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LMX1A LIM homeobox transcription factor 1 alpha [ Homo sapiens (human) ]

Gene ID: 4009, updated on 5-Mar-2024

Summary

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Official Symbol
LMX1Aprovided by HGNC
Official Full Name
LIM homeobox transcription factor 1 alphaprovided by HGNC
Primary source
HGNC:HGNC:6653
See related
Ensembl:ENSG00000162761 MIM:600298; AllianceGenome:HGNC:6653
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LMX1; DFNA7; LMX1.1
Summary
This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (165201867..165356715, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (164548251..164703069, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (165171104..165325952, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 755, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1497 Neighboring gene uncharacterized LOC107985452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:165131828-165132328 Neighboring gene LMX1A antisense RNA 2 Neighboring gene LMX1A antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:165223074-165223646 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:165370087-165370588 Neighboring gene retinoid X receptor gamma Neighboring gene ReSE screen-validated silencer GRCh37_chr1:165446262-165446483 Neighboring gene LRRC52 antisense RNA 1 Neighboring gene PRELID1 pseudogene 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants. Lee SY, et al. Ear Hear, 2022 Nov-Dec 01. PMID 35711095
  2. Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss. Lee SY, et al. Hum Mutat, 2020 Nov. PMID 32840933
  3. Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells. Wu TH, et al. Int J Mol Sci, 2020 Jul 30. PMID 32751497, Free PMC Article
  4. Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction. Wesdorp M, et al. Hum Genet, 2018 May. PMID 29754270, Free PMC Article
  5. LMX1A inhibits metastasis of gastric cancer cells through negative regulation of β-catenin. Feng L, et al. Cell Biol Toxicol, 2016 Apr. PMID 27061089

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
    Title: ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
  2. Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants.
    Title: Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants.
  3. Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
    Title: Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
  4. Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
    Title: Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
  5. Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
    Title: Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
  6. Circular RNA circMTO1 Suppresses RCC Cancer Cell Progression via miR9/LMX1A Axis.
    Title: Circular RNA circMTO1 Suppresses RCC Cancer Cell Progression via miR9/LMX1A Axis.
  7. LINC00682 inhibits gastric cancer cell progression via targeting microRNA-9-LMX1A signaling axis.
    Title: LINC00682 inhibits gastric cancer cell progression via targeting microRNA-9-LMX1A signaling axis.
  8. Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
    Title: Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
  9. Knockdown of ANGPTL4 rescued the tumor suppressive phenotype of LMX1A overexpression, which indicated that LMX1A upregulates ANGPTL4 to exert its role. Mechanistically, we found that LMX1A inhibited the expression of the oncogene C-Myc, which is alleviated by ANGPTL4 knockdown.
    Title: LMX1A inhibits C-Myc expression through ANGPTL4 to exert tumor suppressive role in gastric cancer.
  10. miR-9 selectively targets LMX1A to promote gastric cancer cell progression.
    Title: microRNA-9 selectively targets LMX1A to promote gastric cancer cell progression.
Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal dominant nonsyndromic hearing loss 7
MedGen: C1832379 OMIM: 601412 GeneReviews: Not available
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EBI GWAS Catalog

Description
Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study.
EBI GWAS Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC87616

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
  
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 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 transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cerebellum development IEA
Inferred from Electronic Annotation
more info
  
involved_in dentate gyrus development IEA
Inferred from Electronic Annotation
more info
  
involved_in dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
 PubMed 
involved_in locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in memory IEA
Inferred from Electronic Annotation
more info
  
involved_in midbrain dopaminergic neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in midbrain dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in olfactory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cell growth 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 synapse organization 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
  

General protein information

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Preferred Names
LIM homeobox transcription factor 1-alpha
Names
LIM/homeobox protein 1.1

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.

mRNA and Protein(s)

  1. NM_001174069.2 → NP_001167540.1  LIM homeobox transcription factor 1-alpha

    See identical proteins and their annotated locations for NP_001167540.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Both variants 1 and 4 encode the same protein.
    Source sequence(s)
    AK122800, AK127724, AL390730, BM678780
    Consensus CDS
    CCDS1247.1
    UniProtKB/Swiss-Prot
    B3KXP6, Q0VDB5, Q5VWG4, Q8TE11, Q8TE12
    Related
    ENSP00000294816.2, ENST00000294816.6
    Conserved Domains (3) summary
    cd09370
    Location:35 → 86
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94 → 148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198 → 252
    Homeobox; Homeobox domain

  2. NM_177398.4 → NP_796372.1  LIM homeobox transcription factor 1-alpha

    See identical proteins and their annotated locations for NP_796372.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 4 encode the same protein.
    Source sequence(s)
    AK122800, AK127724, AL160058, AL390730, BM678780
    Consensus CDS
    CCDS1247.1
    UniProtKB/Swiss-Prot
    B3KXP6, Q0VDB5, Q5VWG4, Q8TE11, Q8TE12
    Related
    ENSP00000340226.3, ENST00000342310.7
    Conserved Domains (3) summary
    cd09370
    Location:35 → 86
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94 → 148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198 → 252
    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
    165201867..165356715 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509538.4 → XP_011507840.1  LIM homeobox transcription factor 1-alpha isoform X1

    Conserved Domains (2) summary
    cd09378
    Location:14 → 68
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:118 → 171
    Homeobox; Homeobox domain

  2. XM_011509540.3 → XP_011507842.1  LIM homeobox transcription factor 1-alpha isoform X2

    Conserved Domains (3) summary
    cd09370
    Location:35 → 86
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    pfam00046
    Location:198 → 251
    Homeobox; Homeobox domain
    cl02475
    Location:94 → 148
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    164548251..164703069 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336594.1 → XP_054192569.1  LIM homeobox transcription factor 1-alpha isoform X1

  2. XM_054336595.1 → XP_054192570.1  LIM homeobox transcription factor 1-alpha isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033507.1: Suppressed sequence

    Description
    NM_001033507.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_177399.2: Suppressed sequence

    Description
    NM_177399.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TE12.1 GenPept UniProtKB/Swiss-Prot:Q8TE12

Gene LinkOut

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