EPHX1 p.Pro438=
c.1314G>A · rs45464298 · VCV721093
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.347%, afr)
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 -6.1 | GERP -2.8 |
| Overall | ||
| CADD | 0.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.347%
African / African-American · 260/75,002 alleles
Filtering AF
0.312%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.299%
Overall
0.0206%
333/1,612,726 alleles · rare
exomes 189/1,460,434 · genomes 144/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.347% | 288 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,671 |
| Admixed American | 0.0267% | 3,751 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| South Asian | 0.0033% | 30,339 |
| European (non-Finnish) | 0.00297% | 33,714 |
| East Asian | 0.00223% | 44,882 |
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
- EPHX1
- Protein
- p.Pro438=
- Coding
- c.1314G>A
- MANE Select
- NM_001136018
- dbSNP
- rs45464298
- Type
- single nucleotide variant
- Location
- chr1:225845293 (GRCh38)
- Gene constraint
- LOEUF 1.1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.06
Similar variants
- EPHX1 c.1041-181G>A Benign ★★ same type
- EPHX1 c.183+20G>A Benign ★★ same type
- EPHX1 c.364+114G>C Benign ★★ same type
- EPHX1 c.365-3C>A Benign ★★ same type
- EPHX1 c.592+34G>A Benign ★★ same type
- EPHX1 c.-5-29G>A Benign ★★ same type
- EPHX1 c.-5-45G>A Benign ★★ same type
- EPHX1 c.*35A>C 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/ephx1-p-pro438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown