST00000438806.1_Splice_Site	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein							cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						CCAAAATATACCTTTCGTTGC	0.373																																																0			6											123.0	118.0	119.0					6																	99852478		2203	4300	6503	99959199	SO:0001630	splice_region_variant	25957			AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1102+1G>A	6.37:g.99852478C>T			99959199	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Splice_Site	SNP	-	e7+1	ENST00000369239.5	37	c.1102+1	CCDS5043.1	6	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098077	0.76870	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1563	0.86792	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PNISR	99959199	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.346000	0.79347	2.477000	0.83638	0.551000	0.68910	.	-	-		0.373	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	SFRS18	protein_coding	OTTHUMT00000041598.1	C	NM_032870	Intron	99959199	-1	no_errors	NM_015491	genbank	human	validated	54_36p	splice_site	SNP	1.000	T
RINT1	60561	genome.wustl.edu	37	7	105189127	105189127	+	Missense_Mutation	SNP	A	A	C			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr7:105189127A>C	ENST00000257700.2	+	7	1197	c.966A>C	c.(964-966)agA>agC	p.R322S		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	322	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						ATCACTTCAGAGGGAACCGGC	0.453																																																0			7											168.0	161.0	163.0					7																	105189127		2203	4300	6503	104976363	SO:0001583	missense	60561			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.966A>C	7.37:g.105189127A>C	ENSP00000257700:p.Arg322Ser		104976363	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	HMMPfam_RINT1_TIP1	p.R322S	ENST00000257700.2	37	c.966	CCDS34726.1	7	.	.	.	.	.	.	.	.	.	.	A	9.812	1.183329	0.21870	.	.	ENSG00000135249	ENST00000257700	T	0.24350	1.86	5.93	1.94	0.25998	.	0.628414	0.18012	N	0.154523	T	0.05502	0.0145	N	0.00841	-1.15	0.38252	D	0.941625	B	0.09022	0.002	B	0.08055	0.003	T	0.28964	-1.0027	10	0.06099	T	0.92	-11.9972	4.2531	0.10703	0.667:0.0978:0.0769:0.1583	.	322	Q6NUQ1	RINT1_HUMAN	S	322	ENSP00000257700:R322S	ENSP00000257700:R322S	R	+	3	2	RINT1	104976363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.877000	0.28106	0.460000	0.27045	0.528000	0.53228	AGA	-	HMMPfam_RINT1_TIP1		0.453	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RINT1	protein_coding	OTTHUMT00000348686.1	A	NM_021930		104976363	+1	no_errors	NM_021930	genbank	human	validated	54_36p	missense	SNP	0.993	C
FAM102B	284611	genome.wustl.edu	37	1	109143283	109143283	+	Missense_Mutation	SNP	G	G	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr1:109143283G>T	ENST00000370035.3	+	2	573	c.233G>T	c.(232-234)tGt>tTt	p.C78F	FAM102B_ENST00000405454.1_Missense_Mutation_p.C78F	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	78										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		CTAGATCCTTGTATCTACAGA	0.423																																																0			1											106.0	100.0	102.0					1																	109143283		2203	4300	6503	108944806	SO:0001583	missense	284611			CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"""sym-3 homolog B (C. elegans)"""						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.233G>T	1.37:g.109143283G>T	ENSP00000359052:p.Cys78Phe		108944806	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Missense_Mutation	SNP	HMMPfam_Eeig1	p.C47F	ENST00000370035.3	37	c.140	CCDS30786.2	1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625007	0.87560	.	.	ENSG00000162636	ENST00000370035;ENST00000405454;ENST00000437902	T;T	0.45668	0.89;0.89	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	M	0.89095	3.005	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.71434	-0.4594	10	0.54805	T	0.06	-11.9928	19.0648	0.93106	0.0:0.0:1.0:0.0	.	78	Q5T8I3	F102B_HUMAN	F	78	ENSP00000359052:C78F;ENSP00000386084:C78F	ENSP00000359052:C78F	C	+	2	0	FAM102B	108944806	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	9.008000	0.93601	2.671000	0.90904	0.557000	0.71058	TGT	-	HMMPfam_Eeig1		0.423	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM102B	protein_coding	OTTHUMT00000030188.3	G	NM_001010883		108944806	+1	no_errors	NM_001010883	genbank	human	validated	54_36p	missense	SNP	1.000	T
PTPRZ1	5803	genome.wustl.edu	37	7	121652841	121652841	+	Silent	SNP	G	G	A	rs145804208	byFrequency	TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr7:121652841G>A	ENST00000393386.2	+	12	4152	c.3741G>A	c.(3739-3741)tcG>tcA	p.S1247S	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1247					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTGATGTGTCGCCTACTTCTC	0.368													G|||	2	0.000399361	0.0	0.0	5008	,	,		21852	0.0		0.0	False		,,,				2504	0.002															0			7						G	,,	4,4402	8.1+/-20.4	0,4,2199	139.0	139.0	139.0		,,3741	-11.4	0.0	7	dbSNP_134	139	0,8600		0,0,4300	no	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,,	,,1247/2316	121652841	4,13002	2203	4300	6503	121440077	SO:0001819	synonymous_variant	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3741G>A	7.37:g.121652841G>A			121440077	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	superfamily_Carbonic anhydrase,HMMPfam_Carb_anhydrase,superfamily_Fibronectin type III,HMMSmart_SM00060,HMMPfam_fn3,superfamily_(Phosphotyrosine protein) phosphatases II,HMMSmart_SM00194,HMMPfam_Y_phosphatase,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1	p.S1247	ENST00000393386.2	37	c.3741	CCDS34740.1	7																																																																																			-	NULL		0.368	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRZ1	protein_coding	OTTHUMT00000347288.1	G	NM_002851		121440077	+1	no_errors	NM_002851	genbank	human	reviewed	54_36p	silent	SNP	0.009	A
TMEM225	338661	genome.wustl.edu	37	11	123753867	123753867	+	Missense_Mutation	SNP	C	C	T	rs114749572	byFrequency	TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr11:123753867C>T	ENST00000375026.2	-	4	872	c.656G>A	c.(655-657)cGt>cAt	p.R219H		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	219					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						GGTTACGTGACGTGTTTGGAC	0.418													C|||	13	0.00259585	0.0098	0.0	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.0															0			11						C	HIS/ARG	32,4372	36.8+/-68.6	1,30,2171	178.0	164.0	168.0		656	-0.0	0.0	11	dbSNP_132	168	0,8598		0,0,4299	no	missense	TMEM225	NM_001013743.1	29	1,30,6470	TT,TC,CC		0.0,0.7266,0.2461	benign	219/226	123753867	32,12970	2202	4299	6501	123259077	SO:0001583	missense	338661			AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"""PMP22 claudin domain containing"", ""protein phosphatase 1, regulatory subunit 154"""						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.656G>A	11.37:g.123753867C>T	ENSP00000364166:p.Arg219His		123259077		Missense_Mutation	SNP	NULL	p.R219H	ENST00000375026.2	37	c.656	CCDS31697.1	11	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	7.176	0.588549	0.13812	0.007266	0.0	ENSG00000204300	ENST00000375026	T	0.37584	1.19	3.89	-0.0361	0.13890	.	0.000000	0.45361	D	0.000362	T	0.13884	0.0336	N	0.20986	0.625	0.09310	N	1	B	0.26195	0.144	B	0.18263	0.021	T	0.10730	-1.0617	10	0.52906	T	0.07	-4.2744	6.7241	0.23346	0.0:0.5946:0.0:0.4054	.	219	Q6GV28	TM225_HUMAN	H	219	ENSP00000364166:R219H	ENSP00000364166:R219H	R	-	2	0	TMEM225	123259077	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.764000	0.26532	0.004000	0.14682	-1.619000	0.00793	CGT	-	NULL		0.418	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM225	protein_coding	OTTHUMT00000387260.1	C	NM_001013743		123259077	-1	no_errors	NM_001013743	genbank	human	provisional	54_36p	missense	SNP	0.052	T
