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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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BARHL1
BarH like homeobox 1
Chromosome 9 · 9q34.13
NCBI Gene: 56751Ensembl: ENSG00000125492.11HGNC: HGNC:953UniProt: Q9BZE3
12PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificRNA polymerase II transcription regulatory region sequence-specific DNA bindingregulation of transcription by RNA polymerase IIvenous thromboembolismlaryngeal carcinomaIschemic strokecoronary artery disease
✦AI Summary

BARHL1 (BarH like homeobox 1) is a homeodomain transcription factor that plays a crucial role in cerebellar development and neuronal differentiation. The protein functions as a sequence-specific DNA-binding transcription factor regulating RNA polymerase II-mediated transcription 1. BARHL1 is exclusively expressed in restricted domains of the developing central nervous system, including the diencephalon, dorsal mesencephalon, cerebellar anlage, and dorsal spinal cord interneurons 12. The gene is essential for cerebellar granule cell precursor migration, survival, and differentiation, with expression activated by the transcription factor Math1 in BMP response pathways 12. Mechanistically, BARHL1 controls granule neuron progenitor exit from their germinative niche partly through direct inhibition of T-cell factor (TCF) and regulation of Hes genes 3. In disease contexts, BARHL1 expression is associated with favorable prognosis in medulloblastoma, with higher expression correlating with decreased tumor mitotic activity, increased neuronal differentiation, and prolonged survival in both mouse models and human patients 4. While initially considered a candidate gene for Joubert syndrome due to its chr9 location and cerebellar expression pattern, mutation analysis has excluded BARHL1 from direct pathogenic involvement in this condition 5.

Sources cited
1
BARHL1 is a homeodomain transcription factor expressed exclusively in restricted CNS domains including diencephalon, mesencephalon, cerebellar anlage, and spinal cord
PMID: 16307728
2
BARHL1 expression is induced by Math1 in BMP response pathways and shows differential transcription levels in functionally restricted CNS domains
PMID: 16384683
3
BARHL1 controls granule neuron progenitor exit from germinative niche through direct TCF inhibition and Hes gene regulation
PMID: 38860486
4
Higher BARHL1 expression in medulloblastoma is associated with decreased mitotic activity, increased neuronal differentiation, and prolonged survival
PMID: 21602885
5
BARHL1 was excluded from direct pathogenic involvement in Joubert syndrome through mutation analysis
PMID: 11807898
Disease Associationsⓘ20
venous thromboembolismOpen Targets
0.31Weak
laryngeal carcinomaOpen Targets
0.28Weak
Ischemic strokeOpen Targets
0.21Weak
coronary artery diseaseOpen Targets
0.20Weak
medulloblastomaOpen Targets
0.07Suggestive
deafnessOpen Targets
0.06Suggestive
schizophreniaOpen Targets
0.05Suggestive
joint diseaseOpen Targets
0.05Suggestive
head injuryOpen Targets
0.05Suggestive
Non-syndromic genetic deafnessOpen Targets
0.05Suggestive
malunion fractureOpen Targets
0.05Suggestive
autosomal dominant nonsyndromic hearing lossOpen Targets
0.05Suggestive
diabetes mellitusOpen Targets
0.05Suggestive
autosomal recessive nonsyndromic hearing loss 9Open Targets
0.05Suggestive
hearing loss, autosomal recessiveOpen Targets
0.04Suggestive
crush injuryOpen Targets
0.04Suggestive
central nervous system cancerOpen Targets
0.04Suggestive
ulcerative colitisOpen Targets
0.03Suggestive
ataxia telangiectasiaOpen Targets
0.02Suggestive
HypercholesterolemiaOpen Targets
0.02Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ATOH1Protein interaction85%LHX9Protein interaction77%BARHL2Co-mentioned in literature30%
Tissue Expression6 tissues
Brain
100%
Ovary
0%
Bone Marrow
0%
Heart
0%
Liver
0%
Lung
0%
Gene Interaction Network
Click a node to explore
BARHL1ATOH1LHX9BARHL2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9BZE3
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.42Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.18 [0.09–0.42]
RankingsWhere BARHL1 stands among ~20K protein-coding genes
  • #16,395of 20,598
    Most Researched12
  • #2,208of 17,882
    Most Constrained (LOEUF)0.42 · top quartile
Genes detectedBARHL1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
BARHL1 homeogene, the human ortholog of the mouse Barhl1 involved in cerebellum development, shows regional and cellular specificities in restricted domains of developing human central nervous system.
PMID: 16307728
Biochem Biophys Res Commun · 2006
1.00
2
Differential transcription of Barhl1 homeobox gene in restricted functional domains of the central nervous system suggests a role in brain patterning.
PMID: 16384683
Int J Dev Neurosci · 2006
0.90
3
Barhl1, a gene belonging to a new subfamily of mammalian homeobox genes, is expressed in migrating neurons of the CNS.
PMID: 10814725
Hum Mol Genet · 2000
0.80
4
Expression of BARHL1 in medulloblastoma is associated with prolonged survival in mice and humans.
PMID: 21602885
Oncogene · 2011
0.70
5
Evolutionary relationships and diversification of barhl genes within retinal cell lineages.
PMID: 22103894
BMC Evol Biol · 2011
0.60