FMN2 p.Pro29=
c.87C>A · VCV3353161
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0139%, sas)
Conditions
1
FMN2-related disorder
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 4.6 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 14.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0139%
South Asian · 12/86,530 alleles
Filtering AF
0.00939%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00882%
Overall
0.00943%
149/1,580,578 alleles · ultra-rare
exomes 140/1,431,034 · genomes 9/149,544 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0139% | 7,211 |
| European (non-Finnish) | 0.011% | 9,102 |
| Admixed American | 0.00721% | 13,871 |
| Remaining individualsnot grpmax-eligible | 0.0049% | 20,410 |
| Finnishnot grpmax-eligible | 0.00167% | 59,722 |
| African / African-American | 0.00136% | 73,684 |
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.Pro29=
- Coding
- c.87C>A
- MANE Select
- NM_020066
- Type
- single nucleotide variant
- Location
- chr1:240092196 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 29
- the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- 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
- FMN2 p.Leu1069= 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-pro29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown