Is EP300 p.Pro1858Ala (c.5572C>G) pathogenic?

EP300 p.Pro1858Ala (c.5572C>G) is classified Uncertain significance in EP300 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-11-03). AlphaMissense: likely benign (0.2064); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EP300 p.Pro1858Ala (c.5572C>G)?

EP300 p.Pro1858Ala (c.5572C>G) is associated with Inborn genetic diseases (ClinVar).

How common is EP300 p.Pro1858Ala (c.5572C>G) in the general population?

EP300 p.Pro1858Ala (c.5572C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EP300 p.Pro1858Ala (c.5572C>G)?

AlphaMissense predicts likely benign (score 0.2064) — an in-silico prediction, not a clinical call.

EP300 p.Pro1858Ala

c.5572C>G · rs398123610 · VCV93743

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2064 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2064	likely benign
REVEL	0.332	indeterminate
SaProt	LLR -6.79	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 2.4, phastCons 1
Regional constraint	o/e 1.26	unconstrained · MANE · 1,737 bp · p 6.7e-13 · regional, not allelic
Overall
CADD	21.1	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.Pro1858Ala
Coding: c.5572C>G
MANE Select: NM_001429
dbSNP: rs398123610
Type: single nucleotide variant
Location: chr22:41177283 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.88 · 60 PDB
Residue 1858: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EP300 p.Pro1858Leu Uncertain significance ★ same residue
EP300 p.Arg1055Ter Pathogenic ★★ same condition
EP300 p.Arg1829Cys Likely pathogenic ★★ same condition
EP300 p.Gln1953Ter Likely pathogenic ★★ same condition
EP300 c.3590+4A>T Uncertain significance ★★ same condition
EP300 p.Ala627Val Uncertain significance ★★ ⚠ same condition
EP300 p.Arg1305Cys Uncertain significance ★★ ⚠ same condition
EP300 p.Asn2370Ser 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/ep300-p-pro1858ala (accessed [today's date]).

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