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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LHX9
LIM homeobox 9
Chromosome 1 · 1q31.3
NCBI Gene: 56956Ensembl: ENSG00000143355.16HGNC: HGNC:14222UniProt: H0YL54
25PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingprotein bindingRNA polymerase II transcription regulatory region sequence-specific DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificneurodegenerative diseasenerve plexus diseaserisk-taking behaviourcarpal tunnel syndrome
✦AI Summary

LHX9 (LIM homeobox 9) is a transcription factor primarily known for its role in gonadal development 1. As a DNA-binding protein with sequence-specific double-stranded DNA binding activity, LHX9 functions as an RNA polymerase II-specific transcription factor. During embryonic development, LHX9 is expressed in multiple brain regions, particularly in the developing pineal gland, where it is essential for early pineal gland formation 1. Deletion of Lhx9 in mice results in pineal hypoplasia and causes postnatal hydrocephalus in approximately 70% of mutants by 5-8 weeks of age, indicating LHX9 contributes to maintaining normal brain structure 1. In gonadal development, LHX9 is expressed as a coelomic epithelial marker and is downregulated during the transition to supporting gonadal cell differentiation 2. Beyond developmental roles, LHX9 has emerged as a tumor suppressor. In gliomas, LHX9 expression is decreased, and it functions as a p53-binding protein that inhibits cancer progression by suppressing glycolysis through downregulation of PGK1 3. In gastric cancer, LHX9 expression is elevated and promotes tumor progression through PKM2-mediated glycolytic reprogramming in cancer stem cells 4. Additionally, LHX9 provides neuroprotection to embryonic midbrain and striatal neurons against oxidative stress-induced DNA damage 5. These functions establish LHX9 as a multifunctional transcription factor with critical roles in development, neuroprotection, and cancer biology.

Sources cited
1
LHX9 is essential for pineal gland development; Lhx9 deletion causes pineal hypoplasia and postnatal hydrocephalus in ~70% of mutant mice
PMID: 24647753
2
LHX9 is a coelomic epithelial marker that is downregulated during early supporting gonadal cell differentiation
PMID: 40102860
3
LHX9 is a p53-binding protein; decreased LHX9 in gliomas promotes cancer progression through glycolysis via PGK1 upregulation
PMID: 34536269
4
LHX9 is highly expressed in gastric cancer and promotes progression by enhancing PKM2 activity and glycolytic reprogramming in cancer stem cells
PMID: 37980488
5
LHX9 provides neuroprotective effects on embryonic midbrain and striatal neurons against oxidative stress-induced DNA damage
PMID: 31451602
6
LHX9 gene is conserved across species and mapped to human chromosome 1q; no mutations found in gonadal dysgenesis patients studied
PMID: 11397841
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.52Moderate
nerve plexus diseaseOpen Targets
0.32Weak
risk-taking behaviourOpen Targets
0.31Weak
carpal tunnel syndromeOpen Targets
0.29Weak
hypertrophic cardiomyopathyOpen Targets
0.23Weak
pituitary stalk interruption syndromeOpen Targets
0.13Weak
macular degenerationOpen Targets
0.12Weak
Phenotypic abnormalityOpen Targets
0.12Weak
urinary tract obstructionOpen Targets
0.12Weak
genetic disorderOpen Targets
0.12Weak
myopathyOpen Targets
0.09Suggestive
age-related macular degenerationOpen Targets
0.09Suggestive
COVID-19Open Targets
0.08Suggestive
46,XX gonadal dysgenesisOpen Targets
0.08Suggestive
gliomaOpen Targets
0.08Suggestive
primary ovarian insufficiencyOpen Targets
0.08Suggestive
osteosarcomaOpen Targets
0.08Suggestive
gastric cancerOpen Targets
0.08Suggestive
degeneration of macula and posterior poleOpen Targets
0.07Suggestive
ovarian neoplasmOpen Targets
0.07Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
OTPShared pathway100%LHX4Shared pathway100%LHX5Shared pathway100%NIF3L1Shared pathway100%POU4F1Protein interaction81%LDB1Protein interaction81%
Tissue Expression6 tissues
Ovary
100%
Heart
7%
Liver
5%
Brain
4%
Lung
1%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
LHX9OTPLHX4LHX5NIF3L1POU4F1LDB1
PROTEIN STRUCTURE
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PDB2DMQ · NMR
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.41Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.24 [0.14–0.41]
RankingsWhere LHX9 stands among ~20K protein-coding genes
  • #13,008of 20,598
    Most Researched25
  • #2,123of 17,882
    Most Constrained (LOEUF)0.41 · top quartile
Genes detectedLHX9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus.
PMID: 24647753
Brain Struct Funct · 2015
1.00
2
LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis.
PMID: 34536269
Aging (Albany NY) · 2021
0.90
3
FOXL2 drives the differentiation of supporting gonadal cells in early ovarian development.
PMID: 40102860
Reprod Biol Endocrinol · 2025
0.80
4
Identification of a DNA-methylome-based signature for prognosis prediction in driver gene-negative lung adenocarcinoma.
PMID: 38548216
Cancer Lett · 2024
0.70
5
Transcription factor LHX9 (LIM Homeobox 9) enhances pyruvate kinase PKM2 activity to induce glycolytic metabolic reprogramming in cancer stem cells, promoting gastric cancer progression.
PMID: 37980488
J Transl Med · 2023
0.60