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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. Gene Ontology (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. Binds preferentially to methylated DNA (PubMed:28473536).

Gene Wiki entry for LHX4 Gene

Additional gene information 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

GeneHancer (GH) Regulatory Elements for LHX4 Gene

Promoters and enhancers for LHX4 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
GH01J180229 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 658.8 +1.2 1205 1.3 INSM2 SIN3A GLI4 ZNF2 ZNF335 GLIS2 EGR1 SCRT2 EGR2 SP3 LHX4 GC01P180228 QSOX1 GC01P180221 PIR35029
GH01J179880 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 63.3 -346.0 -345981 4.7 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A TOR1AIP1 ENSG00000272906 LHX4 CEP350 ACBD6 ENSG00000261831 TOR1AIP2 FAM163A AXDND1 GC01P179900
GH01J181086 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 63.3 +863.8 863760 11.6 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 ZNF263 PIR40361 GC01M181092 GC01P181092 LHX4 ACBD6 IER5 ENSG00000225359 MR1 STX6 GC01M181116
GH01J181126 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 80 +900.5 900533 6.2 CLOCK FEZF1 IRF4 ZNF213 E2F8 ZNF548 ZC3H11A MEF2D ZNF610 NBN LHX4 ACBD6 IER5 MR1 KIAA1614 GC01M181116 LINC01732
GH01J181132 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 59.9 +906.1 906113 4.4 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B NEUROD1 SIN3A YBX1 DMAP1 LHX4 ACBD6 IER5 ENSG00000225359 ENSG00000232309 KIAA1614 MR1 STX6 GC01M181116 LINC01732
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX4 gene promoter:
  • Sp1
  • Bach1
  • SRF (504 AA)
  • SRF
  • MyoD
  • GR
  • GR-alpha
  • p300

Genomic Locations for LHX4 Gene

Genomic Locations for LHX4 Gene
50,180 bases
Plus strand
49,960 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

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

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. Binds preferentially to methylated DNA (PubMed:28473536).

Gene Ontology (GO) - Molecular Function for LHX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IDA 28473536
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

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:0006366 transcription by RNA polymerase II IEA --
GO:0008045 motor neuron axon guidance 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

Drugs & Compounds for LHX4 Gene

No Compound Related Data Available

Transcripts for LHX4 Gene

mRNA/cDNA for LHX4 Gene

(5) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(15) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LHX4 Gene

LIM homeobox 4:
Representative Sequences:

Clone Products

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

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 33
  • 99.66 (n)
(Bos Taurus)
Mammalia LXH4 34
  • 99 (a)
LHX4 33
  • 95.04 (n)
(Canis familiaris)
Mammalia LHX4 34 33
  • 95.9 (n)
(Monodelphis domestica)
Mammalia LHX4 34
  • 95 (a)
(Mus musculus)
Mammalia Lhx4 16 34 33
  • 93.08 (n)
(Rattus norvegicus)
Mammalia Lhx4 33
  • 92.91 (n)
(Ornithorhynchus anatinus)
Mammalia LHX4 34
  • 83 (a)
(Gallus gallus)
Aves LHX4 34 33
  • 83.61 (n)
(Anolis carolinensis)
Reptilia LHX4 34
  • 94 (a)
(Danio rerio)
Actinopterygii lhx4 34 33
  • 74.94 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim3 34 35
  • 37 (a)
(Caenorhabditis elegans)
Secernentea ceh-14 34 35
  • 41 (a)
lim-6 35
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2190 34
  • 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)
Evolutionary constrained regions (ECRs) for LHX4: view image

Paralogs for LHX4 Gene

Paralogs for LHX4 Gene

(30) SIMAP similar genes for LHX4 Gene using alignment to 5 proteins:

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 Variation AA Info Type
rs116482990 likely-benign, Combined Pituitary Hormone Deficiency, Dominant 180,274,596(+) C/A/T 3_prime_UTR_variant
rs121912641 pathogenic, Pituitary hormone deficiency, combined 4, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,271,856(+) G/C coding_sequence_variant, missense_variant
rs121912642 pathogenic, Pituitary hormone deficiency, combined 4, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,266,393(+) C/T coding_sequence_variant, missense_variant
rs121912643 pathogenic, Pituitary hormone deficiency, combined 4, Pituitary hormone deficiency, combined, 4 (CPHD4) [MIM:262700] 180,271,497(+) T/G coding_sequence_variant, missense_variant
rs121912644 pathogenic, Pituitary hormone deficiency, combined 4 180,274,568(+) C/A coding_sequence_variant, missense_variant

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)

Additional Variant Information for LHX4 Gene

Human Gene Mutation Database (HGMD)
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 LHX4 Gene

Disorders for LHX4 Gene

MalaCards: The human disease database

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


  • 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.
  • 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}.

Additional Disease Information for LHX4

Genetic Association Database
Human Genome Epidemiology 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 (American journal of human genetics 2001) 2 3 4 22 58
  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 (Endocrine journal 2007) 3 4 22 58
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3 4 58
  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 (The Journal of clinical endocrinology and metabolism 2010) 3 44 58
  5. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 44 58

Products for LHX4 Gene

Sources for LHX4 Gene

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