FMN2 p.Pro989=
c.2967T>G · rs557827551 · VCV2582876
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.13%, amr)
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 -20 | GERP -1.7 |
| Overall | ||
| CADD | 0.585 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.13%
Admixed American · 316/28,054 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.984%
Overall
0.141%
1,318/933,934 alleles · low-frequency
exomes 1,247/904,818 · genomes 71/29,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.13% | 89 |
| Finnishnot grpmax-eligible | 0.979% | 102 |
| East Asian | 0.591% | 169 |
| Remaining individualsnot grpmax-eligible | 0.205% | 488 |
| Ashkenazi Jewishnot grpmax-eligible | 0.162% | 619 |
| South Asian | 0.105% | 957 |
| African / African-American | 0.0867% | 1,154 |
| European (non-Finnish) | 0.0577% | 1,734 |
| Middle Eastern | 0.0435% | 2,298 |
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.Pro989=
- Coding
- c.2967T>G
- MANE Select
- NM_020066
- dbSNP
- rs557827551
- Type
- single nucleotide variant
- Location
- chr1:240207779 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 989
- the fh1 domain; the 'disordered' region
Similar variants
- FMN2 p.Ile183Phe Likely pathogenic ★★ ⚠ same type
- FMN2 p.Ala1691Val Uncertain significance ★★ ⚠ same type
- FMN2 p.Ala367Val Uncertain significance ★★ ⚠ same type
- FMN2 p.Ala508Val Uncertain significance ★★ ⚠ same type
- FMN2 p.Asp352Tyr Uncertain significance ★★ ⚠ same type
- FMN2 p.Gln192Leu Uncertain significance ★★ ⚠ same type
- FMN2 p.Gln210Arg Uncertain significance ★★ ⚠ same type
- FMN2 p.Gly244Ala Uncertain significance ★★ ⚠ 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/fmn2-p-pro989 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown