EP300 p.Arg1311=
c.3933G>A · rs1347207948 · VCV766259
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 1.3 | GERP 0.45, phastCons 1 |
| Overall | ||
| CADD | 8.974 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,014 alleles
Overall
0.000137%
2/1,461,888 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,014 |
| European (non-Finnish) | 8.47e-05% | 1,180,026 |
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.Arg1311=
- Coding
- c.3933G>A
- MANE Select
- NM_001429
- dbSNP
- rs1347207948
- Type
- single nucleotide variant
- Location
- chr22:41168507 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.88 · 60 PDB
- Residue 1311
- an α-helix; the cbp/p300-type hat domain
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-arg1311 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown