EPC1

enhancer of polycomb homolog 1, the group of Tip60/Nua4 histone acetyltransferase complex subunits

Basic information

Region (hg38): 10:32267750-32378798

Links

ENSG00000120616 ∙ NCBI:80314 ∙ OMIM:610999 ∙ HGNC:19876 ∙ Uniprot:Q9H2F5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPC1 gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in EPC1

This is a list of pathogenic ClinVar variants found in the EPC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-32271615-C-T		not specified	Uncertain significance (Jul 19, 2022)
10-32271734-T-C		not specified	Uncertain significance (Nov 09, 2021)
10-32271753-T-A		not specified	Uncertain significance (Oct 04, 2022)
10-32271845-C-T		not specified	Uncertain significance (Mar 16, 2022)
10-32271884-G-A		not specified	Uncertain significance (Nov 09, 2021)
10-32272041-C-T		not specified	Uncertain significance (Dec 13, 2021)
10-32272065-C-T		not specified	Uncertain significance (Mar 25, 2022)
10-32273049-G-A		not specified	Uncertain significance (Feb 27, 2023)
10-32273216-C-T		not specified	Uncertain significance (Jul 14, 2021)
10-32284772-C-T		not specified	Uncertain significance (Oct 06, 2021)
10-32284898-C-T		not specified	Uncertain significance (Jun 29, 2023)
10-32284946-T-C		not specified	Uncertain significance (Feb 15, 2023)
10-32284987-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-32285009-A-C		not specified	Uncertain significance (Jul 17, 2023)
10-32286818-A-G		not specified	Uncertain significance (Aug 02, 2022)
10-32286962-A-T		not specified	Uncertain significance (Dec 05, 2022)
10-32287115-C-T		not specified	Uncertain significance (Apr 05, 2023)
10-32291231-G-C		not specified	Uncertain significance (Mar 20, 2023)
10-32291233-A-G		not specified	Uncertain significance (Jan 23, 2023)
10-32291237-T-C		not specified	Uncertain significance (Jun 27, 2023)
10-32291261-T-C		not specified	Likely benign (Sep 20, 2023)
10-32292503-C-T		not specified	Uncertain significance (Oct 02, 2023)
10-32293002-T-C		not specified	Uncertain significance (Sep 14, 2023)
10-32293708-A-G		not specified	Uncertain significance (Jan 10, 2023)
10-32346869-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPC1	protein_coding	protein_coding	ENST00000263062	15	111048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.41e-7	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	299	460	0.649	0.0000243	5464
Missense in Polyphen		109	223.18	0.48839		2532
Synonymous	0.737	162	174	0.929	0.00000939	1618
Loss of Function	6.30	2	50.2	0.0399	0.00000321	512

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000913	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when directly recruited to sites of DNA damage. {ECO:0000269|PubMed:14966270}.
• Pathway: Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0951

Intolerance Scores

• loftool: 0.0677
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.4

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.833
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Epc1
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription, DNA-templated;regulation of transcription by RNA polymerase II;vascular smooth muscle cell differentiation;regulation of growth;histone H4 acetylation;histone H2A acetylation;negative regulation of gene expression, epigenetic;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;nuclear membrane;Piccolo NuA4 histone acetyltransferase complex;NuA4 histone acetyltransferase complex
• Molecular function: histone acetyltransferase activity;protein binding