Free for academic non-profit institutions. Other users need a Commercial license

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
  • 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
  • CYPHER 3
  • LDB3Z1 3
  • LDB3Z4 3
  • ORACLE 3
  • PDLIM6 3
  • Cypher 2
  • Oracle 2
  • 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 Left Ventricular Noncompaction and Myopathy, Myofibrillar, 4. Gene Ontology (GO) annotations related to this gene include cytoskeletal protein binding and muscle alpha-actinin binding. An important paralog of this gene is PDLIM5.

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

GeneHancer (GH) Regulatory Elements for LDB3 Gene

Promoters and enhancers for LDB3 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
GH10J086662 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 665.2 +2.8 2796 13.3 FEZF1 GLIS2 ATF7 FOS TSHZ1 SMARCB1 ZNF592 GLIS1 NBN WT1 LDB3 OPN4 ENSG00000272631 LOC105378409 GC10M086714
GH10J086519 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 6.4 -145.4 -145400 3.6 PKNOX1 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 FOS SP3 ENSG00000227896 GC10M086521 WAPL GC10M086520 LDB3 GLUD1 GC10P086518 GC10P086490
GH10J086693 Enhancer 0.8 ENCODE dbSUPER 13 +27.3 27289 1.3 CTCF ZNF654 USF1 RB1 TRIM22 REST ZIC2 RAD21 XRCC5 GLIS2 LDB3 OPN4 GC10M086714
GH10J086726 Enhancer 0.8 ENCODE dbSUPER 12.1 +61.0 60989 1.8 MEIS2 PKNOX1 FOXA2 MAFG PPARG ZNF316 NFE2 EMSY MAFK NFE2L2 BMPR1A LDB3 GC10M086714
GH10J086680 Enhancer 0.6 ENCODE dbSUPER 15.2 +14.5 14538 1.2 NFIB ZBTB33 LDB3 OPN4 ENSG00000272631 GC10M086714
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LDB3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LDB3 gene promoter:
  • Pax-4a
  • GATA-1
  • RFX1
  • AP-2gamma

Genomic Locations for LDB3 Gene

Genomic Locations for LDB3 Gene
chr10:86,666,717-86,736,072
(GRCh38/hg38)
Size:
69,356 bases
Orientation:
Plus strand
chr10:88,428,206-88,495,825
(GRCh37/hg19)
Size:
67,620 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

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

HGNC:
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,IEA 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:
  • Ldb3 Ldb3<tm1Chen>

Animal Model Products

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

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 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

mRNA/cDNA 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 ^
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 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 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:

LDB3

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.

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
Systems:
  • cardiovascular
  • immune
  • nervous
  • respiratory
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • ear
  • head
Thorax:
  • heart
  • heart valve
  • lung
Limb:
  • arm
  • forearm
  • lower limb
  • shin
  • thigh
  • upper limb
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia LDB3 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LDB3 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ldb3 16 34 33
  • 82.47 (n)
dog
(Canis familiaris)
Mammalia LDB3 34 33
  • 82.2 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LDB3 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LDB3 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC101750026 33
  • 78.32 (n)
LDB3 34
  • 60 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LDB3 34
  • 59 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia ldb3-prov 33
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75668 33
zebrafish
(Danio rerio)
Actinopterygii ldb3b 34
  • 52 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 34
  • 11 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea alp-1 34
  • 14 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
ManyToMany
-- 34
  • 35 (a)
ManyToMany
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

ENSEMBL:
Gene Tree for LDB3 (if available)
TreeFam:
Gene Tree for LDB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LDB3: view image

Paralogs for LDB3 Gene

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

  • LDB3_HUMAN
  • V5T7C5_HUMAN
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 Variation AA Info Type
rs1011836119 uncertain-significance, Myofibrillar myopathy, ZASP-related 86,716,516(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1060501314 uncertain-significance, Myofibrillar myopathy, ZASP-related 86,687,277(+) GC/TA genic_upstream_transcript_variant, intron_variant
rs1060501315 uncertain-significance, Myofibrillar myopathy, ZASP-related 86,691,894(+) A/G splice_acceptor_variant
rs1060501316 uncertain-significance, Myofibrillar myopathy, ZASP-related 86,692,561(+) C/T coding_sequence_variant, stop_gained
rs1060501317 uncertain-significance, Myofibrillar myopathy, ZASP-related 86,668,714(+) C/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant

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

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

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)

Additional Variant Information for LDB3 Gene

Human Gene Mutation Database (HGMD)
LDB3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LDB3

SNP Genotyping and Copy Number Assay Products

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

Disorders for LDB3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
cardiomyopathy, dilated, 1c, with or without left ventricular noncompaction
  • cmd1c
myopathy, myofibrillar, 4
  • mfm4
late-onset distal myopathy, markesbery-griggs type
  • zasp-related myofibrillar myopathy
myofibrillar myopathy
  • myopathy, myofibrillar, desmin-related
dilated cardiomyopathy
  • cardiomyopathy, familial idiopathic
- 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 form of left ventricular non-compaction, a cardiomyopathy due to myocardial morphogenesis arrest and characterized by a hypertrophic left ventricle, a severely thickened 2-layered myocardium, numerous prominent trabeculations, deep intertrabecular recesses, and poor systolic function. Clinical manifestations are variable. Some affected individuals experience no symptoms at all, others develop heart failure. In some cases, left ventricular non-compaction is associated with other congenital heart anomalies. LVNC3 is an autosomal dominant condition. 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 disk 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.

Additional Disease Information for LDB3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 58
  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 58
  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 58
  4. Cypher/ZASP is a novel A-kinase anchoring protein. (PMID: 23996002) Lin C … Cheng H (The Journal of biological chemistry 2013) 2 3 58
  5. Common susceptibility variants examined for association with dilated cardiomyopathy. (PMID: 20201937) Rampersaud E … Martin ER (Annals of human genetics 2010) 3 44 58

Products for LDB3 Gene

Sources for LDB3 Gene

Content
Loading form....