CYP4V2 p.Pro49=
c.147C>G · rs769901483 · VCV1093082
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00393%, nfe)
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 -2.3 | GERP -4 |
| Overall | ||
| CADD | 6.608 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00393%
European (non-Finnish) · 46/1,170,340 alleles
Filtering AF
0.00301%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00269%
Overall
0.00303%
48/1,586,110 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00393% | 25,442 |
| Remaining individualsnot grpmax-eligible | 0.00325% | 30,767 |
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.Pro49=
- Coding
- c.147C>G
- MANE Select
- NM_207352
- dbSNP
- rs769901483
- Type
- single nucleotide variant
- Location
- chr4:186191970 (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 c.1091-2A>G Pathogenic/Likely pathogenic ★★ same type
- CYP4V2 c.413+1G>A Likely pathogenic ★★ same type
- CYP4V2 c.414-1G>A Pathogenic/Likely pathogenic ★★ same type
- CYP4V2 c.801+1G>A Pathogenic ★★ same type
- CYP4V2 p.Arg232Ter Pathogenic ★★ same type
- CYP4V2 p.Arg390Cys Pathogenic ★★ same type
- CYP4V2 p.Arg390His Pathogenic/Likely pathogenic ★★ same type
- CYP4V2 p.Arg390Leu Likely pathogenic ★★ 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/cyp4v2-p-pro49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown