EP300 p.Pro2003=
c.6009C>T · VCV3353494
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
Conditions
1
EP300-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 0.29 | GERP 0.33, phastCons 0.98 |
| Overall | ||
| CADD | 10.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,180,016 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000753%
11/1,461,596 alleles · very rare
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
- EP300
- Protein
- p.Pro2003=
- Coding
- c.6009C>T
- MANE Select
- NM_001429
- Type
- single nucleotide variant
- Location
- chr22:41177720 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.88 · 60 PDB
- Residue 2003
- the 'disordered' region; the 'interaction with htlv-1 tax' region
Disease context
EP300-related disorder
Similar variants
- EP300 p.Pro2003Thr Benign/Likely benign ★★ ⚠ same residue
- EP300 p.Arg1645Ter Pathogenic ★★ same condition
- EP300 p.Arg200Ter Pathogenic/Likely pathogenic ★★ same condition
- EP300 p.Phe1595Val Pathogenic/Likely pathogenic ★★ same condition
- EP300 p.Arg1324Lys Uncertain significance ★★ ⚠ same condition
- EP300 p.Asn301Asp Uncertain significance ★★ ⚠ same condition
- EP300 p.Asn674Asp Uncertain significance ★★ ⚠ same condition
- EP300 p.Gln570Arg 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-pro2003 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown