FMO3 p.Lys304=
c.912G>A · rs866566270 · VCV2698966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1.5, phastCons 0.003 |
| Overall | ||
| CADD | 2.388 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,064 alleles
Overall
0.000124%
2/1,613,748 alleles · very rare
exomes 2/1,461,488 · genomes 0/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,064 |
| European (non-Finnish) | 8.48e-05% | 1,179,754 |
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.Lys304=
- Coding
- c.912G>A
- MANE Select
- NM_001002294
- dbSNP
- rs866566270
- Type
- single nucleotide variant
- Location
- chr1:171114091 (GRCh38)
- Gene constraint
- LOEUF 1.314 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.50
Similar variants
- 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
- FMO3 p.Arg500Ter 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-lys304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown