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Aliases for LHX3 Gene

Aliases for LHX3 Gene

  • LIM Homeobox 3 2 3 5
  • LIM Homeobox Protein 3 3 4
  • LIM/Homeodomain Protein LHX3 3
  • LIM/Homeobox Protein Lhx3 3
  • M2-LHX3 3
  • CPHD3 3
  • LIM3 3

External Ids for LHX3 Gene

Previous GeneCards Identifiers for LHX3 Gene

  • GC09M130237
  • GC09M130859
  • GC09M132611
  • GC09M134527
  • GC09M136314
  • GC09M138227
  • GC09M139088
  • GC09M108552

Summaries for LHX3 Gene

Entrez Gene Summary for LHX3 Gene

  • This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for LHX3 Gene

LHX3 (LIM Homeobox 3) is a Protein Coding gene. Diseases associated with LHX3 include Pituitary Hormone Deficiency, Combined, 3 and Hypothyroidism Due To Deficient Transcription Factors Involved In Pituitary Development Or Function. Among its related pathways are DAG and IP3 signaling. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and transcription factor activity, RNA polymerase II transcription factor binding. An important paralog of this gene is LHX4.

UniProtKB/Swiss-Prot for LHX3 Gene

  • Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system. Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1.

Gene Wiki entry for LHX3 Gene

Additional gene information for LHX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX3 Gene

Genomics for LHX3 Gene

GeneHancer (GH) Regulatory Elements for LHX3 Gene

Promoters and enhancers for LHX3 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
GH09J136205 Promoter 1 EPDnew 650.7 0.0 -20 0.1 ZNF792 ARID4B BACH1 SIN3A ZNF48 ZSCAN9 RARA GATAD1 ZNF143 EZH2 LHX3 PIR32039
GH09J136203 Promoter 0.6 EPDnew 650.7 +2.0 1951 0.1 EZH2 LHX3 ENSG00000275329
GH09J136189 Enhancer 0.8 FANTOM5 18.2 +15.4 15368 0.5 KLF1 KLF17 ZIC2 HIC1 ZNF335 ZFHX2 GLIS2 ZNF366 PATZ1 ZNF600 LHX3 CAMSAP1 QSOX2 ENSG00000275329
GH09J136224 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.1 -20.6 -20597 3.1 HDGF RB1 ZSCAN4 ARID4B SIN3A ZNF2 IRF4 RAD21 RFX5 SCRT2 LHX3 NACC2 PMPCA ENTR1 QSOX2 OBP2A PIR36610 GC09M136222
GH09J136266 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.1 -62.8 -62821 2.3 HDGF PKNOX1 ARNT ARID4B SIN3A GLI4 YY1 GTF3C2 ZNF121 ZNF213 LOC101928722 SEC16A ENTR1 ANAPC2 GPSM1 MAN1B1 SNHG7 LHX3 NDOR1 ENSG00000283769
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX3 gene promoter:
  • Sp1

Genomic Locations for LHX3 Gene

Genomic Locations for LHX3 Gene
chr9:136,196,250-136,205,128
(GRCh38/hg38)
Size:
8,879 bases
Orientation:
Minus strand
chr9:139,088,096-139,096,955
(GRCh37/hg19)
Size:
8,860 bases
Orientation:
Minus strand

Genomic View for LHX3 Gene

Genes around LHX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX3 Gene

Proteins for LHX3 Gene

  • Protein details for LHX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBR4-LHX3_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx3
    Protein Accession:
    Q9UBR4
    Secondary Accessions:
    • Q5TB39
    • Q5TB40
    • Q9NZB5
    • Q9P0I8
    • Q9P0I9

    Protein attributes for LHX3 Gene

    Size:
    397 amino acids
    Molecular mass:
    43358 Da
    Quaternary structure:
    • Interacts with POU1F1 (PubMed:26612202). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1 (By similarity).

    Alternative splice isoforms for LHX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LHX3 Gene

Post-translational modifications for LHX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX3 Gene

No data available for DME Specific Peptides for LHX3 Gene

Domains & Families for LHX3 Gene

Gene Families for LHX3 Gene

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

Protein Domains for LHX3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UBR4

UniProtKB/Swiss-Prot:

LHX3_HUMAN :
  • The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.
Domain:
  • The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.
genes like me logo Genes that share domains with LHX3: view

Function for LHX3 Gene

Molecular function for LHX3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system. Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1.

Phenotypes From GWAS Catalog for LHX3 Gene

Gene Ontology (GO) - Molecular Function for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001085 RNA polymerase II transcription factor binding IPI 26612202
genes like me logo Genes that share ontologies with LHX3: view
genes like me logo Genes that share phenotypes with LHX3: view

Human Phenotype Ontology for LHX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LHX3 Gene

MGI Knock Outs for LHX3:
  • Lhx3 Lhx3<tm1Lmgd>

Animal Model Products

Targeted motifs for LHX3 Gene
HOMER Transcription Factor Regulatory Elements motif LHX3
  • Consensus sequence: ADBTAATTAR Submotif: canonical Cell Type: Neuron GEO ID: GSE31456

Clone Products

  • Addgene plasmids for LHX3

No data available for Enzyme Numbers (IUBMB) , miRNA and Transcription Factor Targets for LHX3 Gene

Localization for LHX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX3 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 LHX3 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with LHX3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LHX3 Gene

Pathways & Interactions for LHX3 Gene

genes like me logo Genes that share pathways with LHX3: view

Pathways by source for LHX3 Gene

1 GeneGo (Thomson Reuters) pathway for LHX3 Gene

Gene Ontology (GO) - Biological Process for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001890 placenta development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0008045 motor neuron axon guidance IEA --
genes like me logo Genes that share ontologies with LHX3: view

No data available for SIGNOR curated interactions for LHX3 Gene

Drugs & Compounds for LHX3 Gene

(2) Drugs for LHX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for LHX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LHX3: view

Transcripts for LHX3 Gene

mRNA/cDNA for LHX3 Gene

(4) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(16) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LHX3 Gene

LIM homeobox 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for LHX3

Alternative Splicing Database (ASD) splice patterns (SP) for LHX3 Gene

No ASD Table

Relevant External Links for LHX3 Gene

GeneLoc Exon Structure for
LHX3
ECgene alternative splicing isoforms for
LHX3

Expression for LHX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LHX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX3 Gene

This gene is overexpressed in Pituitary (x52.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LHX3 Gene



NURSA nuclear receptor signaling pathways regulating expression of LHX3 Gene:

LHX3

SOURCE GeneReport for Unigene cluster for LHX3 Gene:

Hs.148427

Evidence on tissue expression from TISSUES for LHX3 Gene

  • Nervous system(3.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • face
  • head
  • hypothalamus
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • pharynx
  • pituitary gland
  • skull
  • thyroid
Thorax:
  • breast
  • heart
  • lung
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • liver
  • small intestine
Pelvis:
  • ovary
  • penis
  • prostate
  • rectum
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
genes like me logo Genes that share expression patterns with LHX3: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for LHX3 Gene

Orthologs for LHX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX3 34 33
  • 99.5 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LHX3 34 33
  • 91.54 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LHX3 34 33
  • 90.3 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx3 33
  • 88.47 (n)
mouse
(Mus musculus)
Mammalia Lhx3 16 34 33
  • 88.06 (n)
oppossum
(Monodelphis domestica)
Mammalia LHX3 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves LHX3 34 33
  • 80.14 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LHX3 34
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xlim-3 33
zebrafish
(Danio rerio)
Actinopterygii lhx3 33
  • 73.85 (n)
CABZ01029738.1 34
  • 63 (a)
OneToOne
-- 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009088 33
  • 62.72 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim3 34 35 33
  • 61.64 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-14 34 35
  • 44 (a)
OneToMany
lim-6 35
  • 38 (a)
lim-4 35
  • 38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2190 34
  • 36 (a)
OneToMany
Cin.13878 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13878 33
Species where no ortholog for LHX3 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for LHX3 Gene

ENSEMBL:
Gene Tree for LHX3 (if available)
TreeFam:
Gene Tree for LHX3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LHX3: view image

Paralogs for LHX3 Gene

Paralogs for LHX3 Gene

(19) SIMAP similar genes for LHX3 Gene using alignment to 6 proteins:

  • LHX3_HUMAN
  • F1T0D5_HUMAN
  • F1T0D7_HUMAN
  • F1T0D8_HUMAN
  • F1T0D9_HUMAN
  • Q9HBU2_HUMAN
genes like me logo Genes that share paralogs with LHX3: view

Variants for LHX3 Gene

Sequence variations from dbSNP and Humsavar for LHX3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1013813191 uncertain-significance, Combined Pituitary Hormone Deficiency, Recessive 136,197,164(-) G/T 3_prime_UTR_variant
rs1040918379 uncertain-significance, Combined Pituitary Hormone Deficiency, Recessive 136,196,771(-) G/A 3_prime_UTR_variant
rs104894117 pathogenic, Pituitary hormone deficiency, combined 3, Pituitary hormone deficiency, combined, 3 (CPHD3) [MIM:221750] 136,199,800(-) T/C coding_sequence_variant, missense_variant
rs12237402 uncertain-significance, Combined Pituitary Hormone Deficiency, Recessive 136,196,534(-) C/T 3_prime_UTR_variant
rs137854503 pathogenic, Pituitary hormone deficiency, combined 3, Pituitary hormone deficiency, combined, 3 (CPHD3) [MIM:221750] 136,198,798(-) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for LHX3 Gene

Variant ID Type Subtype PubMed ID
dgv13001n54 CNV gain 21841781
nsv1040564 CNV gain 25217958
nsv469917 CNV loss 18288195
nsv479494 CNV novel sequence insertion 20440878
nsv825173 CNV gain 20364138
nsv951202 CNV deletion 24416366

Variation tolerance for LHX3 Gene

Residual Variation Intolerance Score: 37.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.90; 18.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX3 Gene

Human Gene Mutation Database (HGMD)
LHX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX3 Gene

Disorders for LHX3 Gene

MalaCards: The human disease database

(14) MalaCards diseases for LHX3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LHX3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LHX3_HUMAN
  • Pituitary hormone deficiency, combined, 3 (CPHD3) [MIM:221750]: Combined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD3 is characterized by a complete deficit in all but one (adrenocorticotropin) anterior pituitary hormone and a rigid cervical spine leading to limited head rotation. {ECO:0000269 PubMed:10835633, ECO:0000269 PubMed:17327381, ECO:0000269 PubMed:28302169}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LHX3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LHX3: view

No data available for Genatlas for LHX3 Gene

Publications for LHX3 Gene

  1. Differential activation of pituitary hormone genes by human Lhx3 isoforms with distinct DNA binding properties. (PMID: 10598593) Sloop KW … Rhodes SJ (Molecular endocrinology (Baltimore, Md.) 1999) 2 3 4 22 58
  2. Four novel mutations of the LHX3 gene cause combined pituitary hormone deficiencies with or without limited neck rotation. (PMID: 17327381) Pfaeffle RW … Rhodes SJ (The Journal of clinical endocrinology and metabolism 2007) 3 4 22 58
  3. Serine/threonine/tyrosine phosphorylation of the LHX3 LIM-homeodomain transcription factor. (PMID: 15517599) Parker GE … Rhodes SJ (Journal of cellular biochemistry 2005) 3 4 22 58
  4. Mutations in LHX3 result in a new syndrome revealed by combined pituitary hormone deficiency. (PMID: 10835633) Netchine I … Amselem S (Nature genetics 2000) 3 4 22 58
  5. Analysis of the human LHX3 neuroendocrine transcription factor gene and mapping to the subtelomeric region of chromosome 9. (PMID: 10717474) Sloop KW … Rhodes SJ (Gene 2000) 2 3 22 58

Products for LHX3 Gene

Sources for LHX3 Gene

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