FMN2 p.Pro623=
c.1869A>G · rs147945249 · VCV740479
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.159%, afr)
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 -5 | GERP -4.4 |
| Overall | ||
| CADD | 0.117 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.159%
African / African-American · 119/74,950 alleles
Filtering AF
0.136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.127%
Overall
0.00899%
145/1,612,606 alleles · rare
exomes 87/1,460,322 · genomes 58/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.159% | 630 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,285 |
| Middle Eastern | 0.0165% | 6,056 |
| Admixed American | 0.00504% | 19,857 |
| South Asian | 0.0022% | 45,415 |
| European (non-Finnish) | 8.48e-05% | 1,179,514 |
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.Pro623=
- Coding
- c.1869A>G
- MANE Select
- NM_020066
- dbSNP
- rs147945249
- Type
- single nucleotide variant
- Location
- chr1:240178007 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 623
- 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-pro623 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown