EPHX1 p.Ser450=
c.1350G>C · rs4149230 · VCV1275216
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 15.3%, 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 -4.6 | GERP -2.8 |
| Overall | ||
| CADD | 0.249 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.3%
East Asian · 6,856/44,828 alleles
Filtering AF
15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.9%
Overall
4.58%
73,792/1,610,860 alleles · common
exomes 67,701/1,458,656 · genomes 6,091/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 15.3% | 7 |
| South Asian | 9.15% | 11 |
| Finnishnot grpmax-eligible | 7.9% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 5.65% | 18 |
| Middle Eastern | 5.62% | 18 |
| Admixed American | 5.52% | 18 |
| Remaining individualsnot grpmax-eligible | 4.88% | 20 |
| European (non-Finnish) | 3.8% | 26 |
| African / African-American | 0.658% | 152 |
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.Ser450=
- Coding
- c.1350G>C
- MANE Select
- NM_001136018
- dbSNP
- rs4149230
- Type
- single nucleotide variant
- Location
- chr1:225845329 (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-ser450 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown