Is FMN2 p.Gly950= (c.2850A>G) pathogenic?

FMN2 p.Gly950= (c.2850A>G) is classified Benign in FMN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-08). Low-frequency (popmax 1.39%, eas); Associated with FMN2-related disorder.

What condition is associated with FMN2 p.Gly950= (c.2850A>G)?

FMN2 p.Gly950= (c.2850A>G) is associated with FMN2-related disorder (ClinVar).

How common is FMN2 p.Gly950= (c.2850A>G) in the general population?

FMN2 p.Gly950= (c.2850A>G) is low-frequency (popmax 1.39%, eas) (gnomAD).

FMN2 p.Gly950=

c.2850A>G · rs1378644181 · VCV3041627

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.39%, eas)

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 -2
Overall
CADD	3.045	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.39% East Asian · 509/36,584 alleles

Filtering AF 1.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.25%

Overall 1.15% 15,796/1,376,438 alleles · low-frequency exomes 14,814/1,287,446 · genomes 982/88,992 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	4.13%	24
Ashkenazi Jewishnot grpmax-eligible	1.9%	53
Remaining individualsnot grpmax-eligible	1.5%	66
East Asiangrpmax	1.39%	72
South Asian	1.1%	91
European (non-Finnish)	1.01%	99
Middle Eastern	0.989%	101
Admixed American	0.725%	138
African / African-American	0.365%	274
Amishnot grpmax-eligible	0.16%	624

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Gly950=
Coding: c.2850A>G
MANE Select: NM_020066
dbSNP: rs1378644181
Type: single nucleotide variant
Location: chr1:240207662 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.51 (gnomAD)
Structure: AlphaFold pLDDT 51.48 · 2 PDB
Residue 950: 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-gly950 (accessed [today's date]).

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