FMO3 p.Ser298=
c.894C>T · rs1309541843 · VCV2842448
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -2.1 | GERP -0.95 |
| Overall | ||
| CADD | 6.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,922 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000372%
6/1,613,204 alleles · very rare
exomes 6/1,461,068 · genomes 0/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,461 |
| East Asian | 0.00223% | 44,852 |
| Admixed American | 0.00167% | 59,960 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
| European (non-Finnish) | 8.48e-05% | 1,179,444 |
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.Ser298=
- Coding
- c.894C>T
- MANE Select
- NM_001002294
- dbSNP
- rs1309541843
- Type
- single nucleotide variant
- Location
- chr1:171114073 (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-ser298 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown