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Aliases for LDB3 Gene

Aliases for LDB3 Gene

  • LIM Domain Binding 3 2 3 5
  • Cardiomyopathy, Dilated 1C (Autosomal Dominant) 2 3
  • Z-Band Alternatively Spliced PDZ-Motif Protein 3 4
  • Protein Cypher 3 4
  • Cypher 2 3
  • Oracle 2 3
  • ZASP 3 4
  • Z-Band Alternatively Spliced PDZ Motif Protein 2
  • LIM Domain-Binding Protein 3 3
  • PDZ And LIM Domain 6 3
  • KIAA0613 4
  • LDB3Z1 3
  • LDB3Z4 3
  • PDLIM6 3
  • CMH24 3
  • CMPD3 3
  • LVNC3 3
  • CMD1C 3
  • MFM4 3

External Ids for LDB3 Gene

Previous HGNC Symbols for LDB3 Gene

  • CMD1C

Previous GeneCards Identifiers for LDB3 Gene

  • GC10P087309
  • GC10P087650
  • GC10P088559
  • GC10P088092
  • GC10P088418
  • GC10P082282
  • GC10P088426

Summaries for LDB3 Gene

Entrez Gene Summary for LDB3 Gene

  • This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]

GeneCards Summary for LDB3 Gene

LDB3 (LIM Domain Binding 3) is a Protein Coding gene. Diseases associated with LDB3 include Myopathy, Myofibrillar, 4 and Cardiomyopathy, Dilated, 1C, With Or Without Lvnc. GO annotations related to this gene include cytoskeletal protein binding and muscle alpha-actinin binding. An important paralog of this gene is PDLIM7.

UniProtKB/Swiss-Prot for LDB3 Gene

  • May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.

Gene Wiki entry for LDB3 Gene

Additional gene information for LDB3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDB3 Gene

Genomics for LDB3 Gene

Regulatory Elements for LDB3 Gene

Enhancers for LDB3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H086662 1.4 Ensembl ENCODE dbSUPER 15.1 +2.8 2797 13.3 FEZF1 GLIS2 ATF7 FOS TSHZ1 SMARCB1 ZNF592 GLIS1 NBN WT1 OPN4 LDB3 ENSG00000272631 GC10M086714
GH10H086693 0.9 ENCODE dbSUPER 13 +27.3 27289 1.3 CTCF ZNF654 RB1 TRIM22 REST ZIC2 RAD21 GLIS2 GLIS1 IKZF1 LDB3 OPN4 GC10M086714
GH10H086726 0.9 ENCODE dbSUPER 12.1 +61.0 60990 1.8 PKNOX1 FOXA2 MAFG PPARG ZNF316 NFE2 EMSY MAFK RXRB NFE2L2 BMPR1A LDB3 GC10M086714
GH10H086680 0.7 ENCODE dbSUPER 15.2 +14.5 14539 1.2 NFIB ZBTB33 LDB3 OPN4 ENSG00000272631 GC10M086714
GH10H086436 1.5 Ensembl ENCODE dbSUPER 6.4 -226.5 -226478 7.3 FOXA2 MLX ARID4B DMAP1 TCF12 FOS ATF7 SP5 ZHX2 MXD4 RNU6-780P ENSG00000227896 WAPL LDB3 OPN4 BMPR1A GC10P086443 GC10M086380
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LDB3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for LDB3 Gene

Genomic Locations for LDB3 Gene
69,356 bases
Plus strand

Genomic View for LDB3 Gene

Genes around LDB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LDB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LDB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LDB3 Gene

Proteins for LDB3 Gene

  • Protein details for LDB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM domain-binding protein 3
    Protein Accession:
    Secondary Accessions:
    • A2TDB7
    • A6NIV4
    • B4E3K3
    • Q5K6N9
    • Q5K6P0
    • Q5K6P1
    • Q96FH2
    • Q9Y4Z3
    • Q9Y4Z4
    • Q9Y4Z5

    Protein attributes for LDB3 Gene

    727 amino acids
    Molecular mass:
    77135 Da
    Quaternary structure:
    • Interacts via its LIM domains with various PKC isoforms (By similarity). Interacts via its PDZ domain with the ACTN2 C-terminal region. Interacts with MYOZ1, MYOZ2 and MYOZ3.
    • Sequence=BAA31588.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LDB3 Gene

    Alternative splice isoforms for LDB3 Gene

neXtProt entry for LDB3 Gene

Post-translational modifications for LDB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LDB3 Gene

Domains & Families for LDB3 Gene

Gene Families for LDB3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for LDB3 Gene

Suggested Antigen Peptide Sequences for LDB3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LDB3: view

No data available for UniProtKB/Swiss-Prot for LDB3 Gene

Function for LDB3 Gene

Molecular function for LDB3 Gene

UniProtKB/Swiss-Prot Function:
May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.

Phenotypes From GWAS Catalog for LDB3 Gene

Gene Ontology (GO) - Molecular Function for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005080 protein kinase C binding IEA --
GO:0005515 protein binding IPI 10427098
GO:0008092 cytoskeletal protein binding IPI 17987659
GO:0046872 metal ion binding IEA --
GO:0051371 muscle alpha-actinin binding IEA --
genes like me logo Genes that share ontologies with LDB3: view
genes like me logo Genes that share phenotypes with LDB3: view

Human Phenotype Ontology for LDB3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LDB3 Gene

MGI Knock Outs for LDB3:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LDB3 Gene

Localization for LDB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LDB3 Gene

Cytoplasm, perinuclear region. Cell projection, pseudopodium. Cytoplasm, cytoskeleton. Cytoplasm, myofibril, sarcomere, Z line. Note=Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected throughout the myotubes of differentiated cells. Colocalizes with ACTN2 at the Z-lines.

Subcellular locations from

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 LDB3 gene
Compartment Confidence
cytoskeleton 5
nucleus 4
cytosol 4
mitochondrion 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Focal adhesion sites (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA,IDA 10427098
GO:0030018 Z disc IDA 10427098
GO:0031143 pseudopodium IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with LDB3: view

Pathways & Interactions for LDB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045214 sarcomere organization IEA --
genes like me logo Genes that share ontologies with LDB3: view

No data available for Pathways by source and SIGNOR curated interactions for LDB3 Gene

Drugs & Compounds for LDB3 Gene

No Compound Related Data Available

Transcripts for LDB3 Gene

Unigene Clusters for LDB3 Gene

LIM domain binding 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LDB3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^
SP2: - -
SP3: - - - -
SP4: - - - - -
SP5: - - - - - - - -
SP7: -
SP11: - - - - -

ExUns: 16

Relevant External Links for LDB3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LDB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LDB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LDB3 Gene

This gene is overexpressed in Heart - Left Ventricle (x17.3), Muscle - Skeletal (x14.6), and Heart - Atrial Appendage (x9.7).

Protein differential expression in normal tissues from HIPED for LDB3 Gene

This gene is overexpressed in Heart (42.7) and Fetal heart (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LDB3 Gene

Protein tissue co-expression partners for LDB3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LDB3 Gene:


SOURCE GeneReport for Unigene cluster for LDB3 Gene:


mRNA Expression by UniProt/SwissProt for LDB3 Gene:

Tissue specificity: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain and placenta.

Evidence on tissue expression from TISSUES for LDB3 Gene

  • Muscle(5)
  • Heart(4.9)
  • Nervous system(3.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LDB3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • nervous
  • respiratory
  • skeletal muscle
Head and neck:
  • brain
  • ear
  • head
  • heart
  • heart valve
  • lung
  • arm
  • forearm
  • lower limb
  • shin
  • thigh
  • upper limb
  • blood
  • blood vessel
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with LDB3: view

Orthologs for LDB3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LDB3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LDB3 34
  • 100 (a)
(Bos Taurus)
Mammalia LDB3 34
  • 91 (a)
(Mus musculus)
Mammalia Ldb3 16 34 33
  • 82.47 (n)
(Canis familiaris)
Mammalia LDB3 34 33
  • 82.2 (n)
(Monodelphis domestica)
Mammalia LDB3 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia LDB3 34
  • 76 (a)
(Gallus gallus)
Aves LOC101750026 33
  • 78.32 (n)
LDB3 34
  • 60 (a)
(Anolis carolinensis)
Reptilia LDB3 34
  • 59 (a)
African clawed frog
(Xenopus laevis)
Amphibia ldb3-prov 33
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75668 33
(Danio rerio)
Actinopterygii ldb3b 34
  • 52 (a)
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 34
  • 11 (a)
(Caenorhabditis elegans)
Secernentea alp-1 34
  • 14 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
-- 34
  • 35 (a)
Species where no ortholog for LDB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 LDB3 Gene

Gene Tree for LDB3 (if available)
Gene Tree for LDB3 (if available)

Paralogs for LDB3 Gene

(7) SIMAP similar genes for LDB3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LDB3: view

Variants for LDB3 Gene

Sequence variations from dbSNP and Humsavar for LDB3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs121908336 Pathogenic, Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) [MIM:601493] 86,706,669(+) GCCAT(C/G/T)GCCTC intron-variant, reference, synonymous-codon
rs121908337 Pathogenic, Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) [MIM:601493] 86,681,731(+) AGAGA(C/T)CCTGA intron-variant, reference, missense
rs45487699 Pathogenic, Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) [MIM:601493] 86,681,680(+) GGGCT(C/T)GAGCC intron-variant, reference, missense
rs45514002 Pathogenic, Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) [MIM:601493] 86,726,175(+) GCTGC(A/G)ATTTC reference, missense
rs121908333 Pathogenic 86,687,163(+) GCAAG(A/G)CCACC intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for LDB3 Gene

Variant ID Type Subtype PubMed ID
nsv551783 CNV loss 21841781
nsv524269 CNV loss 19592680
nsv520811 CNV loss 19592680
nsv519805 CNV loss 19592680
nsv517139 CNV gain+loss 19592680
nsv470968 CNV loss 18288195
nsv467411 CNV loss 19166990
nsv1143646 CNV deletion 24896259
nsv1141879 OTHER inversion 24896259
nsv1049754 CNV gain 25217958
esv3624098 CNV loss 21293372
esv3546618 CNV deletion 23714750
esv3354472 CNV insertion 20981092
dgv948n100 CNV gain 25217958
dgv1321n54 CNV loss 21841781
dgv1320n54 CNV gain 21841781
dgv116n27 CNV loss 19166990

Variation tolerance for LDB3 Gene

Residual Variation Intolerance Score: 94.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.44; 71.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LDB3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LDB3 Gene

Disorders for LDB3 Gene

MalaCards: The human disease database

(30) MalaCards diseases for LDB3 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
myopathy, myofibrillar, 4
  • myofibrillar myopathy 4
cardiomyopathy, dilated, 1c, with or without lvnc
  • cardiomyopathy, hypertrophic, 24
ldb3-related dilated cardiomyopathy
  • dilated cardiomyopathy 1c
late-onset distal myopathy, markesbery-griggs type
  • zasp-related myofibrillar myopathy
dilated cardiomyopathy 1c
  • cmdc1
- elite association - COSMIC cancer census association via MalaCards
Search LDB3 in MalaCards View complete list of genes associated with diseases


  • Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) [MIM:601493]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. Cardiomyopathy dilated type 1C is associated with left ventricular non-compaction in some patients. Left ventricular non-compaction is characterized by numerous prominent trabeculations and deep intertrabecular recesses in hypertrophied and hypokinetic segments of the left ventricle. {ECO:0000269 PubMed:14660611, ECO:0000269 PubMed:14662268}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Left ventricular non-compaction 3 (LVNC3) [MIM:601493]: A disease due to an arrest of myocardial morphogenesis. It is characterized by a hypertrophic left ventricle with deep trabeculations and with poor systolic function, with or without associated left ventricular dilation. In some cases, it is associated with other congenital heart anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Myopathy, myofibrillar, 4 (MFM4) [MIM:609452]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disc and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM4 is characterized by distal and proximal muscle weakness with signs of cardiomyopathy and neuropathy. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LDB3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with LDB3: view

No data available for Genatlas for LDB3 Gene

Publications for LDB3 Gene

  1. Mutations in Cypher/ZASP in patients with dilated cardiomyopathy and left ventricular non-compaction. (PMID: 14662268) Vatta M … Towbin JA (Journal of the American College of Cardiology 2003) 2 3 4 60
  2. ZASP: a new Z-band alternatively spliced PDZ-motif protein. (PMID: 10427098) Faulkner G … Lanfranchi G (The Journal of cell biology 1999) 2 3 4 60
  3. Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked β-N-acetylglucosamine-substituted protein in human heart myofibrils. (PMID: 23271734) Leung MC … Marston SB (The Journal of biological chemistry 2013) 2 3 60
  4. Cypher/ZASP is a novel A-kinase anchoring protein. (PMID: 23996002) Lin C … Cheng H (The Journal of biological chemistry 2013) 2 3 60
  5. Common susceptibility variants examined for association with dilated cardiomyopathy. (PMID: 20201937) Rampersaud E … Martin ER (Annals of human genetics 2010) 3 45 60

Products for LDB3 Gene

Sources for LDB3 Gene

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