FMN2 p.Glu551=
c.1653G>A · rs149514160 · VCV435222
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.185%, amr)
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 2.9 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 9.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.185%
Admixed American · 111/60,028 alleles
Filtering AF
0.157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.08%
1,292/1,614,218 alleles · rare
exomes 1,167/1,461,892 · genomes 125/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.185% | 541 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| European (non-Finnish) | 0.0913% | 1,096 |
| Finnishnot grpmax-eligible | 0.0359% | 2,784 |
| African / African-American | 0.0293% | 3,412 |
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.Glu551=
- Coding
- c.1653G>A
- MANE Select
- NM_020066
- dbSNP
- rs149514160
- Type
- single nucleotide variant
- Location
- chr1:240123216 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
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-glu551 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown