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Aliases for LHX1 Gene

Aliases for LHX1 Gene

  • LIM Homeobox 1 2 3 5
  • Homeobox Protein Lim-1 3 4
  • LIM Homeobox Protein 1 3 4
  • LIM-1 3 4
  • LIM1 3 4
  • LIM/Homeobox Protein Lhx1 3
  • HLim-1 4

External Ids for LHX1 Gene

Previous GeneCards Identifiers for LHX1 Gene

  • GC17P034678
  • GC17P037247
  • GC17P035025
  • GC17P035490
  • GC17P032368
  • GC17P035294
  • GC17P031230

Summaries for LHX1 Gene

Entrez Gene Summary for LHX1 Gene

  • This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]

GeneCards Summary for LHX1 Gene

LHX1 (LIM Homeobox 1) is a Protein Coding gene. Diseases associated with LHX1 include Mayer-Rokitansky-Kuster-Hauser Syndrome and Chromosome 17Q12 Deletion Syndrome. Among its related pathways are Ectoderm Differentiation and Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription corepressor activity. An important paralog of this gene is LHX5.

UniProtKB/Swiss-Prot for LHX1 Gene

  • Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Gene Wiki entry for LHX1 Gene

Additional gene information for LHX1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX1 Gene

Genomics for LHX1 Gene

GeneHancer (GH) Regulatory Elements for LHX1 Gene

Promoters and enhancers for LHX1 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
GH17I036934 Enhancer 1.3 FANTOM5 ENCODE 557 -0.7 -738 3.1 ATF1 SIN3A GLI4 ZNF2 ZNF48 GLIS2 ZNF213 ZNF416 KLF7 SP3 LHX1 LHX1-DT AATF ACACA GC17P036813
GH17I036938 Enhancer 0.6 ENCODE 550.8 +1.6 1584 0.2 SUZ12 ETV1 SIN3A REST E2F1 EGR1 GABPB1 EZH2 LHX1-DT LHX1 ENSG00000276707
GH17I036946 Enhancer 0.6 ENCODE 550.8 +1.4 1354 0.2 SUZ12 ETV1 SIN3A REST EGR1 GABPB1 EZH2 ZBTB20 LHX1 LHX1-DT ENSG00000276707
GH17I036939 Enhancer 0.5 ENCODE 550.8 +1.9 1914 0.3 E2F1 EGR1 SUZ12 SIN3A EZH2 LHX1-DT LHX1 ENSG00000276707
GH17I036937 Enhancer 0.5 ENCODE 550.8 +1.0 1014 0.2 CTBP2 ZNF398 ZBTB26 ZBTB20 EZH2 LHX1-DT LHX1 ENSG00000276707
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LHX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX1 gene promoter:

Genomic Locations for LHX1 Gene

Genomic Locations for LHX1 Gene
chr17:36,936,785-36,944,615
(GRCh38/hg38)
Size:
7,831 bases
Orientation:
Plus strand
chr17:35,294,084-35,301,917
(GRCh37/hg19)

Genomic View for LHX1 Gene

Genes around LHX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX1 Gene

Proteins for LHX1 Gene

  • Protein details for LHX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48742-LHX1_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx1
    Protein Accession:
    P48742
    Secondary Accessions:
    • Q3MIW0

    Protein attributes for LHX1 Gene

    Size:
    406 amino acids
    Molecular mass:
    44808 Da
    Quaternary structure:
    • Interacts with LDB1 via the tandem LIM domains.

neXtProt entry for LHX1 Gene

Post-translational modifications for LHX1 Gene

No Post-translational modifications

Other Protein References for LHX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LHX1 Gene

Domains & Families for LHX1 Gene

Gene Families for LHX1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for LHX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P48742

UniProtKB/Swiss-Prot:

LHX1_HUMAN :
  • The LIM domains exert a negative regulatory function and disruption of the LIM domains produces an activated form. In addition, two activation domains and a negative regulatory domain exist C-terminally to the homeobox (By similarity).
Domain:
  • The LIM domains exert a negative regulatory function and disruption of the LIM domains produces an activated form. In addition, two activation domains and a negative regulatory domain exist C-terminally to the homeobox (By similarity).
genes like me logo Genes that share domains with LHX1: view

Function for LHX1 Gene

Molecular function for LHX1 Gene

GENATLAS Biochemistry:
LIM motif containing protein kinase,putative transcription factor,expressed in brain,thymus and tonsillar tissue,involved in transcriptional regulation of neural and lymphoid cell
UniProtKB/Swiss-Prot Function:
Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Gene Ontology (GO) - Molecular Function for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity ISS,IEA --
GO:0003714 transcription corepressor activity ISS --
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LHX1: view
genes like me logo Genes that share phenotypes with LHX1: view

Human Phenotype Ontology for LHX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LHX1 Gene

MGI Knock Outs for LHX1:

Animal Model Products

CRISPR Products

miRNA for LHX1 Gene

Targeted motifs for LHX1 Gene
HOMER Transcription Factor Regulatory Elements motif LHX1
  • Consensus sequence: NNYTAATTAR Submotif: canonical Cell Type: EmbryoCarcinoma GEO ID: GSE70957

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog and Transcription Factor Targets for LHX1 Gene

Localization for LHX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX1 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 LHX1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus ISS --
GO:0043234 protein complex IEA,ISS --
genes like me logo Genes that share ontologies with LHX1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LHX1 Gene

Pathways & Interactions for LHX1 Gene

genes like me logo Genes that share pathways with LHX1: view

Pathways by source for LHX1 Gene

Interacting Proteins for LHX1 Gene

Gene Ontology (GO) - Biological Process for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001655 urogenital system development ISS --
GO:0001656 metanephros development IEA --
GO:0001657 ureteric bud development IEA,ISS --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001702 gastrulation with mouth forming second ISS,IEA --
genes like me logo Genes that share ontologies with LHX1: view

No data available for SIGNOR curated interactions for LHX1 Gene

Drugs & Compounds for LHX1 Gene

No Compound Related Data Available

Transcripts for LHX1 Gene

Unigene Clusters for LHX1 Gene

LIM homeobox 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX1 Gene

No ASD Table

Relevant External Links for LHX1 Gene

GeneLoc Exon Structure for
LHX1
ECgene alternative splicing isoforms for
LHX1

Expression for LHX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LHX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x21.0), Brain - Cerebellum (x20.7), and Kidney - Cortex (x6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LHX1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LHX1 Gene:

LHX1

SOURCE GeneReport for Unigene cluster for LHX1 Gene:

Hs.443727

mRNA Expression by UniProt/SwissProt for LHX1 Gene:

P48742-LHX1_HUMAN
Tissue specificity: Expressed in the brain, thymus, and tonsils. Expressed in samples from patients with chronic myeloid leukemia (CML) and in 58% of acute myeloid leukemia (AML) cell lines.

Evidence on tissue expression from TISSUES for LHX1 Gene

  • Nervous system(4.5)
  • Kidney(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
Thorax:
  • heart
Abdomen:
  • kidney
  • pancreas
Pelvis:
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with LHX1: view

Primer Products

No data available for Protein differential expression in normal tissues and Protein tissue co-expression partners for LHX1 Gene

Orthologs for LHX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX1 33
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia LHX1 33
  • 94.01 (n)
dog
(Canis familiaris)
Mammalia LHX1 33
  • 93.02 (n)
rat
(Rattus norvegicus)
Mammalia Lhx1 33
  • 89 (n)
mouse
(Mus musculus)
Mammalia Lhx1 33 16
  • 88.67 (n)
chicken
(Gallus gallus)
Aves LHX1 33
  • 85.88 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx1 33
  • 79.34 (n)
Str.12750 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.1226 33
zebrafish
(Danio rerio)
Actinopterygii lhx1a 33
  • 76.73 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011134 33
  • 62.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 35 33
  • 60.24 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-11 35
  • 52 (a)
mec-3 35
  • 38 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9454 33
Species where no ortholog for LHX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 LHX1 Gene

ENSEMBL:
Gene Tree for LHX1 (if available)
TreeFam:
Gene Tree for LHX1 (if available)

Paralogs for LHX1 Gene

Paralogs for LHX1 Gene

(18) SIMAP similar genes for LHX1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LHX1: view

Variants for LHX1 Gene

Sequence variations from dbSNP and Humsavar for LHX1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000296484 -- 36,941,031(+) C/A/T intron_variant
rs1000875830 -- 36,938,834(+) AGAG/AG intron_variant
rs1001296353 -- 36,939,606(+) G/C intron_variant
rs1001349723 -- 36,939,353(+) T/C intron_variant
rs1001727182 -- 36,943,378(+) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for LHX1 Gene

Variant ID Type Subtype PubMed ID
esv3640480 CNV gain 21293372
nsv833430 CNV gain+loss 17160897

Variation tolerance for LHX1 Gene

Residual Variation Intolerance Score: 45.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.02; 50.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX1 Gene

Human Gene Mutation Database (HGMD)
LHX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX1 Gene

Disorders for LHX1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LHX1 Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mayer-rokitansky-kuster-hauser syndrome
  • mrkh syndrome
chromosome 17q12 deletion syndrome
  • 17q12 microdeletion syndrome
ureterocele
- elite association - COSMIC cancer census association via MalaCards
Search LHX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX1

genes like me logo Genes that share disorders with LHX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LHX1 Gene

Publications for LHX1 Gene

  1. Cloning, expression, and chromosomal localization to 11p12-13 of a human LIM/HOMEOBOX gene, hLim-1. (PMID: 9212161) Dong WF … Minden MD (DNA and cell biology 1997) 2 3 4 58
  2. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 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. Genetic analysis of Mayer-Rokitansky-Kuster-Hauser syndrome in a large cohort of families. (PMID: 28600106) Williams LS … Layman LC (Fertility and sterility 2017) 3 58

Products for LHX1 Gene

Sources for LHX1 Gene

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