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LHX9 LIM homeobox 9 [ Homo sapiens (human) ]

Gene ID: 56956, updated on 3-Mar-2026
Official Symbol
LHX9provided by HGNC
Official Full Name
LIM homeobox 9provided by HGNC
Primary source
HGNC:HGNC:14222
See related
Ensembl:ENSG00000143355 MIM:606066; AllianceGenome:HGNC:14222
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a member of the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Expression
Biased expression in ovary (RPKM 2.6), testis (RPKM 0.9) and 1 other tissue See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See LHX9 in Genome Data Viewer
Location:
1q31.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (197912464..197935478)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (197171857..197194877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197881594..197904608)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene DENN domain containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1662 Neighboring gene Sharpr-MPRA regulatory region 12429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197757007-197757507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197769368-197770108 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197771590-197772329 Neighboring gene family with sequence similarity 204 member B, pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197779872-197780608 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197782608-197783566 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197783567-197784524 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:197859970-197860527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197887073-197887799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197890605-197891127 Neighboring gene chromosome 1 open reading frame 53 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:198001212-198001386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:198025825-198026449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2284 Neighboring gene Sharpr-MPRA regulatory region 4677 Neighboring gene proline rich 13 pseudogene 1 Neighboring gene NIMA related kinase 7 Neighboring gene VISTA enhancer hs1322 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:198283627-198284283 Neighboring gene NANOG hESC enhancer GRCh37_chr1:198392710-198393375 Neighboring gene uncharacterized LOC105371677

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease. Okutomo K, et al. Respir Investig, 2022 Jan. PMID 34548271
  2. Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY gonadal agenesis and dysgenesis. Ottolenghi C, et al. J Clin Endocrinol Metab, 2001 Jun. PMID 11397841
  3. Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood. Vladimirova V, et al. Neoplasia, 2009 Jul. PMID 19568415, Free PMC Article
  4. LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis. Luo X, et al. Aging (Albany NY), 2021 Sep 17. PMID 34536269, Free PMC Article
  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. Zhao H, et al. J Transl Med, 2023 Nov 18. PMID 37980488, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Transcription factor LHX9 (LIM Homeobox 9) enhances pyruvate kinase PKM2 activity to induce glycolytic metabolic reprogramming in cancer stem cells, promoting gastric cancer progression.
    Title: Transcription factor LHX9 (LIM Homeobox 9) enhances pyruvate kinase PKM2 activity to induce glycolytic metabolic reprogramming in cancer stem cells, promoting gastric cancer progression.
  2. LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis.
    Title: LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis.
  3. Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease.
    Title: Increased LHX9 expression in alveolar epithelial type 2 cells of patients with chronic obstructive pulmonary disease.
  4. that Smurf1 promotes Lhx9 ubiquitylation and is involved in testosterone production in Leydig cells directly
    Title: Smad ubiquitylation regulatory factor 1 promotes LIM-homeobox gene 9 degradation and represses testosterone production in Leydig cells.
  5. LHX9 gene is frequently silenced in pediatric malignant astrocytomas
    Title: Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood.
  6. Lhx9 and Lhx1 serve as a binary switch in controlling the rostral versus caudal longitudinal turning of the caudal commissural axons. Lhx1 determines caudal turning and Lhx9 triggers rostral turning.
    Title: Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1.
Submit: New GeneRIF Correction

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in dorsal spinal cord interneuron anterior axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
LIM/homeobox protein Lhx9
Names
LIM homeobox protein 9

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001014434.2 → NP_001014434.1  LIM/homeobox protein Lhx9 isoform 2

    See identical proteins and their annotated locations for NP_001014434.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1, resulting in a protein that maintains the reading frame but has a shorter N-terminus.
    Source sequence(s)
    AA316988, AJ277915, AL590115, AY273889
    Consensus CDS
    CCDS30962.1
    UniProtKB/Swiss-Prot
    Q9NQ69
    Related
    ENSP00000356360.3, ENST00000367390.7
    Conserved Domains (3) summary
    cd09377
    Location:120 → 178
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:52 → 115
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:262 → 315
    Homeobox; Homeobox domain

  2. NM_001370213.1 → NP_001357142.1  LIM/homeobox protein Lhx9 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL590115
    Related
    ENSP00000356361.1, ENST00000367391.5
    Conserved Domains (3) summary
    cd09377
    Location:129 → 187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    smart00389
    Location:267 → 312
    HOX; Homeodomain

  3. NM_001410927.1 → NP_001397856.1  LIM/homeobox protein Lhx9 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL590115
    Consensus CDS
    CCDS91139.1
    UniProtKB/TrEMBL
    H0YL54
    Related
    ENSP00000453064.1, ENST00000561173.5

  4. NM_020204.3 → NP_064589.2  LIM/homeobox protein Lhx9 isoform 1

    See identical proteins and their annotated locations for NP_064589.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL590115, AY273889
    Consensus CDS
    CCDS1393.1
    UniProtKB/Swiss-Prot
    Q5VUE2, Q5VUE3, Q5VUE6, Q86UH2, Q9BYU6, Q9NQ69, Q9NQ70
    Related
    ENSP00000356357.4, ENST00000367387.6
    Conserved Domains (3) summary
    cd09377
    Location:129 → 187
    LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
    cd09469
    Location:61 → 124
    LIM1_Lhx2; The first LIM domain of Lhx2
    pfam00046
    Location:271 → 324
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    197912464..197935478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509781.3 → XP_011508083.2  LIM/homeobox protein Lhx9 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    197171857..197194877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337758.1 → XP_054193733.1  LIM/homeobox protein Lhx9 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQ69.3 GenPept UniProtKB/Swiss-Prot:Q9NQ69

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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