LAMC3	10319	genome.wustl.edu	37	9	133936540	133936540	+	Silent	SNP	C	C	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr9:133936540C>A	ENST00000361069.4	+	13	2410	c.2277C>A	c.(2275-2277)ggC>ggA	p.G759G	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	759	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCTGCCCTGGCCAGTCGGCCT	0.662																																																0			9											50.0	45.0	47.0					9																	133936540		2203	4300	6503	132926361	SO:0001819	synonymous_variant	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.2277C>A	9.37:g.133936540C>A			132926361	B1APX9|B1APY0|Q59H72	Silent	SNP	HMMSmart_LamNT,HMMPfam_Laminin_N,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,superfamily_SSF57196,PatternScan_EGF_1,PatternScan_EGF_LAM_1,HMMPfam_Laminin_B,PatternScan_EGF_2	p.G759	ENST00000361069.4	37	c.2277	CCDS6938.1	9																																																																																			-	HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,superfamily_SSF57196		0.662	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMC3	protein_coding	OTTHUMT00000054717.3	C	NM_006059		132926361	+1	no_errors	NM_006059	genbank	human	reviewed	54_36p	silent	SNP	0.367	A
GPR112	139378	genome.wustl.edu	37	X	135429258	135429258	+	Silent	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chrX:135429258C>T	ENST00000394143.1	+	6	3684	c.3393C>T	c.(3391-3393)acC>acT	p.T1131T	GPR112_ENST00000412101.1_Silent_p.T926T|GPR112_ENST00000370652.1_Silent_p.T1131T|GPR112_ENST00000394141.1_Silent_p.T926T|GPR112_ENST00000287534.4_Silent_p.T1068T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1131					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTTCTCTACCTCAGTTGATA	0.483																																																0			X											152.0	119.0	130.0					X																	135429258		2203	4300	6503	135256924	SO:0001819	synonymous_variant	139378			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3393C>T	X.37:g.135429258C>T			135256924	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	superfamily_ConA_like_lec_gl,HMMPfam_GPS,HMMSmart_GPS,HMMPfam_7tm_2,PatternScan_G_PROTEIN_RECEP_F2_2	p.T1131	ENST00000394143.1	37	c.3393	CCDS35409.1	X																																																																																			-	NULL		0.483	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GPR112	protein_coding	OTTHUMT00000286639.1	C			135256924	+1	no_errors	NM_153834	genbank	human	validated	54_36p	silent	SNP	0.005	T
A4GNT	51146	genome.wustl.edu	37	3	137843622	137843622	+	Missense_Mutation	SNP	A	A	C			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr3:137843622A>C	ENST00000236709.3	-	3	708	c.507T>G	c.(505-507)gaT>gaG	p.D169E		NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	169					carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						TGGAGATGACATCGGTGTCCA	0.547																																																0			3											88.0	87.0	87.0					3																	137843622		2203	4300	6503	139326312	SO:0001583	missense	51146			AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.507T>G	3.37:g.137843622A>C	ENSP00000236709:p.Asp169Glu		139326312	Q0VDK1|Q0VDK2	Missense_Mutation	SNP	HMMPfam_Gly_transf_sug,HMMPfam_Gb3_synth	p.D169E	ENST00000236709.3	37	c.507	CCDS3097.1	3	.	.	.	.	.	.	.	.	.	.	A	22.2	4.251320	0.80135	.	.	ENSG00000118017	ENST00000236709	D	0.98329	-4.87	5.27	-3.48	0.04739	Glycosyltransferase, DXD sugar-binding motif (1);	0.000000	0.64402	D	0.000001	D	0.98998	0.9658	H	0.95402	3.665	0.38058	D	0.935978	D	0.89917	1.0	D	0.97110	1.0	D	0.99873	1.1099	10	0.87932	D	0	-21.5869	13.4562	0.61199	0.4483:0.0:0.5517:0.0	.	169	Q9UNA3	A4GCT_HUMAN	E	169	ENSP00000236709:D169E	ENSP00000236709:D169E	D	-	3	2	A4GNT	139326312	0.040000	0.19996	0.714000	0.30535	0.994000	0.84299	-0.151000	0.10175	-0.548000	0.06199	0.460000	0.39030	GAT	-	HMMPfam_Gly_transf_sug		0.547	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	A4GNT	protein_coding	OTTHUMT00000357557.1	A	NM_016161		139326312	-1	no_errors	NM_016161	genbank	human	reviewed	54_36p	missense	SNP	0.937	C
EPPK1	83481	genome.wustl.edu	37	8	144942413	144942413	+	Missense_Mutation	SNP	T	T	C	rs201641573	byFrequency	TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr8:144942413T>C	ENST00000525985.1	-	2	5080	c.5009A>G	c.(5008-5010)gAc>gGc	p.D1670G				P58107	EPIPL_HUMAN	epiplakin 1	1670						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GACGATGAGGTCCTTCTGCAT	0.677													T|||	32	0.00638978	0.0	0.0086	5008	,	,		20072	0.002		0.0219	False		,,,				2504	0.002															0			8						T	GLY/ASP	20,3966		1,18,1974	58.0	64.0	62.0		5009	1.3	0.3	8	dbSNP_134	62	165,8119		1,163,3978	no	missense	EPPK1	NM_031308.1	94	2,181,5952	CC,CT,TT		1.9918,0.5018,1.5077	benign	1670/2420	144942413	185,12085	1993	4142	6135	145014401	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5009A>G	8.37:g.144942413T>C	ENSP00000436337:p.Asp1670Gly		145014401	Q76E58|Q9NSU9	Missense_Mutation	SNP	HMMSmart_SM00250,superfamily_Plakin repeat,HMMPfam_Plectin	p.D1645G	ENST00000525985.1	37	c.4934		8	.	.	.	.	.	.	.	.	.	.	T	3.451	-0.111943	0.06881	0.005018	0.019918	ENSG00000227184	ENST00000525985	T	0.61392	0.11	4.95	1.27	0.21489	.	.	.	.	.	T	0.20170	0.0485	N	0.25094	0.71	0.29252	N	0.871898	B	0.02656	0.0	B	0.01281	0.0	T	0.22941	-1.0202	9	0.02654	T	1	.	8.9198	0.35604	0.0:0.1936:0.0:0.8064	.	1670	E9PPU0	.	G	1670	ENSP00000436337:D1670G	ENSP00000436337:D1670G	D	-	2	0	EPPK1	145014401	0.006000	0.16342	0.329000	0.25429	0.086000	0.17979	0.076000	0.14712	0.380000	0.24823	-1.345000	0.01243	GAC	-	superfamily_Plakin repeat,HMMSmart_SM00250		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	EPPK1	protein_coding	OTTHUMT00000382675.1	T	NM_031308		145014401	-1	no_stop_codon:bad_bp_length_for_coding_region	NM_031308	genbank	human	provisional	54_36p	missense	SNP	0.998	C
SCN2A	6326	genome.wustl.edu	37	2	166172039	166172039	+	Missense_Mutation	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr2:166172039G>A	ENST00000375437.2	+	11	1732	c.1442G>A	c.(1441-1443)gGa>gAa	p.G481E	SCN2A_ENST00000357398.3_Missense_Mutation_p.G481E|SCN2A_ENST00000283256.6_Missense_Mutation_p.G481E|SCN2A_ENST00000375427.2_Missense_Mutation_p.G481E	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	481					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGTGGGATAGGAGTTTTTTCA	0.423																																																0			2											66.0	71.0	70.0					2																	166172039		2203	4299	6502	165880285	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1442G>A	2.37:g.166172039G>A	ENSP00000364586:p.Gly481Glu		165880285	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	superfamily_Voltage-gated potassium channels,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,HMMSmart_SM00015,HMMPfam_IQ	p.G481E	ENST00000375437.2	37	c.1442	CCDS33314.1	2	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978098	0.53720	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.96136	-3.92;-3.85;-3.85;-3.85;-3.85	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000009	D	0.95890	0.8662	L	0.36672	1.1	0.39620	D	0.970016	B;D	0.89917	0.378;1.0	B;D	0.97110	0.272;1.0	D	0.95172	0.8291	10	0.39692	T	0.17	.	13.4661	0.61254	0.0709:0.0:0.9291:0.0	.	481;481	Q99250-2;Q99250	.;SCN2A_HUMAN	E	481	ENSP00000406454:G481E;ENSP00000364586:G481E;ENSP00000349973:G481E;ENSP00000283256:G481E;ENSP00000364576:G481E	ENSP00000283256:G481E	G	+	2	0	SCN2A	165880285	0.996000	0.38824	0.206000	0.23566	0.566000	0.35808	4.086000	0.57664	2.788000	0.95919	0.650000	0.86243	GGA	-	NULL		0.423	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SCN2A	protein_coding	OTTHUMT00000102659.2	G	NM_021007		165880285	+1	no_errors	NM_001040142	genbank	human	reviewed	54_36p	missense	SNP	0.197	A
FXR1	8087	genome.wustl.edu	37	3	180680825	180680825	+	Missense_Mutation	SNP	C	C	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr3:180680825C>T	ENST00000357559.4	+	13	1529	c.1145C>T	c.(1144-1146)tCt>tTt	p.S382F	FXR1_ENST00000468861.1_Missense_Mutation_p.S297F|FXR1_ENST00000305586.7_Missense_Mutation_p.S297F|FXR1_ENST00000480918.1_Missense_Mutation_p.S369F|FXR1_ENST00000445140.2_Missense_Mutation_p.S382F|FXR1_ENST00000491062.1_Missense_Mutation_p.S333F	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	382					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			GGTTCTAGGTCTTATAGCGGA	0.393																																																0			3											155.0	159.0	158.0					3																	180680825		2203	4300	6503	182163519	SO:0001583	missense	8087			M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.1145C>T	3.37:g.180680825C>T	ENSP00000350170:p.Ser382Phe		182163519	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	HMMPfam_Agenet,superfamily_Eukaryotic type KH-domain (KH-domain type I),HMMSmart_SM00322,HMMPfam_KH_1	p.S382F	ENST00000357559.4	37	c.1145	CCDS3238.1	3	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084632	0.76642	.	.	ENSG00000114416	ENST00000357559;ENST00000305586;ENST00000491062;ENST00000468861;ENST00000445140;ENST00000480918	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	5.22	5.22	0.72569	.	0.050484	0.85682	D	0.000000	T	0.53818	0.1820	L	0.40543	1.245	0.58432	D	0.999995	D;D;D;D;P;D	0.76494	0.991;0.978;0.978;0.999;0.941;0.99	P;P;P;D;P;P	0.87578	0.877;0.878;0.878;0.998;0.735;0.892	T	0.53995	-0.8359	10	0.59425	D	0.04	-26.9574	19.1372	0.93433	0.0:1.0:0.0:0.0	.	369;333;297;326;382;382	B4DXZ6;E9PFF5;E7EU85;E7ERF5;P51114-2;P51114	.;.;.;.;.;FXR1_HUMAN	F	382;297;333;297;382;369	ENSP00000350170:S382F;ENSP00000307633:S297F;ENSP00000420643:S333F;ENSP00000420515:S297F;ENSP00000388828:S382F;ENSP00000418097:S369F	ENSP00000307633:S297F	S	+	2	0	FXR1	182163519	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.201000	0.65163	2.596000	0.87737	0.467000	0.42956	TCT	-	superfamily_Eukaryotic type KH-domain (KH-domain type I)		0.393	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FXR1	protein_coding	OTTHUMT00000350265.5	C			182163519	+1	no_errors	NM_005087	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
SSFA2	6744	genome.wustl.edu	37	2	182765588	182765588	+	Missense_Mutation	SNP	G	G	T			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr2:182765588G>T	ENST00000431877.2	+	7	848	c.669G>T	c.