Is EP400 p.Pro2797= (c.8391G>A) pathogenic?

EP400 p.Pro2797= (c.8391G>A) is classified Benign in EP400 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Low-frequency (popmax 2.06%, eas); Associated with EP400-related disorder.

What condition is associated with EP400 p.Pro2797= (c.8391G>A)?

EP400 p.Pro2797= (c.8391G>A) is associated with EP400-related disorder (ClinVar).

How common is EP400 p.Pro2797= (c.8391G>A) in the general population?

EP400 p.Pro2797= (c.8391G>A) is low-frequency (popmax 2.06%, eas) (gnomAD).

EP400 p.Pro2797=

c.8391G>A · rs144085795 · VCV3039919

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 2.06%, eas)

Conditions

EP400-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.8	GERP -2.7
Overall
CADD	0.092	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.06% East Asian · 926/44,864 alleles

Filtering AF 1.95% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.91%

Overall 0.0915% 1,477/1,613,572 alleles · low-frequency exomes 1,275/1,461,326 · genomes 202/152,246 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	2.06%	48
Finnishnot grpmax-eligible	0.428%	234
Middle Eastern	0.116%	865
Admixed American	0.0733%	1,364
Remaining individualsnot grpmax-eligible	0.0656%	1,524
South Asian	0.0176%	5,691
European (non-Finnish)	0.0136%	7,374
African / African-American	0.012%	8,325
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,592

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EP400
Protein: p.Pro2797=
Coding: c.8391G>A
MANE Select: NM_015409
dbSNP: rs144085795
Type: single nucleotide variant
Location: chr12:132064724 (GRCh38)
Gene constraint: LOEUF 0.365 · pLI 1.00 (gnomAD)

Full EP400 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EP400-related disorder

Similar variants

EP400 p.Pro2797Ala Uncertain significance ★ same residue
EP400 p.Pro2797Leu Uncertain significance ★ same residue
EP400 p.Gly2702Glu Uncertain significance ★ same condition
EP400 p.Lys1297Arg Uncertain significance ★ same condition
EP400 p.Ser45Pro Uncertain significance ★ same condition
EP400 p.Ser573Phe Uncertain significance ★ same condition
EP400 c.2680-3C>A Uncertain significance same condition
EP400 c.4110+2T>A Uncertain significance same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ep400-p-pro2797 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown