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.... See more...

Aliases for LHX9 Gene

Aliases for LHX9 Gene

  • LIM Homeobox 9 2 3 5
  • LIM/Homeobox Protein Lhx9 3 4
  • LIM Homeobox Protein 9 3 4
  • LHX9 5

External Ids for LHX9 Gene

Previous GeneCards Identifiers for LHX9 Gene

  • GC01P195608
  • GC01P193340
  • GC01P194348
  • GC01P195169
  • GC01P194613
  • GC01P196148
  • GC01P197881
  • GC01P169037

Summaries for LHX9 Gene

Entrez Gene Summary for LHX9 Gene

  • 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]

GeneCards Summary for LHX9 Gene

LHX9 (LIM Homeobox 9) is a Protein Coding gene. Diseases associated with LHX9 include Gonadal Agenesis and 46,Xy Sex Reversal. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and transcription corepressor activity. An important paralog of this gene is LHX2.

UniProtKB/Swiss-Prot Summary for LHX9 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LHX9 Gene

Genomics for LHX9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LHX9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J197915 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 600.4 +5.7 5746 3.9 RNF2 HNRNPL CTCF PRDM10 ZNF629 ZNF512 IKZF1 ZNF692 PRDM1 ZIC2 LHX9 HSALNG0009472 NEK7
GH01J197913 Promoter 0.9 EPDnew Ensembl 600.7 +0.7 699 1.6 POLR2A EZH2 CBX8 SMARCA4 LHX9 C1orf53 HSALNG0009472 NEK7
GH01J197781 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 10.1 -129.0 -129001 3.4 PRDM1 REST DPF2 HDAC1 SOX6 FOXJ2 CEBPB HES1 GATA3 SPI1 DENND1B C1orf53 LHX9 piR-58308-026
GH01J197838 Enhancer 1 FANTOM5 Ensembl ENCODE 10.9 -70.3 -70302 8 GATAD2A CEBPA SOX13 CEBPB FOXA2 MCM5 FOS ZKSCAN1 FOSL1 FOXP1 DENND1B C1orf53 LHX9 RPL24P5 piR-38716-010 piR-58308-026
GH01J197620 Enhancer 0.8 Ensembl 11.2 -291.0 -291002 0.6 GATAD2A FOXA1 RXRB SP1 GABPA CEBPA FOXK2 SOX13 RFX3 CEBPB C1orf53 LHX9 DENND1B piR-38655-001 ENSG00000207139 CRB1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LHX9

Top Transcription factor binding sites by QIAGEN in the LHX9 gene promoter:
  • E47
  • E4BP4
  • Nkx2-5
  • STAT5B

Genomic Locations for LHX9 Gene

Genomic Locations for LHX9 Gene
chr1:197,911,902-197,935,478
(GRCh38/hg38)
Size:
23,577 bases
Orientation:
Plus strand
chr1:197,881,037-197,904,608
(GRCh37/hg19)
Size:
23,572 bases
Orientation:
Plus strand

Genomic View for LHX9 Gene

Genes around LHX9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX9 Gene

Proteins for LHX9 Gene

  • Protein details for LHX9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQ69-LHX9_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx9
    Protein Accession:
    Q9NQ69
    Secondary Accessions:
    • Q5VUE2
    • Q5VUE3
    • Q5VUE6
    • Q86UH2
    • Q9BYU6
    • Q9NQ70

    Protein attributes for LHX9 Gene

    Size:
    397 amino acids
    Molecular mass:
    43976 Da
    Quaternary structure:
    • Interacts with LDB1 and LDB2.

    Three dimensional structures from OCA and Proteopedia for LHX9 Gene

    Alternative splice isoforms for LHX9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LHX9 Gene

Post-translational modifications for LHX9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for LHX9
  • Boster Bio Antibodies for LHX9
  • Santa Cruz Biotechnology (SCBT) Antibodies for LHX9

No data available for DME Specific Peptides for LHX9 Gene

Domains & Families for LHX9 Gene

Gene Families for LHX9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for LHX9 Gene

InterPro:
Blocks:
  • Zn-binding protein, LIM
ProtoNet:

Suggested Antigen Peptide Sequences for LHX9 Gene

GenScript: Design optimal peptide antigens:
  • LIM/homeobox protein Lhx9 (LHX9_HUMAN)
  • LIM homeobox 9 (Q5VUE8_HUMAN)
genes like me logo Genes that share domains with LHX9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LHX9 Gene

Function for LHX9 Gene

Molecular function for LHX9 Gene

UniProtKB/Swiss-Prot Function:
Involved in gonadal development.

Phenotypes From GWAS Catalog for LHX9 Gene

Gene Ontology (GO) - Molecular Function for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LHX9: view
genes like me logo Genes that share phenotypes with LHX9: view

Animal Models for LHX9 Gene

MGI Knock Outs for LHX9:
  • Lhx9 Lhx9<tm1Dodd>
  • Lhx9 Lhx9<tm1Lmgd>
  • Lhx9 Lhx9<tm1.1(cre/ERT2)Gan>
  • Lhx9 Lhx9<tm1And>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX9

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LHX9 Gene

Localization for LHX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX9 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LHX9 gene
Compartment Confidence
nucleus 4
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with LHX9: view

Pathways & Interactions for LHX9 Gene

PathCards logo

SuperPathways for LHX9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0008283 cell proliferation IEA --
GO:0008584 male gonad development IEA --
GO:0008585 female gonad development IEA --
GO:0030182 neuron differentiation IBA 21873635
genes like me logo Genes that share ontologies with LHX9: view

No data available for Pathways by source and SIGNOR curated interactions for LHX9 Gene

Drugs & Compounds for LHX9 Gene

No Compound Related Data Available

Transcripts for LHX9 Gene

mRNA/cDNA for LHX9 Gene

3 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX9

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12
SP1: -
SP2: - - -
SP3: - - -
SP4: -
SP5:

Relevant External Links for LHX9 Gene

GeneLoc Exon Structure for
LHX9

Expression for LHX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LHX9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX9 Gene

This gene is overexpressed in Ovary (x20.8) and Testis (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LHX9 Gene



Protein tissue co-expression partners for LHX9 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LHX9

SOURCE GeneReport for Unigene cluster for LHX9 Gene:

Hs.442578

Evidence on tissue expression from TISSUES for LHX9 Gene

  • Nervous system(3.3)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with LHX9: view

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX9 Gene

Orthologs for LHX9 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LHX9 30 31
  • 99.83 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LHX9 30 31
  • 96.14 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lhx9 30 17 31
  • 94.71 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LHX9 30 31
  • 94.44 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lhx9 30
  • 94.37 (n)
Oppossum
(Monodelphis domestica)
Mammalia LHX9 31
  • 91 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LHX9 31
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LHX9 30 31
  • 88.27 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LHX9 31
  • 91 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lhx9 30
  • 77.89 (n)
African clawed frog
(Xenopus laevis)
Amphibia lhx9-A 30
Zebrafish
(Danio rerio)
Actinopterygii lhx9 30 31
  • 80.68 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta ap 31
  • 35 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ttx-3 31
  • 31 (a)
OneToMany
Species where no ortholog for LHX9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for LHX9 Gene

ENSEMBL:
Gene Tree for LHX9 (if available)
TreeFam:
Gene Tree for LHX9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LHX9: view image

Paralogs for LHX9 Gene

(14) SIMAP similar genes for LHX9 Gene using alignment to 3 proteins:

  • LHX9_HUMAN
  • H0Y330_HUMAN
  • H0YL54_HUMAN
genes like me logo Genes that share paralogs with LHX9: view

Variants for LHX9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LHX9 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
777332 Benign: not provided 197,929,226(+) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for LHX9 Gene

Structural Variations from Database of Genomic Variants (DGV) for LHX9 Gene

Variant ID Type Subtype PubMed ID
dgv44e201 CNV deletion 23290073
dgv558n100 CNV gain 25217958
esv1002483 CNV deletion 20482838
esv2143475 CNV deletion 18987734
esv2520814 CNV deletion 19546169
esv2660965 CNV deletion 23128226
esv2721095 CNV deletion 23290073
esv2721117 CNV deletion 23290073
esv2762214 CNV gain 21179565
esv3513 CNV loss 18987735
esv3544755 CNV deletion 23714750
esv3588508 CNV loss 21293372
esv8658 CNV loss 19470904
nsv1071825 CNV deletion 25765185
nsv1110664 CNV insertion 24896259
nsv1122440 CNV deletion 24896259
nsv506971 OTHER sequence alteration 20534489
nsv958115 CNV deletion 24416366

Variation tolerance for LHX9 Gene

Residual Variation Intolerance Score: 29.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.34; 26.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX9 Gene

Disorders for LHX9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LHX9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
gonadal agenesis
46,xy sex reversal
  • 46 xy gonadal dysgenesis
- elite association - COSMIC cancer census association via MalaCards
Search LHX9 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with LHX9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LHX9 Gene

Publications for LHX9 Gene

  1. Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1. (PMID: 19545367) Avraham O … Klar A (Neural development 2009) 3 23
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  3. Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY gonadal agenesis and dysgenesis. (PMID: 11397841) Ottolenghi C … McElreavey K (The Journal of clinical endocrinology and metabolism 2001) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Smad ubiquitylation regulatory factor 1 promotes LIM-homeobox gene 9 degradation and represses testosterone production in Leydig cells. (PMID: 29565736) Hu F … Zhang L (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2018) 3

Products for LHX9 Gene

Sources for LHX9 Gene