(667-669)caG>caT	p.Q223H	SSFA2_ENST00000409001.1_Missense_Mutation_p.Q223H|SSFA2_ENST00000428267.2_Missense_Mutation_p.Q70H|SSFA2_ENST00000320370.7_Missense_Mutation_p.Q223H	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	223						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TGAGTGCTCAGATGCAACGGA	0.318																																																0			2											58.0	60.0	59.0					2																	182765588		2203	4299	6502	182473833	SO:0001583	missense	6744			M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.669G>T	2.37:g.182765588G>T	ENSP00000388731:p.Gln223His		182473833	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	NULL	p.Q223H	ENST00000431877.2	37	c.669	CCDS46467.1	2	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444227	0.63067	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267	T;T;T;T	0.30981	1.85;1.61;1.83;1.51	5.97	-8.24	0.01029	.	0.055211	0.64402	D	0.000001	T	0.51601	0.1684	M	0.76002	2.32	0.38076	D	0.936534	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.994;0.994;0.996	T	0.70110	-0.4962	10	0.66056	D	0.02	-14.4297	21.9459	0.99964	0.3195:0.0:0.6805:0.0	.	70;223;223;223	E7END2;E9PHV5;P28290;P28290-3	.;.;SSFA2_HUMAN;.	H	223;223;223;70	ENSP00000388731:Q223H;ENSP00000314669:Q223H;ENSP00000387319:Q223H;ENSP00000409867:Q70H	ENSP00000314669:Q223H	Q	+	3	2	SSFA2	182473833	0.633000	0.27181	0.494000	0.27515	0.996000	0.88848	-0.025000	0.12413	-2.019000	0.00942	-0.137000	0.14449	CAG	-	NULL		0.318	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SSFA2	protein_coding	OTTHUMT00000255793.2	G	NM_006751		182473833	+1	no_errors	NM_006751	genbank	human	validated	54_36p	missense	SNP	0.873	T
UGT1A6	54578	genome.wustl.edu	37	2	234652364	234652364	+	Intron	SNP	G	G	A			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr2:234652364G>A	ENST00000305139.6	+	2	1000				UGT1A3_ENST00000482026.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|DNAJB3_ENST00000449667.1_RNA|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000608381.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	TCGCCATAGCGGTCATAGATA	0.622																																																0			2											120.0	132.0	128.0					2																	234652364		2032	4197	6229	234317103	SO:0001627	intron_variant	414061			M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.862-23316G>A	2.37:g.234652364G>A			234317103	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	superfamily_DnaJ_N,HMMSmart_DnaJ,HMMPfam_DnaJ,PatternScan_DNAJ_1	p.R67C	ENST00000305139.6	37	c.199	CCDS2507.1	2																																																																																			-	superfamily_DnaJ_N		0.622	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAJB3	protein_coding	OTTHUMT00000130988.1	G	NM_205862		234317103	-1	no_errors	NM_001001394	genbank	human	validated	54_36p	missense	SNP	0.720	A
VARS	7407	genome.wustl.edu	37	6	31760607	31760608	+	Frame_Shift_Ins	INS	-	-	CGGACACA			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	-	-					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr6:31760607_31760608insCGGACACA	ENST00000375663.3	-	4	1027_1028	c.587_588insTGTGTCCG	c.(586-588)cggfs	p.-196fs	VARS_ENST00000444930.2_5'UTR	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase						gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	ATTCTGGCTGCCGGACACACGT	0.554																																																0			6																																								31868587	SO:0001589	frameshift_variant	7407			BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.580_587dupTGTGTCCG	6.37:g.31760608_31760615dupCGGACACA	ENSP00000364815:p.Arg196fs		31868586	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Frame_Shift_Ins	INS	HMMPfam_GST_N,superfamily_Glutathione S-transferase (GST) C-terminal domain,HMMPfam_GST_C,superfamily_Nucleotidylyl transferase,HMMPfam_tRNA-synt_1,PatternScan_AA_TRNA_LIGASE_I,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases,HMMPfam_Anticodon_1	p.Q197fs	ENST00000375663.3	37	c.588_587	CCDS34412.1	6																																																																																			-	superfamily_Glutathione S-transferase (GST) C-terminal domain,HMMPfam_GST_C		0.554	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VARS	protein_coding	OTTHUMT00000076619.2	-	NM_006295		31868587	-1	no_errors	NM_006295	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	CGGACACA
CDK12	51755	genome.wustl.edu	37	17	37650879	37650880	+	Frame_Shift_Ins	INS	-	-	A	rs191899574		TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	-	-					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr17:37650879_37650880insA	ENST00000447079.4	+	5	2384_2385	c.2351_2352insA	c.(2350-2355)cgaagtfs	p.S785fs	CDK12_ENST00000430627.2_Frame_Shift_Ins_p.S785fs	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	785	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						TTAatccaccgaagtgttgtta	0.406			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																													Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0			17																																								34904406	SO:0001589	frameshift_variant	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2353dupA	17.37:g.37650881_37650881dupA	ENSP00000398880:p.Ser785fs		34904405	A7E2B2|B4DYX4|B9EIQ6|O94978	Frame_Shift_Ins	INS	superfamily_Protein kinase-like (PK-like),HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Pkinase,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_ST	p.S785fs	ENST00000447079.4	37	c.2351_2352	CCDS11337.1	17																																																																																			-	superfamily_Protein kinase-like (PK-like),HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Pkinase		0.406	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CRKRS	protein_coding	OTTHUMT00000256941.4	-	NM_016507		34904406	+1	no_errors	NM_016507	genbank	human	validated	54_36p	frame_shift_ins	INS	0.449:0.384	A
HIPK1	204851	genome.wustl.edu	37	1	114483657	114483662	+	In_Frame_Del	DEL	ATTAAA	ATTAAA	-			TCGA-20-1684-01A-01W-0633-09	TCGA-20-1684-10A-01W-0633-09	ATTAAA	ATTAAA					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	41fbfa93-8a31-461e-800a-23142842d0df	37f8a8d6-27ce-43b4-9e13-ac2e11fffdd0	g.chr1:114483657_114483662delATTAAA	ENST00000369558.1	+	2	884_889	c.652_657delATTAAA	c.(652-657)attaaadel	p.IK218del	HIPK1_ENST00000426820.2_In_Frame_Del_p.IK218del|HIPK1_ENST00000369559.4_In_Frame_Del_p.IK218del|HIPK1_ENST00000369554.2_In_Frame_Del_p.IK218del|HIPK1_ENST00000369561.4_In_Frame_Del_p.IK218del|HIPK1_ENST00000369555.2_In_Frame_Del_p.IK218del			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	218	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATTGTGGCTATTAAAATCTTGAAGA	0.466																																																0			1																																								114285185	SO:0001651	inframe_deletion	204851			AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.652_657delATTAAA	1.37:g.114483657_114483662delATTAAA	ENSP00000358571:p.Ile218_Lys219del		114285180	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	In_Frame_Del	DEL	superfamily_Protein kinase-like (PK-like),HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Pkinase,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_ST	p.KI219in_frame_del	ENST00000369558.1	37	c.652_657	CCDS867.1	1																																																																																			(deletion:cds_exon[114284529,114285604])	superfamily_Protein kinase-like (PK-like),HMMSmart_SM00219,HMMSmart_SM00220,HMMPfam_Pkinase,PatternScan_PROTEIN_KINASE_ATP		0.466	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	HIPK1	protein_coding	OTTHUMT00000033127.1	ATTAAA	NM_198268		114285185	+1	no_errors	NM_198268	genbank	human	reviewed	54_36p	in_frame_del	DEL	1.000:1.000:1.000:1.000:1.000:0.997	-
