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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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LHX1
LIM homeobox 1
Chromosome 17 · 17q12
NCBI Gene: 3975Ensembl: ENSG00000273706.6HGNC: HGNC:6593UniProt: P48742
37PubMed Papers
0Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingsequence-specific double-stranded DNA bindingDNA-binding transcription factor activityRNA polymerase II transcription regulatory region sequence-specific DNA binding
✦AI Summary

LHX1 (LIM homeobox 1) is a sequence-specific DNA-binding transcription factor essential for embryonic development and organogenesis. During early development, LHX1 marks the anterior visceral endoderm and is critical for gastrulation axis formation 1. LHX1 plays a central role in kidney development, where it is expressed in PAX8+ renal vesicles that differentiate into nephron structures including podocytes, proximal tubules, and distal tubules 2. The gene is also vital for embryonic head development, where LHX1 regulates morphogenetic movements through modulation of WNT signaling and transcriptional control of target genes via interactions with transcription factor complexes 3. Clinically, LHX1 dysfunction is implicated in multiple pathologies. Loss-of-function variants in LHX1 and deletions in the 17q12 region (containing LHX1) are associated with Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome, characterized by uterine and vaginal agenesis 4. In pathological contexts, LHX1 can function as an oncogenic driver; in esophageal squamous cell carcinoma, LHX1 overexpression forms a positive feedback loop with UHRF1 and NKX2-5, promoting tumor growth through epigenetic dysregulation 5. Aberrant LHX1 expression also contributes to preterm birth by inducing endoplasmic reticulum stress via IRE-1/XBP1/CHOP pathway activation 6. Additionally, LHX1-derived long non-coding RNA (LHX1-DT) suppresses renal cell carcinoma progression through miR-590-5p sponging 7. LHX1 is recognized as an oncogenic homeoprotein in medulloblastoma 8.

Sources cited
1
LHX1 is expressed in PAX8+ renal vesicles during nephron differentiation from human pluripotent stem cell-derived nephron progenitor cells
PMID: 26458176
2
LHX1 is a conserved marker of the anterior visceral endoderm during early primate gastrulation and axis formation
PMID: 35709828
3
LHX1 deletions (17q12) are associated with Mayer-Rokitansky-Küster-Hauser syndrome, a congenital condition causing uterine and vaginal agenesis
PMID: 38699388
4
LHX1 forms a positive feedback loop with UHRF1 and NKX2-5 in esophageal squamous cell carcinoma, promoting oncogenic gene expression through epigenetic dysregulation
PMID: 40307990
5
LHX1 is a transcription factor that regulates morphogenetic movement of head tissue precursors and modulates WNT signaling during embryonic head development
PMID: 31111476
6
LHX1 is one of eleven travelling homeoproteins associated with medulloblastoma pathogenesis
PMID: 40760093
7
LHX1 overexpression induces endoplasmic reticulum stress via IRE-1/XBP1/CHOP pathway activation and promotes preterm birth
PMID: 39027525
8
LHX1-DT long non-coding RNA is stabilized by m6A reader IGF2BP2 and inhibits renal cell carcinoma progression by sponging miR-590-5p
PMID: 40527909
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
LDB2Protein interaction86%SSBP3Protein interaction86%SSBP4Protein interaction86%CCNKProtein interaction84%NEUROG2Protein interaction81%EVX1Protein interaction76%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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LHX1LDB2SSBP3SSBP4CCNKNEUROG2EVX1
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt P48742
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.55Moderately Constrained
pLIⓘ
0.92Intolerant
Observed/Expected LoF0.32 [0.19–0.55]
RankingsWhere LHX1 stands among ~20K protein-coding genes
  • #10,644of 20,598
    Most Researched37
  • #3,551of 17,882
    Most Constrained (LOEUF)0.55 · top quartile
Genes detectedLHX1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Nephron organoids derived from human pluripotent stem cells model kidney development and injury.
PMID: 26458176
Nat Biotechnol · 2015
1.00
2
Spatial profiling of early primate gastrulation in utero.
PMID: 35709828
Nature · 2022
0.90
3
Genetics of Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome: advancements and implications.
PMID: 38699388
Front Endocrinol (Lausanne) · 2024
0.80
4
NKX2-5/LHX1 and UHRF1 Establishing a Positive Feedback Regulatory Circuitry Drives Esophageal Squamous Cell Carcinoma through Epigenetic Dysregulation.
PMID: 40307990
Adv Sci (Weinh) · 2025
0.70
5
Mechanistic insights from the LHX1-driven molecular network in building the embryonic head.
PMID: 31111476
Dev Growth Differ · 2019
0.60