FMN2 p.Pro1156=
c.3468A>T · rs773418922 · VCV3025338
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.31%, mid)
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 -1.6 | GERP -1.8 |
| Overall | ||
| CADD | 1.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.31%
Middle Eastern · 8/242 alleles
Filtering AF
2.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.3%
Overall
1.33%
1,356/102,330 alleles · low-frequency
exomes 1,355/101,974 · genomes 1/356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.31% | 30 |
| South Asian | 2.68% | 37 |
| African / African-American | 2.18% | 46 |
| Remaining individualsnot grpmax-eligible | 1.76% | 57 |
| East Asian | 1.31% | 76 |
| Ashkenazi Jewishnot grpmax-eligible | 1.23% | 81 |
| European (non-Finnish) | 1.19% | 84 |
| Admixed American | 1.02% | 98 |
| Finnishnot grpmax-eligible | 0.847% | 118 |
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.Pro1156=
- Coding
- c.3468A>T
- MANE Select
- NM_020066
- dbSNP
- rs773418922
- Type
- single nucleotide variant
- Location
- chr1:240208280 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 1156
- 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-pro1156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown