FMN2 p.Pro999=
c.2997T>A · rs1572063197 · VCV3036377
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.117%, mid)
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 -15 | GERP -0.39 |
| Overall | ||
| CADD | 3.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
Middle Eastern · 1/856 alleles
Filtering AF
0.000532%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000291%
Overall
0.00279%
9/323,152 alleles · rare
exomes 9/309,356 · genomes 0/13,796 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.117% | 856 |
| East Asian | 0.00907% | 11,020 |
| Remaining individualsnot grpmax-eligible | 0.00769% | 12,998 |
| Finnishnot grpmax-eligible | 0.00422% | 23,682 |
| South Asian | 0.00401% | 24,928 |
| European (non-Finnish) | 0.00185% | 54,179 |
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.Pro999=
- Coding
- c.2997T>A
- MANE Select
- NM_020066
- dbSNP
- rs1572063197
- Type
- single nucleotide variant
- Location
- chr1:240207809 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 999
- the fh1 domain; the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- FMN2 p.Pro999Leu 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-pro999 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown