FMN2 p.Pro958=
c.2874T>A · rs1305894508 · VCV2640140
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0347%, afr)
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 -2.4 | GERP -2.1 |
| Overall | ||
| CADD | 0.685 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0347%
African / African-American · 13/37,432 alleles
Filtering AF
0.0205%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0162%
Overall
0.00905%
100/1,105,522 alleles · ultra-rare
exomes 53/1,055,210 · genomes 47/50,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0347% | 2,879 |
| South Asian | 0.0194% | 5,151 |
| Admixed American | 0.0157% | 6,376 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0147% | 6,799 |
| Finnishnot grpmax-eligible | 0.00754% | 13,259 |
| European (non-Finnish) | 0.00718% | 13,931 |
| Remaining individualsnot grpmax-eligible | 0.00473% | 21,122 |
| East Asian | 0.00381% | 26,258 |
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.Pro958=
- Coding
- c.2874T>A
- MANE Select
- NM_020066
- dbSNP
- rs1305894508
- Type
- single nucleotide variant
- Location
- chr1:240207686 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 958
- the fh1 domain; the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- FMN2 p.Pro958Leu Benign ★★ ⚠ 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-pro958 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown