This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in ... See more...

Aliases for LMCD1 Gene

Aliases for LMCD1 Gene

  • LIM And Cysteine Rich Domains 1 2 3 5
  • Dyxin 2 3 4
  • LIM And Cysteine-Rich Domains Protein 1 3 4
  • LMCD1 5

External Ids for LMCD1 Gene

Previous GeneCards Identifiers for LMCD1 Gene

  • GC03P008472

Summaries for LMCD1 Gene

Entrez Gene Summary for LMCD1 Gene

  • This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

GeneCards Summary for LMCD1 Gene

LMCD1 (LIM And Cysteine Rich Domains 1) is a Protein Coding gene. Diseases associated with LMCD1 include Mixed Cell Uveal Melanoma and Lidocaine Allergy. Among its related pathways are Surfactant metabolism and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity. An important paralog of this gene is TES.

UniProtKB/Swiss-Prot Summary for LMCD1 Gene

  • Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LMCD1 Gene

Genomics for LMCD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LMCD1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LMCD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LMCD1

Top Transcription factor binding sites by QIAGEN in the LMCD1 gene promoter:
  • AREB6
  • Bach2
  • CREB
  • Nkx6-1
  • p53
  • PPAR-gamma1
  • PPAR-gamma2
  • RSRFC4
  • STAT1

Genomic Locations for LMCD1 Gene

Latest Assembly
chr3:8,501,807-8,574,668
(GRCh38/hg38)
Size:
72,862 bases
Orientation:
Plus strand

Previous Assembly
chr3:8,543,509-8,616,354
(GRCh37/hg19 by Entrez Gene)
Size:
72,846 bases
Orientation:
Plus strand

chr3:8,543,393-8,609,805
(GRCh37/hg19 by Ensembl)
Size:
66,413 bases
Orientation:
Plus strand

Genomic View for LMCD1 Gene

Genes around LMCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMCD1 Gene

Proteins for LMCD1 Gene

  • Protein details for LMCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZU5-LMCD1_HUMAN
    Recommended name:
    LIM and cysteine-rich domains protein 1
    Protein Accession:
    Q9NZU5
    Secondary Accessions:
    • B4DG80

    Protein attributes for LMCD1 Gene

    Size:
    365 amino acids
    Molecular mass:
    40833 Da
    Quaternary structure:
    • Interacts with GATA1 and GATA4 (By similarity). Interacts with beta-dystroglycan. Interacts with GATA6.

    Alternative splice isoforms for LMCD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMCD1 Gene

Post-translational modifications for LMCD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

  • Abcam antibodies for LMCD1

No data available for DME Specific Peptides for LMCD1 Gene

Domains & Families for LMCD1 Gene

Gene Families for LMCD1 Gene

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

Protein Domains for LMCD1 Gene

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

Suggested Antigen Peptide Sequences for LMCD1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52480, highly similar to LIM and cysteine-rich domains protein 1 (B4DEY6_HUMAN)
  • cDNA FLJ55018, highly similar to LIM and cysteine-rich domains protein 1 (B4DG80_HUMAN)
  • Dyxin (LMCD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NZU5

UniProtKB/Swiss-Prot:

LMCD1_HUMAN :
  • The LIM zinc-binding domains and the Cys-rich region mediate interaction with GATA6.
Domain:
  • The LIM zinc-binding domains and the Cys-rich region mediate interaction with GATA6.
genes like me logo Genes that share domains with LMCD1: view

Function for LMCD1 Gene

Molecular function for LMCD1 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway.
GENATLAS Biochemistry:
LIM and cysteine-rich domains 1

Phenotypes From GWAS Catalog for LMCD1 Gene

Gene Ontology (GO) - Molecular Function for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding IPI 32296183
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LMCD1: view
genes like me logo Genes that share phenotypes with LMCD1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMCD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LMCD1 Gene

Localization for LMCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMCD1 Gene

Cytoplasm. Nucleus. Note=May shuttle between the cytoplasm and the nucleus. {ECO:0000250}.

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 LMCD1 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
  • Cell Junctions (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with LMCD1: view

Pathways & Interactions for LMCD1 Gene

PathCards logo

SuperPathways for LMCD1 Gene

genes like me logo Genes that share pathways with LMCD1: view

Pathways by source for LMCD1 Gene

2 Reactome pathways for LMCD1 Gene

Gene Ontology (GO) - Biological Process for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0010611 regulation of cardiac muscle hypertrophy IMP 20026769
GO:0044267 cellular protein metabolic process TAS --
GO:0070886 positive regulation of calcineurin-NFAT signaling cascade IMP 20026769
genes like me logo Genes that share ontologies with LMCD1: view

No data available for SIGNOR curated interactions for LMCD1 Gene

Drugs & Compounds for LMCD1 Gene

No Compound Related Data Available

Transcripts for LMCD1 Gene

mRNA/cDNA for LMCD1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMCD1

Alternative Splicing Database (ASD) splice patterns (SP) for LMCD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8
SP1: - - -
SP2:
SP3: -
SP4: - - -
SP5:

Relevant External Links for LMCD1 Gene

GeneLoc Exon Structure for
LMCD1

Expression for LMCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LMCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMCD1 Gene

This gene is overexpressed in Muscle - Skeletal (x7.1) and Artery - Aorta (x7.0).

Protein differential expression in normal tissues from HIPED for LMCD1 Gene

This gene is overexpressed in Spleen (13.0), Urinary Bladder (7.3), Uterus (6.6), and Bone marrow stromal cell (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LMCD1 Gene



Protein tissue co-expression partners for LMCD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LMCD1

SOURCE GeneReport for Unigene cluster for LMCD1 Gene:

Hs.475353

mRNA Expression by UniProt/SwissProt for LMCD1 Gene:

Q9NZU5-LMCD1_HUMAN
Tissue specificity: Expressed in the heart (at protein level). Expressed in many tissues with highest abundance in skeletal muscle.

Evidence on tissue expression from TISSUES for LMCD1 Gene

  • Nervous system(4.6)
  • Eye(4.4)
  • Liver(4.3)
  • Muscle(3.1)
  • Lung(2.9)
  • Heart(2.8)
genes like me logo Genes that share expression patterns with LMCD1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LMCD1 Gene

Orthologs for LMCD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LMCD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LMCD1 29 30
  • 99.18 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LMCD1 29 30
  • 91.64 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LMCD1 29 30
  • 90.82 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lmcd1 29 16 30
  • 87.31 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lmcd1 29
  • 87.03 (n)
Oppossum
(Monodelphis domestica)
Mammalia LMCD1 30
  • 84 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LMCD1 30
  • 82 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LMCD1 29 30
  • 73.28 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LMCD1 30
  • 68 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii lmcd1 29 30
  • 60.43 (n)
OneToOne
zgc56533 29
Fruit Fly
(Drosophila melanogaster)
Insecta Tes 30
  • 13 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea tes-1 30
  • 22 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 26 (a)
OneToMany
Species where no ortholog for LMCD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for LMCD1 Gene

ENSEMBL:
Gene Tree for LMCD1 (if available)
TreeFam:
Gene Tree for LMCD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMCD1: view image
Alliance of Genome Resources:
Additional Orthologs for LMCD1

Paralogs for LMCD1 Gene

Paralogs for LMCD1 Gene

(5) SIMAP similar genes for LMCD1 Gene using alignment to 6 proteins:

  • LMCD1_HUMAN
  • B4DEY6_HUMAN
  • C9IYS1_HUMAN
  • F5GX84_HUMAN
  • F8WB09_HUMAN
  • H7C3D2_HUMAN
genes like me logo Genes that share paralogs with LMCD1: view

Variants for LMCD1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LMCD1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LMCD1 Gene

Variant ID Type Subtype PubMed ID
dgv2652e59 CNV duplication 20981092
dgv2653e59 CNV tandem duplication 20981092
dgv4677n100 CNV gain 25217958
esv1238714 CNV insertion 17803354
esv2724875 CNV deletion 23290073
esv3423947 CNV duplication 20981092
nsv1009343 CNV gain 25217958
nsv1011096 CNV loss 25217958
nsv1011935 CNV loss 25217958
nsv1074567 CNV deletion 25765185
nsv1117326 CNV tandem duplication 24896259
nsv519789 CNV loss 19592680
nsv820839 CNV duplication 20802225
nsv821979 CNV loss 20364138
nsv821980 CNV loss 20364138
nsv956829 CNV deletion 24416366

Variation tolerance for LMCD1 Gene

Residual Variation Intolerance Score: 87.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.78; 47.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMCD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMCD1
Leiden Open Variation Database (LOVD)
LMCD1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LMCD1 Gene

Disorders for LMCD1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for LMCD1 Gene - From: COP

Disorder Aliases PubMed IDs
mixed cell uveal melanoma
  • intraocular mixed cell type melanoma
lidocaine allergy
  • lidoderm allergy
choroid cancer
  • choroid neoplasm
orthostatic intolerance
  • neurocirculatory asthenia
melanoma, uveal
  • uveal melanoma
- elite association - COSMIC cancer census association via MalaCards
Search LMCD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LMCD1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LMCD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LMCD1 Gene

Publications for LMCD1 Gene

  1. LMCD1/Dyxin is a novel transcriptional cofactor that restricts GATA6 function by inhibiting DNA binding. (PMID: 16199866) Rath N … Morrisey EE (Molecular and cellular biology 2005) 3 4 22
  2. Identification of a novel LIM domain gene, LMCD1, and chromosomal localization in human and mouse. (PMID: 10662546) Bespalova IN … Burmeister M (Genomics 2000) 2 3 4
  3. LIM and cysteine-rich domains 1 regulates cardiac hypertrophy by targeting calcineurin/nuclear factor of activated T cells signaling. (PMID: 20026769) Bian ZY … Li H (Hypertension (Dallas, Tex. : 1979) 2010) 3 4
  4. 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 40
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for LMCD1 Gene

Sources for LMCD1 Gene