Is FOXG1 p.Pro111fs (c.332del) pathogenic?

FOXG1 p.Pro111fs (c.332del) is classified Likely pathogenic in FOXG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-04). No allele count reported in gnomAD v4.1 (AN 1,255,418); Associated with FOXG1 disorder.

What condition is associated with FOXG1 p.Pro111fs (c.332del)?

FOXG1 p.Pro111fs (c.332del) is associated with FOXG1 disorder (ClinVar).

How common is FOXG1 p.Pro111fs (c.332del) in the general population?

FOXG1 p.Pro111fs (c.332del) is no allele count reported in gnomAD v4.1 (AN 1,255,418) (gnomAD).

FOXG1 p.Pro111fs

c.332del · VCV4854824

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,255,418)

Conditions

FOXG1 disorder

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 0.28	GERP -2.8, phastCons 0.99
Region caveats
Repeat context	tandem	(CGC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,255,418). 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: FOXG1
Protein: p.Pro111fs
Coding: c.332del
MANE Select: NM_005249
Type: Deletion
Location: chr14:28767610 (GRCh38)
Gene constraint: LOEUF 0.36 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.79 · 1 PDB
Residue 111: the 'disordered' region

Full FOXG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

FOXG1 disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For FOXG1 syndrome (Orphanet):

Onset: Neonatal

Similar variants

FOXG1 p.Pro111_Pro112dup Conflicting classifications of pathogenicity ★ same residue
FOXG1 p.Gln86fs Pathogenic ★★★ same condition
FOXG1 p.Gln70_Pro76del Benign ★★★ same condition
FOXG1 p.Gln70_Pro77del Benign ★★★ same condition
FOXG1 p.Gln70_Pro78del Benign ★★★ same condition
FOXG1 p.Pro80del Benign ★★★ same condition
FOXG1 p.Arg320fs Pathogenic ★★ same condition
FOXG1 p.Arg88fs 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/foxg1-p-pro111fs (accessed [today's date]).

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