Is FMN2 p.Pro1048= (c.3144C>T) pathogenic?

FMN2 p.Pro1048= (c.3144C>T) is classified Likely benign in FMN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-05). Absent from gnomAD v4.1; Associated with FMN2-related disorder.

What condition is associated with FMN2 p.Pro1048= (c.3144C>T)?

FMN2 p.Pro1048= (c.3144C>T) is associated with FMN2-related disorder (ClinVar).

How common is FMN2 p.Pro1048= (c.3144C>T) in the general population?

FMN2 p.Pro1048= (c.3144C>T) is absent from gnomAD v4.1 (gnomAD).

FMN2 p.Pro1048=

c.3144C>T · rs1666487002 · VCV3029532

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 540,874)

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 -1.4
Overall
CADD	4.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 540,874). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FMN2
Protein: p.Pro1048=
Coding: c.3144C>T
MANE Select: NM_020066
dbSNP: rs1666487002
Type: single nucleotide variant
Location: chr1:240207956 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.51 (gnomAD)
Structure: AlphaFold pLDDT 51.48 · 2 PDB
Residue 1048: 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-pro1048 (accessed [today's date]).

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