LHX3 LIM homeobox 3 [Homo sapiens (human)] - Gene

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: all
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Genomic context

Location:: 9q34.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (136196250..136205128, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (148425793..148434671, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (139088096..139096974, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Generation and optimization of highly pure motor neurons from human induced pluripotent stem cells via lentiviral delivery of transcription factors.
Title: Generation and optimization of highly pure motor neurons from human induced pluripotent stem cells via lentiviral delivery of transcription factors.
LHX3 expression is significantly increased in carcinoma tissues, and associated with clinical stage and metastasis of patients. LHX3 expression is much higher in the advanced-stage patients than the early-stage patients, and is sharply increased in metastasic patients.
Title: LHX3 is an advanced-stage prognostic biomarker and metastatic oncogene in hepatocellular carcinoma.
Study did not identify HESX1 and LHX3 mutations by Sanger in brazilian patients with combined pituitary hormone deficiency
Title: Molecular analysis of brazilian patients with combined pituitary hormone deficiency and orthotopic posterior pituitary lobe reveals eight different PROP1 alterations with three novel mutations.
Further functional studies show that forced expression of LHX3 in lung cancer cells obviously promotes cell proliferation and invasion, whereas inhibits cell apoptosis. In summary, LHX3 is an early-stage and radiosensitivity prognostic biomarker, and a novel potential oncogene in lung adenocarcinoma .
Title: LHX3 is an early stage and radiosensitivity prognostic biomarker in lung adenocarcinoma.
investigated the specific mutations in PROP1, POU1F1, LHX3, and HESX1 genes in patients with combined pituitary hormone deficiency (CPHD) in Turkey
Title: Molecular analysis of PROP1, POU1F1, LHX3, and HESX1 in Turkish patients with combined pituitary hormone deficiency: a multicenter study.
LHX3 is upregulated in high-grade oligodendroglioma.
Title: Lhx3 is required to maintain cancer cell development of high-grade oligodendroglioma.
The downstream enhancer region of LHX3 in regulating gene expression at the cellular level during development, is reported.
Title: Cell-specific actions of a human LHX3 gene enhancer during pituitary and spinal cord development.
Data suggest that low serum FSH (follicle stimulating hormone) levels in men with SNP in promoter region of FSHB (FSH beta subunit; -211G/T) result from reduced LHX3 binding to FSHB promoter and down-regulation of FSHB transcription in gonadotrophs.
Title: A human FSHB promoter SNP associated with low FSH levels in men impairs LHX3 binding and basal FSHB transcription.
The present study was unable to confirm a significant association of all of the three SNPs, rs12338076 in LHX3-QSOX2, and rs1457595 and rs17032362 in IGF1, with adult height in our study population.
Title: Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population; wide-ranging comparison of each SNP genotype distribution.
descriprion of pediatric patients with combined pituitary hormone deficiency with a novel mutation in LHX3; the T194R mutation affects a critical residue in the LHX3 protein; study extends understanding of phenotypic features, molecular mechanism and developmental course associated with mutations in the LHX3 gene
Title: A recessive mutation resulting in a disabling amino acid substitution (T194R) in the LHX3 homeodomain causes combined pituitary hormone deficiency.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

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 EBI GWAS CatalogPubMed
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-14818 (e-PCR)
- UniSTS:64929

NoName (e-PCR)
- UniSTS:482009

NoName (e-PCR)
- UniSTS:480757

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info
enables transcription coactivator binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in inner ear development	IEP Inferred from Expression Pattern more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	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 regulation of DNA-templated transcription	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

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx3

Names: LIM homeobox protein 3; LIM/homeodomain protein LHX3

NCBI Reference Sequences (RefSeq)

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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

NG_008097.1 RefSeqGene

Range

4982..13860

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001363746.1 → NP_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:79 → 134

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:17 → 71

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:149 → 202

Homeobox; Homeobox domain

pfam04503
Location:247 → 368

SSDP; Single-stranded DNA binding protein, SSDP
NM_014564.5 → NP_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:95 → 150

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:33 → 87

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:165 → 218

Homeobox; Homeobox domain
NM_178138.6 → NP_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:90 → 145

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:28 → 82

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:160 → 213

Homeobox; Homeobox domain