Is FOXL2 p.Pro310fs (c.927del) pathogenic?

FOXL2 p.Pro310fs (c.927del) is classified Likely pathogenic in FOXL2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-04). No gnomAD frequency available for this variant; Associated with blepharophimosis, ptosis, and epicanthus inversus syndrome.

What condition is associated with FOXL2 p.Pro310fs (c.927del)?

FOXL2 p.Pro310fs (c.927del) is associated with blepharophimosis, ptosis, and epicanthus inversus syndrome (ClinVar).

How common is FOXL2 p.Pro310fs (c.927del) in the general population?

FOXL2 p.Pro310fs (c.927del) is no gnomAD frequency available for this variant (gnomAD).

FOXL2 p.Pro310fs

c.927del · rs2473811785 · VCV2572197

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

blepharophimosis, ptosis, and epicanthus inversus syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.3	GERP 3.1, phastCons 1
Region caveats
Repeat context	tandem	(GGC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: FOXL2
Protein: p.Pro310fs
Coding: c.927del
MANE Select: NM_023067
dbSNP: rs2473811785
Type: Deletion
Location: chr3:138945796 (GRCh38)
Gene constraint: LOEUF 1.913 · pLI 0.03 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.89 · 2 PDB
Residue 310: the 'disordered' region

Full FOXL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

blepharophimosis, ptosis, and epicanthus inversus syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FOXL2 p.Gly269fs Pathogenic ★★ same condition
FOXL2 p.Ala221fs Pathogenic ★ same condition
FOXL2 p.Ala225fs Pathogenic ★ same condition
FOXL2 p.Ala227fs Pathogenic ★ same condition
FOXL2 p.Ala229fs Pathogenic ★ same condition
FOXL2 p.Ala283fs Pathogenic ★ same condition
FOXL2 p.Ala328fs Pathogenic ★ same condition
FOXL2 p.Gly250fs Pathogenic ★ 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/foxl2-p-pro310fs (accessed [today's date]).

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