EPC2

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

Basic information

Region (hg38): 2:148644440-148788495

Links

ENSG00000135999 ∙ NCBI:26122 ∙ OMIM:611000 ∙ HGNC:24543 ∙ Uniprot:Q52LR7 ∙ 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 EPC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPC2 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					4	4
missense			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	0	5

Variants in EPC2

This is a list of pathogenic ClinVar variants found in the EPC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-148645031-C-T		not specified	Uncertain significance (Nov 23, 2022)
2-148645035-C-T			Benign (Jun 19, 2018)
2-148645054-G-A		not specified	Uncertain significance (Nov 02, 2023)
2-148645072-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-148690218-A-G		not specified	Uncertain significance (Jun 24, 2022)
2-148690323-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-148743628-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-148743636-A-G		not specified	Uncertain significance (Apr 25, 2022)
2-148743679-T-C		not specified	Uncertain significance (Jul 27, 2022)
2-148743735-A-G		not specified	Uncertain significance (Dec 15, 2022)
2-148743737-T-G		not specified	Uncertain significance (Dec 11, 2024)
2-148753927-C-T		not specified	Uncertain significance (Jan 21, 2025)
2-148753967-A-G		not specified	Uncertain significance (Apr 23, 2024)
2-148753991-A-T		not specified	Uncertain significance (Mar 06, 2025)
2-148754002-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-148754012-G-A		not specified	Uncertain significance (May 24, 2024)
2-148754035-C-T		not specified	Uncertain significance (Feb 26, 2025)
2-148754067-T-G		not specified	Uncertain significance (Jan 16, 2024)
2-148754142-C-T			Benign (Dec 31, 2019)
2-148761874-A-G			Benign (Dec 31, 2019)
2-148762693-G-A		not specified	Uncertain significance (Mar 25, 2024)
2-148765027-C-T		not specified	Uncertain significance (May 01, 2024)
2-148765052-C-G		not specified	Uncertain significance (Jun 21, 2022)
2-148765088-A-G		not specified	Uncertain significance (Sep 06, 2022)
2-148765094-G-A		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPC2	protein_coding	protein_coding	ENST00000258484	14	143122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000181	124626	0	6	124632	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	251	404	0.622	0.0000198	5294
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000649	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.783
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.680

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epc2
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; vision/eye phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: DNA repair;regulation of transcription by RNA polymerase II;histone acetylation
• Cellular component: Piccolo NuA4 histone acetyltransferase complex
• Molecular function: histone acetyltransferase activity