EP400 p.Pro1586=
c.4758A>G · rs7133119 · VCV1314961
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 71.3%, afr) — too common for a highly-penetrant pathogenic allele
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 -5.4 | GERP -3.1 |
| Overall | ||
| CADD | 0.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
71.3%
African / African-American · 53,391/74,834 alleles
Filtering AF
70.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 70.6%
Overall
15.3%
246,232/1,613,106 alleles · common
exomes 201,214/1,460,890 · genomes 45,018/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 71.3% | 1 |
| South Asian | 21.1% | 5 |
| Finnishnot grpmax-eligible | 19% | 5 |
| Middle Eastern | 19% | 5 |
| Remaining individualsnot grpmax-eligible | 17.8% | 6 |
| Amishnot grpmax-eligible | 16% | 6 |
| Admixed American | 15.9% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 15.9% | 6 |
| East Asian | 12% | 8 |
| European (non-Finnish) | 11% | 9 |
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.Pro1586=
- Coding
- c.4758A>G
- MANE Select
- NM_015409
- dbSNP
- rs7133119
- Type
- single nucleotide variant
- Location
- chr12:132023844 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
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.Ala1764= Benign ★★ same type
- EP400 p.Ala244= Likely benign ★★ same type
- EP400 p.Ala2803= 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-pro1586 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown