U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LHX3 LIM homeobox 3 [ Homo sapiens (human) ]

Gene ID: 8022, updated on 1-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