FOXG1

Chr 14

forkhead box G1

Also known as: BF1, BF2, FHKL3, FKH2, FKHL1, FKHL2, FKHL3, FKHL4

NCBI Gene: 2290ENSG00000176165UniProt: P55316

This locus encodes a member of the fork-head transcription factor family. The encoded protein, which functions as a transcriptional repressor, is highly expressed in neural tissues during brain development. Mutations at this locus have been associated with Rett syndrome and a diverse spectrum of neurodevelopmental disorders defined as part of the FOXG1 syndrome. This gene is disregulated in many types of cancer and is the target of multiple microRNAs that regulate the proliferation of tumor cells. [provided by RefSeq, Jul 2020]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtRett syndrome congenital variant

Clinical highlights

Gene-disease validity (ClinGen)
FOXG1 disorder · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
2
Active trials
66
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.33
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — FOXG1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.33LOEUF
pLI 0.944
Z-score 2.79
OE 0.00 (0.00–0.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
3.49Z-score
OE missense 0.36 (0.30–0.43)
84 obs / 234.3 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.33)
0≤0.351.4
Missense OE?0.36 (0.30–0.43)
0≤0.61.4
Synonymous OE?1.29
0≤1.21.6
LoF obs/exp: 0 / 9.1Missense obs/exp: 84 / 234.3Syn Z: -2.38

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

FOXG1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

VCEP specificationsRett/Angelman-like DisordersReleased
Specifications ↗Panel ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients