FMO3 p.Phe109fs
c.327_329delinsAC · VCV3573951
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
trimethylaminuria
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -4 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- FMO3
- Protein
- p.Phe109fs
- Coding
- c.327_329delinsAC
- MANE Select
- NM_001002294
- Type
- Indel
- Location
- chr1:171107680 (GRCh38)
- Gene constraint
- LOEUF 1.314 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.50
Similar variants
- FMO3 p.Ala52fs Likely pathogenic ★ same condition
- FMO3 p.Arg387Cys Likely pathogenic ★ same condition
- FMO3 c.484+2T>G Likely pathogenic ★★ same condition
- FMO3 c.828-2A>G Likely pathogenic ★★ same condition
- FMO3 p.Arg131fs Pathogenic/Likely pathogenic ★★ same condition
- FMO3 p.Arg223Gln Likely pathogenic ★★ same condition
- FMO3 p.Arg223Trp Likely pathogenic ★★ same condition
- FMO3 p.Arg238Gln Pathogenic/Likely pathogenic ★★ same condition
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-phe109fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown