Is EP300 p.Ala2129Ser (c.6385G>T) pathogenic?

EP300 p.Ala2129Ser (c.6385G>T) is classified Uncertain significance in EP300 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-28). AlphaMissense: likely benign (0.0769); Absent from gnomAD v4.1.

How common is EP300 p.Ala2129Ser (c.6385G>T) in the general population?

EP300 p.Ala2129Ser (c.6385G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EP300 p.Ala2129Ser (c.6385G>T)?

AlphaMissense predicts likely benign (score 0.0769) — an in-silico prediction, not a clinical call.

EP300 p.Ala2129Ser

c.6385G>T · VCV3361632

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0769 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0769	likely benign
REVEL	0.194	benign-leaning
SaProt	LLR -6.78	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.6	GERP 1.3, phastCons 1
Regional constraint	o/e 1.26	unconstrained · MANE · 1,737 bp · p 6.7e-13 · regional, not allelic
Overall
CADD	21.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EP300
Protein: p.Ala2129Ser
Coding: c.6385G>T
MANE Select: NM_001429
Type: single nucleotide variant
Location: chr22:41178096 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.88 · 60 PDB
Residue 2129: the 'interaction with htlv-1 tax' region; the 'interaction with ncoa2' region; the 'disordered' region

Full EP300 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EP300 c.1282+1G>A Pathogenic/Likely pathogenic ★★ same type
EP300 c.3671+1G>A Pathogenic/Likely pathogenic ★★ same type
EP300 c.3729-2A>G Pathogenic/Likely pathogenic ★★ same type
EP300 c.3857A>G Pathogenic/Likely pathogenic ★★ ⚠ same type
EP300 p.Arg1055Ter Pathogenic ★★ same type
EP300 p.Arg1312Ter Pathogenic ★★ same type
EP300 p.Arg1356Ter Pathogenic ★★ same type
EP300 p.Arg1462Ter Pathogenic ★★ same type

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/ep300-p-ala2129ser (accessed [today's date]).

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