CYP4V2 p.Ala41=
c.123G>A · rs963304343 · VCV3027683
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.048%, eas)
Conditions
1
inherited retinal dystrophy
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 0.25 | GERP -0.97 |
| Overall | ||
| CADD | 7.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.048%
East Asian · 21/43,790 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.027%
Overall
0.00145%
23/1,590,168 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.048% | 2,085 |
| European (non-Finnish) | 0.000171% | 585,844 |
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
- CYP4V2
- Protein
- p.Ala41=
- Coding
- c.123G>A
- MANE Select
- NM_207352
- dbSNP
- rs963304343
- Type
- single nucleotide variant
- Location
- chr4:186191946 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.05
Similar variants
- CYP4V2 p.Ala41Val Benign/Likely benign ★★ same residue
- CYP4V2 c.1091-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CYP4V2 c.414-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CYP4V2 c.801+1G>A Pathogenic ★★ same condition
- CYP4V2 p.Arg232Ter Pathogenic ★★ same condition
- CYP4V2 p.Gly134Ter Pathogenic ★★ same condition
- CYP4V2 p.Ile111Thr Pathogenic ★★ same condition
- CYP4V2 p.Leu173Trp Pathogenic/Likely pathogenic ★★ same condition
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/cyp4v2-p-ala41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown