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LHX4 LIM homeobox 4 [ Homo sapiens (human) ]

Gene ID: 89884, updated on 1-Mar-2024

Summary

Official Symbol
LHX4provided by HGNC
Official Full Name
LIM homeobox 4provided by HGNC
Primary source
HGNC:HGNC:21734
See related
Ensembl:ENSG00000121454 MIM:602146; AllianceGenome:HGNC:21734
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
CPHD4
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 1.2), placenta (RPKM 0.8) and 24 other tissues See more
Orthologs
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Genomic context

See LHX4 in Genome Data Viewer
Location:
1q25.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (180228375..180278984)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (179583799..179634371)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (180199399..180248119)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2159 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180134845-180135502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180135503-180136160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180136161-180136816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180136817-180137474 Neighboring gene quiescin sulfhydryl oxidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180162034-180162705 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1382 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180213501-180214248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180217481-180217981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180218267-180219247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180223097-180223616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180227074-180227843 Neighboring gene Sharpr-MPRA regulatory region 8966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180240649-180241576 Neighboring gene LHX4 antisense RNA 1 Neighboring gene acyl-CoA binding domain containing 6 Neighboring gene MPRA-validated peak481 silencer Neighboring gene MPRA-validated peak482 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:180295724-180296224 Neighboring gene MPRA-validated peak483 silencer Neighboring gene MPRA-validated peak484 silencer Neighboring gene uncharacterized LOC124904702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2162 Neighboring gene uncharacterized LOC105371637

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
Short stature-pituitary and cerebellar defects-small sella turcica syndrome
MedGen: C2678408 OMIM: 262700 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2022-04-25)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2022-04-25)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ22769

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic process 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 transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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
 

General protein information

Preferred Names
LIM/homeobox protein Lhx4
Names
LIM homeobox protein 4

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

  1. NG_008081.1 RefSeqGene

    Range
    4992..49747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_033343.4NP_203129.1  LIM/homeobox protein Lhx4

    See identical proteins and their annotated locations for NP_203129.1

    Status: REVIEWED

    Source sequence(s)
    AF179849, AL139141, BC011759, BX954266
    Consensus CDS
    CCDS1338.1
    UniProtKB/Swiss-Prot
    Q8NHE0, Q8NHM1, Q8TCJ1, Q8WWX2, Q969G2, Q969W2
    UniProtKB/TrEMBL
    A0A0S2Z5S4
    Related
    ENSP00000263726.2, ENST00000263726.4
    Conserved Domains (3) summary
    cd09376
    Location:89144
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09468
    Location:3081
    LIM1_Lhx4; The first LIM domain of Lhx4
    pfam00046
    Location:160214
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    180228375..180278984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510105.3XP_011508407.1  LIM/homeobox protein Lhx4 isoform X1

    See identical proteins and their annotated locations for XP_011508407.1

    Conserved Domains (3) summary
    cd09376
    Location:2883
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    pfam00046
    Location:99152
    Homeobox; Homeobox domain
    cl02475
    Location:120
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  2. XM_011510106.4XP_011508408.1  LIM/homeobox protein Lhx4 isoform X1

    See identical proteins and their annotated locations for XP_011508408.1

    Conserved Domains (3) summary
    cd09376
    Location:2883
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    pfam00046
    Location:99152
    Homeobox; Homeobox domain
    cl02475
    Location:120
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  3. XM_011510108.3XP_011508410.1  LIM/homeobox protein Lhx4 isoform X2

    See identical proteins and their annotated locations for XP_011508410.1

    Conserved Domains (2) summary
    cd09376
    Location:1469
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    pfam00046
    Location:85138
    Homeobox; Homeobox domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    179583799..179634371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339483.1XP_054195458.1  LIM/homeobox protein Lhx4 isoform X1

  2. XM_054339484.1XP_054195459.1  LIM/homeobox protein Lhx4 isoform X1

  3. XM_054339485.1XP_054195460.1  LIM/homeobox protein Lhx4 isoform X2