Gene
FOXG1
forkhead box G1
- HGNC 3811(opens in a new tab)
- Ensembl gene ENSG00000176165(opens in a new tab)
- NCBI Gene 2290(opens in a new tab)
Summary
- Cytogenetic location
- 14q12
- Coordinates
- Chromosome 14: 28,766,787–28,770,277 (GRCh38)
- Exons
- 1 exon across 3.5 kb
- Protein
- 489 amino acids
- Also known as
- HFK2, QIN, BF1, HFK1, HFK3, HBF-3
- Previous symbols
- FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A
- MANE Select transcript
- ENST00000313071.7NM_005249.5
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Epilepsy (Full Panel)
- Atypical Rett Syndrome
A neurodevelopmental disorder that is diagnosed when a child presents with a Rett-like syndrome but does not fulfill all the diagnostic criteria for typical Rett syndrome (classic/typical RTT).
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
How FOXG1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Variants with a page
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 3.5 kb of the gene's 3.5 kb; 1,470 of those bases code for the protein.
How a genome test reads FOXG1
172
positions in FOXG1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 3.5 kb of FOXG1, introns included, not only the 3.5 kb of exons.
Variants with a page (14)
The FOXG1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| E154Gfs*301 | c.460dup | Exon 1 | 28,767,732 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| G224S | c.670G>A | Exon 1 | 28,767,949 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| G250S | c.748G>A | Exon 1 | 28,768,027 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| G267S | c.799G>A | Exon 1 | 28,768,078 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| I207T | c.620T>C | Exon 1 | 28,767,899 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| I229L | c.685A>C | Exon 1 | 28,767,964 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| L189V | c.565C>G | Exon 1 | 28,767,844 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| M191I | c.573G>A | Exon 1 | 28,767,852 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| N187K | c.561C>A | Exon 1 | 28,767,840 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| N236D | c.706A>G | Exon 1 | 28,767,985 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
Traits linked to FOXG1
The Human Phenotype Ontology lists these as features of the rare conditions FOXG1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Absent speech development
- Delayed ability to sit
- Delayed ability to walk
- Delayed speech and language development
- Global developmental delay
- Intellectual disability, severe
- Poor social interactions
- Seizure affecting one half of brain
Show 45 more traits
- Simplified gyral pattern
- Underdeveloped frontal lobe
- Encephalopathy
- Epilepsy
- Loss of developmental milestones
- Repetitive movements
- Underdevelopment of part of brain called corpus callosum
- Abnormality of coordination
- Agenesis of corpus callosum
- Decreased reflex response
- Difficulty sleeping
- EEG abnormality
- EEG with multifocal slow activity
- Inappropriate crying
- Intellectual disability
- Irritability
- Teeth grinding
- Abnormal corpus callosum morphology
- Abnormal gait
- Abnormal myelination
- Ataxia
- Attention deficit
- Autism
- Behavioral abnormality
- Brain degeneration
- Degeneration of cerebrum
- Delayed CNS myelination
- Diminished deep tendon reflex
- Disorder of involuntary muscle movements
- Fewer and broader ridges in brain
- Hypsarrhythmia
- Impulsivity
- Involuntary movements
- Jerking
- Mental deterioration
- Tremor
- Unsteady walk
- Repeated seizures without recovery between them
- Apraxia
- Chorea
- Dystonia
- Involuntary writhing movements in fingers, hands, toes, and feet
- Motor delay
- Poor eye contact
- Tongue thrusting
Abnormality of head or neck
- Progressively abnormally small cranium
- Abnormally small head
- Bulbous nose
- Depressed nasal bridge
- Drooping lower lip
- Eye folds
- Tented mouth
- Abnormally large tongue
Show 13 more traits
- Big lower jaw
- Downward slanting of the opening between the eyelids
- Excessive salivation
- Fullness of eyelids
- Narrow opening between the eyelids
- Prominent metopic ridge
- Short nose
- Smooth philtrum
- Failure of development of between one and six teeth
- High forehead
- Drooling
- Midface retrusion
- Thin red part of the upper lip
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). FOXG1 gene: forkhead box G1. Retrieved 17 October 2026, from https://dantelabs.com/genes/foxg1
Dante Labs. FOXG1 gene: forkhead box G1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/foxg1
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