FMO3 p.Ser493=
c.1479G>A · rs766383334 · VCV260068
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.281%, mid)
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 -6.5 | GERP -3.7 |
| Overall | ||
| CADD | 0.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.281%
Middle Eastern · 17/6,056 alleles
Filtering AF
0.179%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.00601%
97/1,613,954 alleles · rare
exomes 84/1,461,632 · genomes 13/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.281% | 356 |
| South Asian | 0.0494% | 2,024 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| European (non-Finnish) | 0.0017% | 58,993 |
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
- FMO3
- Protein
- p.Ser493=
- Coding
- c.1479G>A
- MANE Select
- NM_001002294
- dbSNP
- rs766383334
- Type
- single nucleotide variant
- Location
- chr1:171117322 (GRCh38)
- Gene constraint
- LOEUF 1.314 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.50
Similar variants
- FMO3 p.Ser493Leu Likely benign ★ same residue
- FMO3 c.484+2T>G Likely pathogenic ★★ same type
- FMO3 c.828-2A>G Likely pathogenic ★★ same type
- FMO3 p.Arg223Gln Likely pathogenic ★★ same type
- FMO3 p.Arg223Trp Likely pathogenic ★★ same type
- FMO3 p.Arg238Gln Pathogenic/Likely pathogenic ★★ same type
- FMO3 p.Arg238Ter Pathogenic/Likely pathogenic ★★ same type
- FMO3 p.Arg492Trp Pathogenic/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/fmo3-p-ser493 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown