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    LHX3 LIM homeobox 3 [ Homo sapiens (human) ]

    Gene ID: 8022, updated on 5-Mar-2024

    Summary

    Official Symbol
    LHX3provided by HGNC
    Official Full Name
    LIM homeobox 3provided by HGNC
    Primary source
    HGNC:HGNC:6595
    See related
    Ensembl:ENSG00000107187 MIM:600577; AllianceGenome:HGNC:6595
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LIM3; CPHD3; M2-LHX3
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LHX3 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136196250..136205128, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148425793..148434671, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139088096..139096974, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902307 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:138912910-138913832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138913833-138914753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138915830-138916368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138916406-138916996 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138921801-138922013 Neighboring gene NACC family member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223743486-223744062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138947679-138948279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138948280-138948879 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138948880-138949481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138966482-138967232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138972585-138973346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138978791-138979750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138982379-138983071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138985151-138985842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138995039-138995738 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138999932-139000544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139001156-139001768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139001769-139002380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139002381-139002992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139008667-139009242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139009243-139009818 Neighboring gene uncharacterized LOC107987142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139010972-139011548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139011549-139012123 Neighboring gene transmembrane protein 250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139027429-139027969 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139037051-139037363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139038646-139039577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139044229-139044797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139048359-139048859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139060941-139061592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139061593-139062243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139067483-139068316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139079110-139079610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139082169-139083115 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139083116-139084061 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139089541-139090232 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139090233-139090922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139100281-139100832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139100833-139101382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139103280-139104056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139107853-139108356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29302 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:139119971-139121170 Neighboring gene quiescin sulfhydryl oxidase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139131059-139131587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139139693-139140547 Neighboring gene 9q34.3 QSOX2 distal recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20505 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139159307-139159682 Neighboring gene coiled-coil domain containing 187 Neighboring gene uncharacterized LOC124902308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20506

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Non-acquired combined pituitary hormone deficiency with spine abnormalities
    MedGen: C3489787 OMIM: 221750 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp762A2013

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner ear development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in medial motor column neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in motor neuron axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in placenta development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in prolactin secreting cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in somatotropin secreting cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spinal cord association neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spinal cord motor neuron cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thyroid-stimulating hormone-secreting cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventral spinal cord interneuron specification IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    LIM/homeobox protein Lhx3
    Names
    LIM homeobox protein 3
    LIM/homeodomain protein LHX3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008097.1 RefSeqGene

      Range
      4982..13860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001363746.1NP_001350675.1  LIM/homeobox protein Lhx3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AB593064, AL138781
      Consensus CDS
      CCDS87713.1
      UniProtKB/TrEMBL
      F1T0D7
      Related
      ENSP00000483080.1, ENST00000619587.1
      Conserved Domains (4) summary
      cd09376
      Location:79134
      LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
      cd09467
      Location:1771
      LIM1_Lhx3b; The first LIM domain of Lhx3b
      pfam00046
      Location:149202
      Homeobox; Homeobox domain
      pfam04503
      Location:247368
      SSDP; Single-stranded DNA binding protein, SSDP
    2. NM_014564.5NP_055379.1  LIM/homeobox protein Lhx3 isoform b

      See identical proteins and their annotated locations for NP_055379.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the 5' UTR and coding sequence, compared to variant 1. The resulting isoform (b) has a longer and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AB593066, AL138781, CK300529
      Consensus CDS
      CCDS6995.1
      UniProtKB/TrEMBL
      F1T0D9
      Related
      ENSP00000360811.3, ENST00000371746.9
      Conserved Domains (3) summary
      cd09376
      Location:95150
      LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
      cd09467
      Location:3387
      LIM1_Lhx3b; The first LIM domain of Lhx3b
      pfam00046
      Location:165218
      Homeobox; Homeobox domain
    3. NM_178138.6NP_835258.1  LIM/homeobox protein Lhx3 isoform a

      See identical proteins and their annotated locations for NP_835258.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript. This transcript encodes two proteins; isoform a and M2-LHX3, which is generated by an internal translation initiation codon.
      Source sequence(s)
      AB593062, AL138781, CK300529
      Consensus CDS
      CCDS6994.1
      UniProtKB/Swiss-Prot
      Q5TB39, Q5TB40, Q9NZB5, Q9P0I8, Q9P0I9, Q9UBR4
      UniProtKB/TrEMBL
      F1T0D5
      Related
      ENSP00000360813.4, ENST00000371748.10
      Conserved Domains (3) summary
      cd09376
      Location:90145
      LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
      cd09467
      Location:2882
      LIM1_Lhx3b; The first LIM domain of Lhx3b
      pfam00046
      Location:160213
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      136196250..136205128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017015168.1XP_016870657.1  LIM/homeobox protein Lhx3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      148425793..148434671 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363881.1XP_054219856.1  LIM/homeobox protein Lhx3 isoform X1