FMO3 p.Ser137=
c.411G>A · rs146587449 · VCV2832491
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -3.5 | GERP -4 |
| Overall | ||
| CADD | 0.344 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,868 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000992%
16/1,613,690 alleles · very rare
exomes 13/1,461,604 · genomes 3/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,717 |
| East Asian | 0.00223% | 44,854 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,460 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000763% | 131,096 |
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.Ser137=
- Coding
- c.411G>A
- MANE Select
- NM_001002294
- dbSNP
- rs146587449
- Type
- single nucleotide variant
- Location
- chr1:171107764 (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-ser137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown