Is FOXG1 p.Pro65= (c.195G>T) pathogenic?

FOXG1 p.Pro65= (c.195G>T) is classified Likely benign in FOXG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-24). No allele count reported in gnomAD v4.1 (AN 1,064,400); Associated with FOXG1 disorder.

What condition is associated with FOXG1 p.Pro65= (c.195G>T)?

FOXG1 p.Pro65= (c.195G>T) is associated with FOXG1 disorder (ClinVar).

How common is FOXG1 p.Pro65= (c.195G>T) in the general population?

FOXG1 p.Pro65= (c.195G>T) is no allele count reported in gnomAD v4.1 (AN 1,064,400) (gnomAD).

FOXG1 p.Pro65=

c.195G>T · rs774144312 · VCV1543906

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 1,064,400)

Conditions

FOXG1 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 2.6	GERP -0.87, phastCons 1
Overall
CADD	12.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,064,400). 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.Pro65=
Coding: c.195G>T
MANE Select: NM_005249
dbSNP: rs774144312
Type: single nucleotide variant
Location: chr14:28767474 (GRCh38)
Gene constraint: LOEUF 0.36 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.79 · 1 PDB
Residue 65: 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.Pro65Ser Uncertain significance ★ ⚠ same residue
FOXG1 p.Pro65_Gln71del Conflicting classifications of pathogenicity ★ same residue
FOXG1 p.Arg230Leu Likely pathogenic ★★★ same condition
FOXG1 p.Asn187Lys Pathogenic ★★★ same condition
FOXG1 p.Asn236Asp Likely pathogenic ★★★ same condition
FOXG1 p.Gly224Ser Likely pathogenic ★★★ same condition
FOXG1 p.Gly250Ser Likely pathogenic ★★★ same condition
FOXG1 p.Gly267Ser 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-pro65 (accessed [today's date]).

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