Is FMN2 p.Pro1079= (c.3237A>T) pathogenic?

FMN2 p.Pro1079= (c.3237A>T) is classified Likely benign in FMN2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-06-14). Low-frequency (popmax 4.07%, mid); Associated with FMN2-related disorder.

What condition is associated with FMN2 p.Pro1079= (c.3237A>T)?

FMN2 p.Pro1079= (c.3237A>T) is associated with FMN2-related disorder (ClinVar).

How common is FMN2 p.Pro1079= (c.3237A>T) in the general population?

FMN2 p.Pro1079= (c.3237A>T) is low-frequency (popmax 4.07%, mid) (gnomAD).

FMN2 p.Pro1079=

c.3237A>T · rs141917612 · VCV3052114

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.07%, mid)

Conditions

FMN2-related disorder

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 -0.066	GERP -1.2, phastCons 0.58
Overall
CADD	1.253	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.07% Middle Eastern · 10/246 alleles

Filtering AF 2.96% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.85%

Overall 2.05% 2,030/98,962 alleles · low-frequency exomes 2,018/95,358 · genomes 12/3,604 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	4.07%	25
South Asian	3.24%	31
East Asian	3.04%	33
Ashkenazi Jewishnot grpmax-eligible	2.99%	33
Remaining individualsnot grpmax-eligible	2.68%	37
European (non-Finnish)	2.21%	45
African / African-American	1.93%	52
Admixed American	1.66%	60
Finnishnot grpmax-eligible	0.441%	227

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.Pro1079=
Coding: c.3237A>T
MANE Select: NM_020066
dbSNP: rs141917612
Type: single nucleotide variant
Location: chr1:240208049 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.51 (gnomAD)
Structure: AlphaFold pLDDT 51.48 · 2 PDB
Residue 1079: the fh1 domain; the 'disordered' region

Full FMN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-pro1079 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown