FMN2 p.Gly930=
c.2790C>A · rs769741561 · VCV2640135
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00232%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.39 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -2.4 |
| Overall | ||
| CADD | 0.257 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00232%
East Asian · 1/43,094 alleles
Filtering AF
0.000507%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000371%
Overall
0.000884%
14/1,584,142 alleles · very rare
exomes 11/1,437,166 · genomes 3/146,976 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00232% | 43,094 |
| South Asian | 0.0023% | 43,490 |
| European (non-Finnish) | 0.000945% | 105,864 |
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.Gly930=
- Coding
- c.2790C>A
- MANE Select
- NM_020066
- dbSNP
- rs769741561
- Type
- single nucleotide variant
- Location
- chr1:240207602 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 930
- the fh1 domain; the 'disordered' region
Similar variants
- FMN2 p.Gly930_Ala951del Likely benign ★ same residue
- 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
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-gly930 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown