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Aliases for LHX9 Gene

Aliases for LHX9 Gene

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

External Ids for LHX9 Gene

Previous GeneCards Identifiers for LHX9 Gene

  • GC01P195608
  • GC01P193340
  • GC01P194348
  • GC01P195169
  • GC01P194613
  • GC01P196148
  • 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 Frasier Syndrome. 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 for LHX9 Gene

  • Involved in gonadal development.

Additional gene information for LHX9 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX9 Gene

Genomics for LHX9 Gene

GeneHancer (GH) Regulatory Elements for LHX9 Gene

Promoters and enhancers for LHX9 Gene
GeneHancer (GH) Identifier GH Type GH
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 650.4 +5.1 5093 2.6 GLI4 ZNF2 ZNF48 YY1 GLIS2 KLF7 KLF13 SP3 TSHZ1 SMARCB1 LHX9 GC01P198155
GH01J197912 Promoter 0.7 EPDnew 650.7 +0.6 559 0.1 SUZ12 EZH2 LHX9 GC01P198155
GH01J197781 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 10.1 -128.7 -128748 2.7 HDAC1 MEIS2 TEAD4 TAL1 ZBTB40 CHAMP1 ZNF664 GATA3 FOS SMARCE1 DENND1B C1orf53 LHX9
GH01J198465 Enhancer 0.9 Ensembl ENCODE 10.7 +553.6 553642 0.9 CTCF CEBPG BRCA1 RAD21 RFX5 GATA3 ZNF143 SMC3 SMARCA5 ZNF654 ATP6V1G3 LHX9 C1orf53 LOC105371677 GC01P198285
GH01J198461 Enhancer 0.7 FANTOM5 ENCODE 10.7 +550.7 550701 1.3 STAT1 JUND MAFF JUN MAFK ATP6V1G3 LHX9 C1orf53 LOC105371677 GC01P198285
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LHX9 Gene

Genomic Locations for LHX9 Gene
23,577 bases
Plus strand
23,572 bases
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:
    Recommended name:
    LIM/homeobox protein Lhx9
    Protein Accession:
    Secondary Accessions:
    • Q5VUE2
    • Q5VUE3
    • Q5VUE6
    • Q86UH2
    • Q9BYU6
    • Q9NQ70

    Protein attributes for LHX9 Gene

    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


neXtProt entry for LHX9 Gene

Post-translational modifications for LHX9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LHX9 Gene

Domains & Families for LHX9 Gene

Gene Families for LHX9 Gene

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

Protein Domains for LHX9 Gene

Suggested Antigen Peptide Sequences for LHX9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LHX9: view

No data available for 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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IEA --
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<tm1Lmgd>
  • Lhx9 Lhx9<tm1Dodd>
  • Lhx9 Lhx9<tm1And>
  • Lhx9 Lhx9<tm1.1(cre/ERT2)Gan>

Animal Model Products

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

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 5
cytosol 2

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:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LHX9: view

Pathways & Interactions 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:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0008283 cell proliferation IEA --
GO:0008584 male gonad development IEA --
GO:0008585 female gonad development IEA --
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

Unigene Clusters for LHX9 Gene

LIM homeobox 9:
Representative Sequences:

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: -

Relevant External Links for LHX9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LHX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of LHX9 Gene:


SOURCE GeneReport for Unigene cluster for LHX9 Gene:


Evidence on tissue expression from TISSUES for LHX9 Gene

  • Nervous system(2.9)
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
(Pan troglodytes)
Mammalia LHX9 34 33
  • 99.83 (n)
(Canis familiaris)
Mammalia LHX9 34 33
  • 96.14 (n)
(Mus musculus)
Mammalia Lhx9 16 34 33
  • 94.71 (n)
(Bos Taurus)
Mammalia LHX9 34 33
  • 94.44 (n)
(Rattus norvegicus)
Mammalia Lhx9 33
  • 94.37 (n)
(Monodelphis domestica)
Mammalia LHX9 34
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia LHX9 34
  • 67 (a)
(Gallus gallus)
Aves LHX9 34 33
  • 88.27 (n)
(Anolis carolinensis)
Reptilia LHX9 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx9 33
  • 77.89 (n)
African clawed frog
(Xenopus laevis)
Amphibia lhx9-A 33
(Danio rerio)
Actinopterygii lhx9 34 33
  • 80.68 (n)
fruit fly
(Drosophila melanogaster)
Insecta ap 34
  • 35 (a)
(Caenorhabditis elegans)
Secernentea ttx-3 34
  • 31 (a)
Species where no ortholog for LHX9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

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

Paralogs for LHX9 Gene

Paralogs for LHX9 Gene

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

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

Variants for LHX9 Gene

Sequence variations from dbSNP and Humsavar for LHX9 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000093342 -- 197,934,122(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000188878 -- 197,916,527(+) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000355963 -- 197,911,458(+) G/A upstream_transcript_variant
rs1000640398 -- 197,929,495(+) T/A 3_prime_UTR_variant, intron_variant
rs1000709761 -- 197,922,742(+) T/A intron_variant

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

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
frasier syndrome
  • fs
- elite association - COSMIC cancer census association via MalaCards
Search LHX9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX9

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 22 58
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  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 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Widespread macromolecular interaction perturbations in human genetic disorders. (PMID: 25910212) Sahni N … Vidal M (Cell 2015) 3 58

Products for LHX9 Gene

Sources for LHX9 Gene

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