EP400 p.Ala1764=
c.5292G>A · rs34531099 · VCV747137
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.776%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -3.2 |
| Overall | ||
| CADD | 0.457 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.776%
African / African-American · 582/75,030 alleles
Filtering AF
0.723%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.703%
Overall
0.0398%
643/1,614,162 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.776% | 129 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Admixed American | 0.0333% | 3,001 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.000254% | 393,345 |
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
- EP400
- Protein
- p.Ala1764=
- Coding
- c.5292G>A
- MANE Select
- NM_015409
- dbSNP
- rs34531099
- Type
- single nucleotide variant
- Location
- chr12:132028199 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Residue 1764
- an α-helix
Similar variants
- EP400 p.Thr664Ala Uncertain significance ★★ same type
- EP400 c.1435+8G>A Benign ★★ same type
- EP400 c.7027-9C>T Benign ★★ same type
- EP400 p.Ala146= Likely benign ★★ same type
- EP400 p.Ala1649Thr Benign/Likely benign ★★ same type
- EP400 p.Ala244= Likely benign ★★ same type
- EP400 p.Ala2803= Likely benign ★★ same type
- EP400 p.Ala524= Likely benign ★★ 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/ep400-p-ala1764 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown