EP400 p.Pro2507=
c.7521A>C · rs979171090 · VCV769838
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.27%, eas) — 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 -5.5 | GERP -2.6 |
| Overall | ||
| CADD | 0.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.27%
East Asian · 2,036/21,972 alleles
Filtering AF
8.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.8%
Overall
3.04%
33,017/1,085,304 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 9.27% | 11 |
| Finnishnot grpmax-eligible | 6.76% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 4.93% | 20 |
| Remaining individualsnot grpmax-eligible | 4.7% | 21 |
| Middle Eastern | 4.34% | 23 |
| European (non-Finnish) | 2.97% | 34 |
| Admixed American | 2.09% | 48 |
| African / African-American | 1.88% | 53 |
| Amishnot grpmax-eligible | 1.13% | 88 |
| South Asian | 0.848% | 118 |
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.Pro2507=
- Coding
- c.7521A>C
- MANE Select
- NM_015409
- dbSNP
- rs979171090
- Type
- single nucleotide variant
- Location
- chr12:132053390 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Residue 2507
- a β-strand
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-pro2507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown