EPC2

protein-coding

enhancer of polycomb homolog 2, the group of Tip60/Nua4 histone acetyltransferase complex subunits

Gene summary

Predicted to enable protein-macromolecule adaptor activity. Involved in positive regulation of double-strand break repair via homologous recombination and regulation of cell cycle. Predicted to be located in nucleus. Predicted to be part of NuA4 histone acetyltransferase complex and piccolo histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015630.4

Inheritance

—

ClinVar variants

U:84B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr2:148,644,440-148,788,495

External References & Databases

Ensembl (ENSG00000135999)

Transcript & Mutation Effects

hg38 • Region Span ~144.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EPC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015630.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					4 clinvar	4
missense			80 clinvar			80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	84	0	4	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015630.4	RefSeq	NP_056445.3	14	MANE Select
ENST00000258484.11	Ensembl	ENSP00000258484.6	14	MANE Select
ENST00000397424.2	Ensembl	ENSP00000380569.2	4	Standard
ENST00000409654.5	Ensembl	ENSP00000387097.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA repair
regulation of transcription by RNA polymerase II
histone acetylation

Molecular Function

histone acetyltransferase activity

Cellular Component

Piccolo NuA4 histone acetyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258484
Coding exons: 14
Length: 143122
Individuals with no LoFs: 124626
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124632
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.70	251	404	0.622	0.0000198	5294
Missense (PolyPhen)		32	98.025	0.32645		1287
Synonymous	-0.450	150	143	1.05	0.00000705	1501
Loss of Function	5.53	2	39.6	0.0506	0.00000222	499

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in transcription or DNA repair. {ECO:0000250}.;

Recessive Scores

pRec: 0.160

Intolerance Scores

LoFtool: 0.254
RVIS EVS: -0.29
RVIS percentile EVS: 33.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.680

Gene Damage Prediction

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