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Aliases for LHX4 Gene

Aliases for LHX4 Gene

  • LIM Homeobox 4 2 3 5
  • LIM Homeobox Protein 4 3 4
  • LIM/Homeobox Protein Lhx4 3
  • CPHD4 3

External Ids for LHX4 Gene

Previous GeneCards Identifiers for LHX4 Gene

  • GC01P177723
  • GC01P175627
  • GC01P176719
  • GC01P177438
  • GC01P176931
  • GC01P178466
  • GC01P180199
  • GC01P151430

Summaries for LHX4 Gene

Entrez Gene Summary for LHX4 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 involved in the control of differentiation and development of the pituitary gland. Mutations in this gene cause combined pituitary hormone deficiency 4. [provided by RefSeq, Dec 2010]

GeneCards Summary for LHX4 Gene

LHX4 (LIM Homeobox 4) is a Protein Coding gene. Diseases associated with LHX4 include Pituitary Hormone Deficiency, Combined, 4 and Pituitary Stalk Interruption Syndrome. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LHX3.

UniProtKB/Swiss-Prot for LHX4 Gene

  • May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

Gene Wiki entry for LHX4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX4 Gene

Genomics for LHX4 Gene

Regulatory Elements for LHX4 Gene

Enhancers for LHX4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G181132 2.1 FANTOM5 Ensembl ENCODE dbSUPER 44 +906.1 906113 4.4 DMAP1 YBX1 ZNF548 ZNF263 SP3 TBX21 ZFP41 MEF2D ZNF585B GLIS1 LHX4 IER5 ACBD6 KIAA1614 MR1 STX6 GC01M181116 LINC01732
GH01G181126 2 FANTOM5 Ensembl ENCODE dbSUPER 21.7 +900.5 900534 6.2 FEZF1 ZNF548 ZNF263 TBX21 MEF2D ZNF610 GLIS1 NBN NR2C1 KDM1A ACBD6 LHX4 KIAA1614 IER5 MR1 GC01M181116 LINC01732
GH01G181117 1.7 Ensembl ENCODE dbSUPER 20.3 +889.9 889879 3.3 CREB3L1 AGO1 FEZF1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 MEF2D LHX4 ACBD6 GC01M181116 LINC01732
GH01G181086 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +863.8 863760 11.6 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 IER5 MR1 ACBD6 KIAA1614 LHX4 STX6 GC01M181092 GC01M181116
GH01G179880 1.5 ENCODE dbSUPER 14.3 -346.0 -345982 4.7 CREB3L1 AGO1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 LHX4 TOR3A ENSG00000261831 TOR1AIP2 FAM163A AXDND1 ENSG00000272906 GC01P179900
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LHX4 on UCSC Golden Path with GeneCards custom track

Promoters for LHX4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000016526 1297 1001 FEZF1 GLI4 ZNF2 GLIS2 ZNF263 SP3 REST ZNF610 SMARCA4 ZSCAN16

Genomic Location for LHX4 Gene

180,228,803 bp from pter
180,278,982 bp from pter
50,180 bases
Plus strand

Genomic View for LHX4 Gene

Genes around LHX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX4 Gene

Proteins for LHX4 Gene

  • Protein details for LHX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM/homeobox protein Lhx4
    Protein Accession:
    Secondary Accessions:
    • Q8NHE0
    • Q8NHM1
    • Q8TCJ1
    • Q8WWX2
    • Q969W2

    Protein attributes for LHX4 Gene

    390 amino acids
    Molecular mass:
    43124 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB62817.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LHX4 Gene

neXtProt entry for LHX4 Gene

Post-translational modifications for LHX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX4 Gene

No data available for DME Specific Peptides for LHX4 Gene

Domains & Families for LHX4 Gene

Gene Families for LHX4 Gene

Protein Domains for LHX4 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LHX4: view

No data available for UniProtKB/Swiss-Prot for LHX4 Gene

Function for LHX4 Gene

Molecular function for LHX4 Gene

UniProtKB/Swiss-Prot Function:
May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

Gene Ontology (GO) - Molecular Function for LHX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LHX4: view
genes like me logo Genes that share phenotypes with LHX4: view

Human Phenotype Ontology for LHX4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LHX4 Gene

MGI Knock Outs for LHX4:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LHX4 Gene

Localization for LHX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX4 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 LHX4 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for LHX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LHX4: view

Pathways & Interactions for LHX4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LHX4 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:0008045 motor neuron axon guidance IEA --
GO:0009887 animal organ morphogenesis IEA --
genes like me logo Genes that share ontologies with LHX4: view

No data available for Pathways by source and SIGNOR curated interactions for LHX4 Gene

Transcripts for LHX4 Gene

mRNA/cDNA for LHX4 Gene

Unigene Clusters for LHX4 Gene

LIM homeobox 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LHX4 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6
SP1: -

Relevant External Links for LHX4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LHX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LHX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX4 Gene

This gene is overexpressed in Testis (x5.1).

NURSA nuclear receptor signaling pathways regulating expression of LHX4 Gene:


SOURCE GeneReport for Unigene cluster for LHX4 Gene:


Evidence on tissue expression from TISSUES for LHX4 Gene

  • Muscle(4)
  • Nervous system(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cheek
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • pituitary gland
  • skull
  • thyroid
  • tongue
  • breast
  • chest wall
  • clavicle
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • adrenal gland
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • urinary bladder
  • uterus
  • vagina
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood
  • blood vessel
  • coagulation system
  • hair
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with LHX4: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for LHX4 Gene

Orthologs for LHX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LHX4 34 35
  • 99.66 (n)
(Bos Taurus)
Mammalia LXH4 35
  • 99 (a)
LHX4 34
  • 95.04 (n)
(Canis familiaris)
Mammalia LHX4 34 35
  • 95.9 (n)
(Monodelphis domestica)
Mammalia LHX4 35
  • 95 (a)
(Mus musculus)
Mammalia Lhx4 34 16 35
  • 93.08 (n)
(Rattus norvegicus)
Mammalia Lhx4 34
  • 92.91 (n)
(Ornithorhynchus anatinus)
Mammalia LHX4 35
  • 83 (a)
(Gallus gallus)
Aves LHX4 34 35
  • 83.61 (n)
(Anolis carolinensis)
Reptilia LHX4 35
  • 94 (a)
(Danio rerio)
Actinopterygii lhx4 34 35
  • 74.94 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim3 36 35
  • 48 (a)
(Caenorhabditis elegans)
Secernentea ceh-14 36 35
  • 57 (a)
lim-6 36
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2190 35
  • 34 (a)
Species where no ortholog for LHX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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 LHX4 Gene

Gene Tree for LHX4 (if available)
Gene Tree for LHX4 (if available)

Paralogs for LHX4 Gene

Paralogs for LHX4 Gene

genes like me logo Genes that share paralogs with LHX4: view

Variants for LHX4 Gene

Sequence variations from dbSNP and Humsavar for LHX4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121912641 Pathogenic, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,271,856(+) GAAGG(C/G)CCAAA nc-transcript-variant, reference, missense
rs121912642 Pathogenic, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,266,393(+) ACAGG(C/T)GCTTC reference, missense
rs121912643 Pathogenic, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,271,497(+) GCAGC(G/T)GTCCT nc-transcript-variant, reference, missense
rs145433128 Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,274,571(+) ATCCT(A/C)CTTTT intron-variant, nc-transcript-variant, reference, missense
rs121912644 Pathogenic 180,274,568(+) ATCAT(A/C)CTCCT intron-variant, nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for LHX4 Gene

Variant ID Type Subtype PubMed ID
dgv474n100 CNV gain 25217958
dgv476n100 CNV gain 25217958
esv23910 CNV loss 19812545
esv2660683 CNV deletion 23128226
esv2661645 CNV deletion 23128226
esv29505 CNV loss 19812545
esv3588063 CNV loss 21293372
esv3588064 CNV loss 21293372
nsv1013076 CNV gain 25217958
nsv466239 CNV gain 19166990
nsv548345 CNV gain 21841781
nsv832004 CNV gain 17160897
nsv946527 CNV duplication 23825009

Variation tolerance for LHX4 Gene

Residual Variation Intolerance Score: 38.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.81; 93.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LHX4 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX4 Gene

Disorders for LHX4 Gene

MalaCards: The human disease database

(12) MalaCards diseases for LHX4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LHX4 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving LHX4 may be a cause of acute lymphoblastic leukemia. Translocation t(1;14)(q25;q32) with IGHG1. {ECO:0000269 PubMed:11567216}.
  • Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700]: Combined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD4 is characterized by complete or partial deficiencies of growth hormone, thyroid-stimulating hormone, luteinizing hormone, follicle stimulating hormone and adrenocorticotropic hormone. Clinical features include short stature, cerebellar defects, and small sella turcica. {ECO:0000269 PubMed:17527005, ECO:0000269 PubMed:18073311}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LHX4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with LHX4: view

No data available for Genatlas for LHX4 Gene

Publications for LHX4 Gene

  1. Syndromic short stature in patients with a germline mutation in the LIM homeobox LHX4. (PMID: 11567216) Machinis K. … Amselem S. (Am. J. Hum. Genet. 2001) 2 3 4 22 64
  2. A novel missense mutation (P366T) of the LHX4 gene causes severe combined pituitary hormone deficiency with pituitary hypoplasia, ectopic posterior lobe and a poorly developed sella turcica. (PMID: 17527005) Tajima T. … Fujieda K. (Endocr. J. 2007) 3 4 22 64
  3. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F. … Nebel A. (Mutat. Res. 2010) 3 46 64
  4. Mutation and gene copy number analyses of six pituitary transcription factor genes in 71 patients with combined pituitary hormone deficiency: identification of a single patient with LHX4 deletion. (PMID: 20534763) Dateki S. … Ogata T. (J. Clin. Endocrinol. Metab. 2010) 3 46 64
  5. Three novel missense mutations within the LHX4 gene are associated with variable pituitary hormone deficiencies. (PMID: 18073311) Pfaeffle R.W. … Rhodes S.J. (J. Clin. Endocrinol. Metab. 2008) 3 4 64

Products for LHX4 Gene

Sources for LHX4 Gene

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