FMN2 p.Leu798=
c.2394C>T · rs569497003 · VCV3045005
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.203%, amr)
Conditions
1
FMN2-related disorder
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 -9.8 | GERP -3.8 |
| Overall | ||
| CADD | 0.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.203%
Admixed American · 122/60,008 alleles
Filtering AF
0.174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.163%
Overall
0.00855%
138/1,614,008 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.203% | 492 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,251 |
| South Asian | 0.0022% | 45,541 |
| European (non-Finnish) | 0.000932% | 107,269 |
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
- FMN2
- Protein
- p.Leu798=
- Coding
- c.2394C>T
- MANE Select
- NM_020066
- dbSNP
- rs569497003
- Type
- single nucleotide variant
- Location
- chr1:240207206 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 798
- the fh1 domain; the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- FMN2 p.Leu798Val Uncertain significance ★ ⚠ same residue
- FMN2 p.Ala951= Likely benign ★★ same condition
- FMN2 p.Ala973= Benign/Likely benign ★★ same condition
- FMN2 p.Gly1005= Likely benign ★★ same condition
- FMN2 p.Gly1007= Likely benign ★★ same condition
- FMN2 p.Gly1062= Likely benign ★★ same condition
- FMN2 p.Gly941= Likely benign ★★ same condition
- FMN2 p.Leu1058= Likely benign ★★ 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/fmn2-p-leu798 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown