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. Alterna... See more...

Aliases for LMX1A Gene

Aliases for LMX1A Gene

  • LIM Homeobox Transcription Factor 1 Alpha 2 3 5
  • LIM Homeobox Transcription Factor 1-Alpha 3 4
  • LIM/Homeobox Protein 1.1 3 4
  • LMX1.1 2 3
  • LIM Homeobox Transcription Factor 1, Alpha 2
  • LIM/Homeobox Protein LMX1A 4
  • LMX-1.1 4
  • DFNA7 3
  • LMX1A 5
  • LMX1 3

External Ids for LMX1A Gene

Previous HGNC Symbols for LMX1A Gene

  • LMX1

Previous GeneCards Identifiers for LMX1A Gene

  • GC01U990100
  • GC01M160823
  • GC01M161868
  • GC01M162360
  • GC01M162358
  • GC01M161902
  • GC01M163437
  • GC01M136417

Summaries for LMX1A Gene

Entrez Gene Summary for LMX1A Gene

  • 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]

GeneCards Summary for LMX1A Gene

LMX1A (LIM Homeobox Transcription Factor 1 Alpha) is a Protein Coding gene. Diseases associated with LMX1A include Deafness, Autosomal Dominant 7 and Ovarian Mucinous Cystadenocarcinoma. Among its related pathways are Dopaminergic Neurogenesis. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LMX1B.

UniProtKB/Swiss-Prot Summary for LMX1A Gene

  • Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).

Gene Wiki entry for LMX1A Gene

Additional gene information for LMX1A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LMX1A Gene

Genomics for LMX1A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LMX1A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J165356 Promoter 0.5 Ensembl 600.7 +0.3 314 0.8 EZH2 SIN3A LMX1A HSALNG0008131 PBX1
GH01J165355 Promoter 0.4 EPDnew 600.7 +0.9 923 0.1 EZH2 LMX1A HSALNG0008131 PBX1
GH01J165258 Enhancer 0.8 Ensembl 11.1 +97.8 97848 1.9 GATAD2A CTCF ZNF629 RFX1 RFX5 JUND FOXA1 REST ZNF24 SP1 LMX1A LMX1A-AS2 HSALNG0008130 HSALNG0008131 PBX1
GH01J165162 Enhancer 0.8 Ensembl ENCODE 10.9 +193.8 193814 1.4 FOXA1 ZNF600 ZFX ZBTB48 ZBTB17 MBD2 GATA3 STAT1 NFIB ZSCAN16 LMX1A-AS1 LMX1A piR-61514-022 lnc-LMX1A-4 PBX1
GH01J165593 Enhancer 0.8 Ensembl ENCODE 10 -236.7 -236708 1.2 CTCF REST RAD21 TRIM22 ZNF524 SMC3 ZBTB17 SKIL ZNF654 ZNF2 MGST3 LRRC52 RXRG LMX1A RF00005-020 TRK-CTT13-1 LRRC52-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LMX1A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LMX1A

Top Transcription factor binding sites by QIAGEN in the LMX1A gene promoter:
  • AREB6
  • CP2
  • IRF-7A
  • ITF-2
  • Nkx2-5
  • NRSF form 1
  • NRSF form 2
  • Tal-1beta
  • TBP

Genomic Locations for LMX1A Gene

Genomic Locations for LMX1A Gene
chr1:165,201,867-165,356,715
(GRCh38/hg38)
Size:
154,849 bases
Orientation:
Minus strand
chr1:165,171,104-165,325,952
(GRCh37/hg19)
Size:
154,849 bases
Orientation:
Minus strand

Genomic View for LMX1A Gene

Genes around LMX1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMX1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMX1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMX1A Gene

Proteins for LMX1A Gene

  • Protein details for LMX1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TE12-LMX1A_HUMAN
    Recommended name:
    LIM homeobox transcription factor 1-alpha
    Protein Accession:
    Q8TE12
    Secondary Accessions:
    • B3KXP6
    • Q0VDB5
    • Q5VWG4
    • Q8TE11

    Protein attributes for LMX1A Gene

    Size:
    382 amino acids
    Molecular mass:
    42747 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LMX1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMX1A Gene

Post-translational modifications for LMX1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LMX1A Gene

No data available for DME Specific Peptides for LMX1A Gene

Domains & Families for LMX1A Gene

Gene Families for LMX1A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for LMX1A Gene

InterPro:
Blocks:
  • Zn-binding protein, LIM
ProtoNet:

Suggested Antigen Peptide Sequences for LMX1A Gene

GenScript: Design optimal peptide antigens:
  • LIM/homeobox protein LMX1A (LMX1A_HUMAN)
  • LIM homeobox transcription factor 1, alpha, isoform CRA_a (Q6NZ39_HUMAN)
genes like me logo Genes that share domains with LMX1A: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LMX1A Gene

Function for LMX1A Gene

Molecular function for LMX1A Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).
GENATLAS Biochemistry:
transcriptional regulator of insulin gene,with the LIM-homeo domain (lmx-1),expressed in pancreatic islets,expressed in limb mesenchyme through WNT7A induction,involved in dorsoventral polarity of vertebrate limb (dorsal differentiation)

Phenotypes From GWAS Catalog for LMX1A Gene

Gene Ontology (GO) - Molecular Function for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding ISS --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25814554
genes like me logo Genes that share ontologies with LMX1A: view
genes like me logo Genes that share phenotypes with LMX1A: view

Human Phenotype Ontology for LMX1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LMX1A Gene

MGI Knock Outs for LMX1A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMX1A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LMX1A Gene

Localization for LMX1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMX1A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMX1A gene
Compartment Confidence
nucleus 5
golgi apparatus 3
extracellular 2
cytoskeleton 2
mitochondrion 2
cytosol 2
plasma membrane 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with LMX1A: view

Pathways & Interactions for LMX1A Gene

PathCards logo

SuperPathways for LMX1A Gene

SuperPathway Contained pathways
1 Dopaminergic Neurogenesis
genes like me logo Genes that share pathways with LMX1A: view

Pathways by source for LMX1A Gene

1 BioSystems pathway for LMX1A Gene

Gene Ontology (GO) - Biological Process for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001558 regulation of cell growth IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007411 axon guidance IEA --
GO:0007417 central nervous system development IEA --
genes like me logo Genes that share ontologies with LMX1A: view

No data available for SIGNOR curated interactions for LMX1A Gene

Drugs & Compounds for LMX1A Gene

No Compound Related Data Available

Transcripts for LMX1A Gene

mRNA/cDNA for LMX1A Gene

4 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMX1A

Alternative Splicing Database (ASD) splice patterns (SP) for LMX1A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: - - - -
SP2: - - -
SP3:

Relevant External Links for LMX1A Gene

GeneLoc Exon Structure for
LMX1A

Expression for LMX1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LMX1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMX1A Gene

This gene is overexpressed in Pituitary (x14.1) and Testis (x7.4).

Protein differential expression in normal tissues from HIPED for LMX1A Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LMX1A Gene



Protein tissue co-expression partners for LMX1A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LMX1A

SOURCE GeneReport for Unigene cluster for LMX1A Gene:

Hs.667312

mRNA Expression by UniProt/SwissProt for LMX1A Gene:

Q8TE12-LMX1A_HUMAN
Tissue specificity: Isoform 1 is expressed in many tissues. Not found in heart, liver, spleen and testis. Relatively highly expressed in fetal brain. Isoform LMX1A-4AB is expressed in testis.

Evidence on tissue expression from TISSUES for LMX1A Gene

  • Nervous system(2.8)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with LMX1A: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LMX1A Gene

Orthologs for LMX1A Gene

This gene was present in the common ancestor of animals.

Orthologs for LMX1A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LMX1A 30 31
  • 99.65 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LMX1A 30 31
  • 94.07 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LMX1A 31
  • 94 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LMX1A 30 31
  • 93.11 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lmx1a 30
  • 91.1 (n)
Mouse
(Mus musculus)
Mammalia Lmx1a 30 17 31
  • 90.92 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LMX1A 30 31
  • 80.96 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LMX1A 31
  • 77 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100492433 30
  • 72.49 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12464 30
Zebrafish
(Danio rerio)
Actinopterygii lmx1a 31
  • 55 (a)
OneToOne
Dr.13964 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG4328 31
  • 26 (a)
ManyToMany
CG32105 31
  • 25 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea lim-6 31
  • 37 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 32 (a)
ManyToMany
-- 31
  • 23 (a)
ManyToMany
Species where no ortholog for LMX1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for LMX1A Gene

ENSEMBL:
Gene Tree for LMX1A (if available)
TreeFam:
Gene Tree for LMX1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMX1A: view image

Paralogs for LMX1A Gene

(11) SIMAP similar genes for LMX1A Gene using alignment to 2 proteins:

  • LMX1A_HUMAN
  • Q6NZ39_HUMAN
genes like me logo Genes that share paralogs with LMX1A: view

Variants for LMX1A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LMX1A Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
726824 Benign: not provided 165,355,551(-) G/A SYNONYMOUS_VARIANT
777953 Benign: not provided 165,205,901(-) G/A SYNONYMOUS_VARIANT
812515 Pathogenic: Deafness, autosomal dominant 7 165,210,725(-) C/G MISSENSE_VARIANT
812516 Pathogenic: Deafness, autosomal dominant 7 165,249,614(-) C/G MISSENSE_VARIANT
rs763320093 Conflicting Interpretations: Autosomal-Recessive Hereditary Hearing Impairment; Sensorineural hearing loss; not provided 165,203,923(-) A/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for LMX1A Gene

Structural Variations from Database of Genomic Variants (DGV) for LMX1A Gene

Variant ID Type Subtype PubMed ID
dgv57e214 CNV loss 21293372
esv1005410 CNV deletion 20482838
esv1310421 CNV deletion 17803354
esv2678124 CNV deletion 23128226
esv2719084 CNV deletion 23290073
esv3587802 CNV gain 21293372
nsv1119734 CNV deletion 24896259
nsv952229 CNV deletion 24416366

Variation tolerance for LMX1A Gene

Residual Variation Intolerance Score: 15.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMX1A Gene

Human Gene Mutation Database (HGMD)
LMX1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMX1A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMX1A Gene

Disorders for LMX1A Gene

MalaCards: The human disease database

(6) MalaCards diseases for LMX1A Gene - From: OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal dominant 7
  • dfna7
ovarian mucinous cystadenocarcinoma
  • mucinous cystadenocarcinoma of ovary
arthrogryposis, distal, type 1a
  • da1a
chromosome 14q11-q22 deletion syndrome
  • 14q11.2 microdeletion syndrome
obsessive-compulsive disorder
  • ocd
- elite association - COSMIC cancer census association via MalaCards
Search LMX1A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LMX1A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LMX1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LMX1A Gene

Publications for LMX1A Gene

  1. Cloning, expression and genomic structure of human LMX1A, and variant screening in Pima Indians. (PMID: 12062816) Thameem F … Prochazka M (Gene 2002) 3 4 41
  2. Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study. (PMID: 21177773) Moyer AM … Weinshilboum RM (Toxicological sciences : an official journal of the Society of Toxicology 2011) 3 41
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Preliminary evidence that polymorphisms in dopamine-related transcription factors LMX1A, LMX1B and PITX3 are associated with schizophrenia. (PMID: 20570600) Bergman O … Eriksson E (Progress in neuro-psychopharmacology & biological psychiatry 2010) 3 41
  5. Do polymorphisms in transcription factors LMX1A and LMX1B influence the risk for Parkinson's disease? (PMID: 19189040) Bergman O … Nissbrandt H (Journal of neural transmission (Vienna, Austria : 1996) 2009) 3 41

Products for LMX1A Gene

Sources for LMX1A Gene