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. [p... See more...

Aliases for LHX1 Gene

Aliases for LHX1 Gene

  • LIM Homeobox 1 2 3 5
  • LIM/Homeobox Protein Lhx1 3 4
  • Homeobox Protein Lim-1 3 4
  • LIM Homeobox Protein 1 3 4
  • LIM-1 3 4
  • LIM1 3 4
  • 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 Chromosome 17Q12 Deletion Syndrome and Mayer-Rokitansky-Kuster-Hauser Syndrome. Among its related pathways are Neural Crest Differentiation and Ectoderm 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 Summary 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 , Rfam classification 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
GH17J036935 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE 756.9 +0.1 116 5 ZNF362 ZNF701 ZNF148 ZNF473 SP7 ZSCAN21 PRDM1 ZNF404 EGR1 KLF14 LHX1 LHX1-DT AATF ACACA ENSG00000276707
GH17J037088 Enhancer 1.4 VISTA FANTOM5 Ensembl ENCODE dbSUPER 10.6 +154.6 154588 7.5 CTCF ZNF362 MAFK ZNF687 ZNF384 PRDM10 RFX1 ZNF316 SCRT2 ELF1 LHX1 C17orf78 lnc-SYNRG-5 RPS2P49 ACACA
GH17J036978 Enhancer 1.4 VISTA UCNEbase Ensembl ENCODE 9.7 +43.1 43116 3 ZNF362 PRDM1 ZNF680 PKNOX1 ZNF512 ZEB2 ZXDB OSR2 PRDM4 KLF8 ENSG00000277911 AATF LHX1
GH17J036870 Enhancer 0.9 Ensembl ENCODE 11.5 -66.2 -66238 0.5 ZBTB6 MAFK TRIM24 ZBTB33 SMARCC1 ATF1 NFE2L2 CEBPB ZNF692 ZNF316 LHX1 piR-50437-285 piR-50437-286 LHX1-DT
GH17J037079 Enhancer 1 Ensembl ENCODE dbSUPER 10.6 +146.5 146501 7.8 POLR2A HLF CEBPG CEBPA RXRA CEBPB SCRT2 SCRT1 ATF3 MNT LHX1 lnc-SYNRG-5 ENSG00000278638 ACACA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX1 gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • E2F
  • p53

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)
Size:
7,834 bases
Orientation:
Plus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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:
  • Homeobox protein Lim-1 (LHX1_HUMAN)
  • LHX1 protein (Q58F18_HUMAN)

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

UniProtKB/Swiss-Prot Function:
Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.
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

Phenotypes From GWAS Catalog for LHX1 Gene

Gene Ontology (GO) - Molecular Function for LHX1 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 ISA --
GO:0001158 enhancer sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity ISS,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:
  • Lhx1 Lhx1<tm1Bhr>
  • Lhx1 Lhx1<tm1a(EUCOMM)Wtsi>
  • Lhx1 Lhx1<tm1Tmj>
  • Lhx1 Lhx1<tm3Bhr>

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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX1

Clone Products

No data available for Enzyme Numbers (IUBMB) 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:0005634 nucleus ISS,IBA --
GO:0005667 transcription factor complex IEA --
GO:0032991 protein-containing complex ISS,IEA --
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

SIGNOR curated interactions for LHX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for LHX1 Gene

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

Drugs & Compounds for LHX1 Gene

No Compound Related Data Available

Transcripts for LHX1 Gene

mRNA/cDNA for LHX1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX1

Clone 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
Regions:
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

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 32
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia LHX1 32
  • 94.01 (n)
dog
(Canis familiaris)
Mammalia LHX1 32
  • 93.02 (n)
rat
(Rattus norvegicus)
Mammalia Lhx1 32
  • 89 (n)
mouse
(Mus musculus)
Mammalia Lhx1 17 32
  • 88.67 (n)
chicken
(Gallus gallus)
Aves LHX1 32
  • 85.88 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx1 32
  • 79.34 (n)
Str.12750 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.1226 32
zebrafish
(Danio rerio)
Actinopterygii lhx1a 32 32
  • 76.73 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011134 32
  • 62.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 34 32
  • 60.24 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-11 34
  • 52 (a)
mec-3 34
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.9454 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9454 32
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)
Aminode:
Evolutionary constrained regions (ECRs) for LHX1: view image

Paralogs for LHX1 Gene

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

  • LHX1_HUMAN
  • Q58F18_HUMAN
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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LHX1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
chromosome 17q12 deletion syndrome
  • 17q12 microdeletion syndrome
mayer-rokitansky-kuster-hauser syndrome
  • mrkh syndrome
ureterocele
allan-herndon-dudley syndrome
  • ahds
- 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 56
  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 56
  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 56
  4. The Lim1 oncogene as a new therapeutic target for metastatic human renal cell carcinoma. (PMID: 30076415) Hamaidi I … Massfelder T (Oncogene 2019) 3 56
  5. Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina. (PMID: 28061432) Zhang W … Wang B (Oncotarget 2017) 3 56

Products for LHX1 Gene

Sources for LHX1 Gene