EPHX1 p.Val413=
c.1239G>A · rs45540739 · VCV771319
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.91%, 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 |
|---|---|---|
| Pangolin | Δ0.30 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 0.34, phastCons 0.97 |
| Overall | ||
| CADD | 0.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.91%
Admixed American · 2,946/60,024 alleles
Filtering AF
4.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.7%
Overall
0.227%
3,667/1,614,160 alleles · low-frequency
exomes 2,983/1,461,854 · genomes 684/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.91% | 20 |
| East Asian | 0.274% | 365 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| African / African-American | 0.112% | 893 |
| South Asian | 0.078% | 1,283 |
| European (non-Finnish) | 0.0242% | 4,126 |
| Finnishnot grpmax-eligible | 0.0203% | 4,927 |
| Middle Eastern | 0.0166% | 6,040 |
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.Val413=
- Coding
- c.1239G>A
- MANE Select
- NM_001136018
- dbSNP
- rs45540739
- Type
- single nucleotide variant
- Location
- chr1:225845218 (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-val413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown