Is EP300 p.Arg580Gly (c.1738C>G) pathogenic?

EP300 p.Arg580Gly (c.1738C>G) is classified Uncertain significance in EP300 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-29). AlphaMissense: likely pathogenic (0.9991); Absent from gnomAD v4.1.

How common is EP300 p.Arg580Gly (c.1738C>G) in the general population?

EP300 p.Arg580Gly (c.1738C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EP300 p.Arg580Gly (c.1738C>G)?

AlphaMissense predicts likely pathogenic (score 0.9991) — an in-silico prediction, not a clinical call.

EP300 p.Arg580Gly

c.1738C>G · VCV3343151

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9991 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9991	likely pathogenic · top 4% in EP300
REVEL	0.882	moderately pathogenic-leaning
SaProt	LLR -14.40	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 2.3, phastCons 1
Regional constraint	o/e 0.49	unconstrained · MANE · 3,373 bp · p 3.9e-07 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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.Arg580Gly
Coding: c.1738C>G
MANE Select: NM_001429
Type: single nucleotide variant
Location: chr22:41137768 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.88 · 60 PDB
Residue 580: an α-helix; the kix domain; a modified residue (asymmetric dimethylarginine; by carm1)

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

Similar variants

EP300 p.Arg580Ter Pathogenic ★ same residue
EP300 p.Arg580Gln Conflicting classifications of pathogenicity ★ same residue
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

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-arg580gly (accessed [today's date]).

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