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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 2 3
  • Z-Band Alternatively Spliced PDZ-Motif Protein 3 4
  • Protein Cypher 3 4
  • ZASP 3 4
  • PDZ And LIM Domain 6 3
  • KIAA0613 4
  • Cypher 2
  • Oracle 2
  • CYPHER 3
  • LDB3Z1 3
  • LDB3Z4 3
  • ORACLE 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 Cardiomyopathy, Dilated, 1C, With Or Without Lvnc and Myopathy, Myofibrillar, 4. GO annotations related to this gene include cytoskeletal protein binding and muscle alpha-actinin binding. An important paralog of this gene is FHL3.

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

No data available for 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LDB3 on UCSC Golden Path with GeneCards custom track

Genomic Location for LDB3 Gene

Chromosome:
10
Start:
86,666,717 bp from pter
End:
86,736,072 bp from pter
Size:
69,356 bases
Orientation:
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:
    O75112-LDB3_HUMAN
    Recommended name:
    LIM domain-binding protein 3
    Protein Accession:
    O75112
    Secondary Accessions:
    • A2TDB7
    • A6NIV4
    • B4E3K3
    • Q5K6N9
    • Q5K6P0
    • Q5K6P1
    • Q96FH2
    • Q9Y4Z3
    • Q9Y4Z4
    • Q9Y4Z5

    Protein attributes for LDB3 Gene

    Size:
    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.
    SequenceCaution:
    • 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

Proteomics data for LDB3 Gene at MOPED

Post-translational modifications for LDB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for LDB3

No data available for DME Specific Peptides for LDB3 Gene

Domains & Families for LDB3 Gene

Protein Domains for LDB3 Gene

Suggested Antigen Peptide Sequences for LDB3 Gene

Graphical View of Domain Structure for InterPro Entry

O75112

UniProtKB/Swiss-Prot:

LDB3_HUMAN :
  • Contains 3 LIM zinc-binding domains.
Domain:
  • Contains 3 LIM zinc-binding domains.
  • Contains 1 PDZ (DHR) domain.
genes like me logo Genes that share domains with LDB3: view

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.

Gene Ontology (GO) - Molecular Function for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 10427098
GO:0008092 cytoskeletal protein binding IPI 17987659
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:

Flow Cytometry 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

COMPARTMENTS
Jensen Localization Image for LDB3 Gene COMPARTMENTS Subcellular localization image for LDB3 gene
Compartment Confidence
cytoskeleton 5
cytosol 4
nucleus 4
mitochondrion 2
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton IDA 10427098
genes like me logo Genes that share ontologies with LDB3: view

Pathways & Interactions for LDB3 Gene

SuperPathways for LDB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LDB3 Gene

None

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:

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 ^
SP1:
SP2: - -
SP3: - - - -
SP4: - - - - -
SP5: - - - - - - - -
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11: - - - - -
SP12:

ExUns: 16
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for LDB3 Gene

GeneLoc Exon Structure for
LDB3
ECgene alternative splicing isoforms for
LDB3

Expression for LDB3 Gene

mRNA expression in normal human tissues 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



SOURCE GeneReport for Unigene cluster for LDB3 Gene Hs.657271

mRNA Expression by UniProt/SwissProt for LDB3 Gene

O75112-LDB3_HUMAN
Tissue specificity: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain and placenta.
genes like me logo Genes that share expression patterns with LDB3: view

Protein tissue co-expression partners for LDB3 Gene

- Elite partner

Primer Products

Orthologs for LDB3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LDB3 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia LDB3 35
  • 82.2 (n)
  • 84.09 (a)
LDB3 36
  • 72 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ldb3 35
  • 82.47 (n)
  • 86.53 (a)
Ldb3 16
Ldb3 36
  • 82 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LDB3 36
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LDB3 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LDB3 36
  • 76 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LDB3 36
  • 100 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC101750026 35
  • 78.32 (n)
  • 85.31 (a)
LDB3 36
  • 60 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LDB3 36
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75668 35
African clawed frog
(Xenopus laevis)
Amphibia ldb3-prov 35
zebrafish
(Danio rerio)
Actinopterygii ldb3b 36
  • 52 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 36
  • 11 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea alp-1 36
  • 14 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 35 (a)
ManyToMany
-- 36
  • 40 (a)
ManyToMany
Species with no ortholog for LDB3:
  • 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

ENSEMBL:
Gene Tree for LDB3 (if available)
TreeFam:
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
rs3740343 - 86,679,436(+) ACGGC(A/G)TCAAC reference, missense, utr-variant-5-prime
rs45487699 Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C) 86,681,680(+) GGGCT(C/T)GAGCC intron-variant, reference, missense
VAR_024010 Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C)
VAR_024011 Cardiomyopathy, dilated 1C, with or without left ventricular non-compaction (CMD1C)
rs45618633 - 86,718,772(+) GCTTC(A/G/T)TCTGT reference, missense

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

Variant ID Type Subtype PubMed ID
nsv467411 CNV Loss 19166990
nsv470968 CNV Loss 18288195
dgv116n27 CNV Loss 19166990
dgv793n71 CNV Gain 21882294
nsv524269 CNV Loss 19592680
nsv895836 CNV Loss 21882294
nsv517139 CNV Gain+Loss 19592680
nsv895857 CNV Loss 21882294
nsv520811 CNV Loss 19592680
nsv519805 CNV Loss 19592680

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)
LDB3

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

Disorders for LDB3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
cardiomyopathy, dilated, 1c, with or without lvnc
  • cardiomyopathy, hypertrophic, 24
myopathy, myofibrillar, 4
  • myofibrillar myopathy 4
late-onset distal myopathy, markesbery-griggs type
  • zasp-related myofibrillar myopathy
ldb3-related dilated cardiomyopathy
  • cmd1c
left ventricular noncompaction 3, with or without dilated cardiomyopathy
  • left ventricular noncompaction 3
- elite association - COSMIC cancer census association via MalaCards
Search LDB3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LDB3_HUMAN
  • 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 neuromuscular disorder 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)
LDB3
Human Genome Epidemiology (HuGE) Navigator
LDB3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LDB3
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 J.A. (J. Am. Coll. Cardiol. 2003) 2 3 4 67
  2. Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked I^-N-acetylglucosamine-substituted protein in human heart myofibrils. (PMID: 23271734) Leung M.C. … Marston S.B. (J. Biol. Chem. 2013) 2 3
  3. Cypher/ZASP is a novel A-kinase anchoring protein. (PMID: 23996002) Lin C. … Cheng H. (J. Biol. Chem. 2013) 2 3
  4. Barth syndrome associated with compound hemizygosity and heterozygosity of the TAZ and LDB3 genes. (PMID: 17394203) Marziliano N. … Arbustini E. (Am. J. Med. Genet. A 2007) 3 23
  5. Zasp/Cypher internal ZM-motif containing fragments are sufficient to co-localize with alpha-actinin--analysis of patient mutations. (PMID: 16476425) Klaavuniemi T. … YlAonne J. (Exp. Cell Res. 2006) 3 23

Products for LDB3 Gene

Sources for LDB3 Gene

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