Is FMN2 p.Pro1020= (c.3060T>C) pathogenic?

FMN2 p.Pro1020= (c.3060T>C) is classified Likely benign in FMN2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-05-01). Rare (popmax 0.907%, afr); Associated with FMN2-related disorder.

What condition is associated with FMN2 p.Pro1020= (c.3060T>C)?

FMN2 p.Pro1020= (c.3060T>C) is associated with FMN2-related disorder (ClinVar).

How common is FMN2 p.Pro1020= (c.3060T>C) in the general population?

FMN2 p.Pro1020= (c.3060T>C) is rare (popmax 0.907%, afr) (gnomAD).

FMN2 p.Pro1020=

c.3060T>C · rs762630179 · VCV2640157

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.907%, afr)

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 -20	GERP -1.8
Overall
CADD	0.929	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.907% African / African-American · 30/3,308 alleles

Filtering AF 0.653% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.567%

Overall 0.267% 341/127,946 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.907%	110
East Asian	0.778%	129
Middle Eastern	0.719%	139
Ashkenazi Jewishnot grpmax-eligible	0.518%	193
Remaining individualsnot grpmax-eligible	0.426%	235
South Asian	0.42%	238
European (non-Finnish)	0.225%	444
Finnishnot grpmax-eligible	0.136%	735
Admixed American	0.0679%	1,474

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.Pro1020=
Coding: c.3060T>C
MANE Select: NM_020066
dbSNP: rs762630179
Type: single nucleotide variant
Location: chr1:240207872 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.51 (gnomAD)
Structure: AlphaFold pLDDT 51.48 · 2 PDB
Residue 1020: 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-pro1020 (accessed [today's date]).

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