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LDB3 Gene

protein-coding   GIFtS: 58
GCID: GC10P088426

LIM Domain Binding 3

(Previous names: cardiomyopathy, dilated 1C (autosomal dominant))
(Previous symbol: CMD1C)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LIM Domain Binding 31 2     cypher1
CMD1C1 2 5     oracle1
ZASP2 3 5     LDB3Z12
Cardiomyopathy, Dilated 1C (Autosomal Dominant)1 2     LDB3Z42
Z-Band Alternatively Spliced PDZ Motif Protein1 2     ORACLE2
Protein Cypher2 3     PDLIM62
Z-Band Alternatively Spliced PDZ-Motif Protein2 3     LIM Domain-Binding Protein 32
CYPHER2 5     PDZ And LIM Domain 62
LVNC32 5     KIAA06133
MFM42 5     KIAA016135

External Ids:    HGNC: 157101   Entrez Gene: 111552   Ensembl: ENSG000001223677   OMIM: 6059065   UniProtKB: O751123   

Export aliases for LDB3 gene to outside databases

Previous GC identifers: GC10P087309 GC10P087650 GC10P088559 GC10P088092 GC10P088418 GC10P082282


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 left ventricular noncompaction 3, with or without dilated cardiomyopathy, and zaspopathy. GO annotations related to this gene include muscle alpha-actinin binding and cytoskeletal protein binding. An important paralog of this gene is LIMS1.

UniProtKB/Swiss-Prot: LDB3_HUMAN, O75112
Function: 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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000010.11  NT_030059.14  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LDB3 gene promoter:
         RFX1   AP-2gamma   Pax-4a   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLDB3 promoter sequence
   Search Chromatin IP Primers for LDB3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LDB3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q22.3-q23.2   Ensembl cytogenetic band:  10q23.2   HGNC cytogenetic band: 10q22.3-q23.2

LDB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LDB3 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P088426:  view genomic region     (about GC identifiers)

Start:
88,428,206 bp from pter      End:
88,495,825 bp from pter
Size:
67,620 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LDB3_HUMAN, O75112 (See protein sequence)
Recommended Name: LIM domain-binding protein 3  
Size: 727 amino acids; 77135 Da
Subunit: 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 caution: Sequence=BAA31588.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for LDB3:
1RGW (3D)    
Secondary accessions: A2TDB7 A6NIV4 B4E3K3 Q5K6N9 Q5K6P0 Q5K6P1 Q96FH2 Q9Y4Z3 Q9Y4Z4 Q9Y4Z5
Alternative splicing: 7 isoforms:  O75112-1   O75112-2   O75112-3   O75112-4   O75112-5   O75112-6   O75112-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LDB3: NX_O75112

Explore proteomics data for LDB3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See LDB3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_001073583.1  NP_001073584.1  NP_001073585.1  NP_001165081.1  NP_001165082.1  NP_009009.1  

    ENSEMBL proteins: 
     ENSP00000361136   ENSP00000355296   ENSP00000401437   ENSP00000409148   ENSP00000263067  
     ENSP00000263066   ENSP00000361126   ENSP00000311913   ENSP00000438866  

    LDB3 Human Recombinant Protein Products:

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    Novus Biologicals LDB3 Protein
    Novus Biologicals LDB3 Lysate
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for LDB3

    LDB3 Antibody Products:

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    Abcam antibodies for LDB3
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    ThermoFisher Antibodies for LDB3
    LSBio Antibodies in human, mouse, rat for LDB3

    LDB3 Assay Products:

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    Cloud-Clone Corp. ELISAs for LDB3
    Cloud-Clone Corp. CLIAs for LDB3


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR006643 ZASP
     IPR001478 PDZ
     IPR001781 Znf_LIM

    Graphical View of Domain Structure for InterPro Entry O75112

    ProtoNet protein and cluster: O75112

    2 Blocks protein domains:
    IPB001478 PDZ/DHR/GLGF domain
    IPB001781 Zn-binding protein


    UniProtKB/Swiss-Prot: LDB3_HUMAN, O75112
    Similarity: Contains 3 LIM zinc-binding domains
    Similarity: Contains 1 PDZ (DHR) domain


    LDB3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: LDB3_HUMAN, O75112
    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): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005080protein kinase C binding IEA--
    GO:0005515protein binding IPI10427098
    GO:0008092cytoskeletal protein binding IPI17987659
    GO:0008270zinc ion binding IEA--
    GO:0051371muscle alpha-actinin binding IEA--
         
    LDB3 for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Ldb3):
     behavior/neurological  cardiovascular system  digestive/alimentary  growth/size/body  homeostasis/metabolism 
     mortality/aging  muscle  respiratory system 

    LDB3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LDB3
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LDB3
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LDB3

    miRNA
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    Block miRNA regulation of human, mouse, rat LDB3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LDB3 (see all 48):
    hsa-miR-579 hsa-miR-607 hsa-let-7d hsa-let-7a-2* hsa-miR-342-3p hsa-miR-10b* hsa-let-7g hsa-let-7a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Predesigned siRNA for gene silencing in human, mouse, rat LDB3

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    GenScript: all cDNA clones in your preferred vector (see all 6): LDB3 (NM_001080114)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LDB3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LDB3

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LDB3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    LDB3_HUMAN, O75112: 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: 

    CompartmentConfidence
    cytoskeleton5
    cytosol3
    nucleus3
    mitochondrion2

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005856cytoskeleton IDA10427098
    GO:0030018Z disc IDA10427098
    GO:0031143pseudopodium IEA--
    GO:0048471perinuclear region of cytoplasm IEA--

    LDB3 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LDB3
    Interactions:

        Search GeneGlobe Interaction Network for LDB3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for LDB3 (O751123 ENSP000003552964) via UniProtKB, MINT, STRING, and/or I2D (see all 82)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACTN2P356093, ENSP000003555374I2D: score=4 STRING: ENSP00000355537
    MYOZ3Q8TDC03, ENSP000002971304I2D: score=4 STRING: ENSP00000297130
    PRKCBP057713, ENSP000003053554I2D: score=3 STRING: ENSP00000305355
    PRKCDQ056553, ENSP000003316024I2D: score=3 STRING: ENSP00000331602
    PRKCZQ055133, ENSP000003678304I2D: score=3 STRING: ENSP00000367830
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0045214sarcomere organization IEA--

    LDB3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LDB3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LDB3 gene (6 alternative transcripts): 
    NM_001080114.1  NM_001080115.1  NM_001080116.1  NM_001171610.1  NM_001171611.1  NM_007078.2  

    Unigene Cluster for LDB3:

    LIM domain binding 3
    Hs.657271  [show with all ESTs]
    Unigene Representative Sequence: NM_001171610
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372066(uc001kdr.3) ENST00000361373 ENST00000477489(uc009xta.2)
    ENST00000429277(uc010qmm.2 uc001kdv.3) ENST00000458213(uc009xsz.3 uc001kdu.3)
    ENST00000352360 ENST00000263066 ENST00000372056(uc001kdt.3 uc009xsy.3)
    ENST00000310944(uc001kds.3) ENST00000542786

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat LDB3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LDB3 (see all 48):
    hsa-miR-579 hsa-miR-607 hsa-let-7d hsa-let-7a-2* hsa-miR-342-3p hsa-miR-10b* hsa-let-7g hsa-let-7a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LDB3
    Clone
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    OriGene clones in human, mouse for LDB3 (see all 37)
    OriGene ORF clones in mouse, rat for LDB3
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): LDB3 (NM_001080114)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LDB3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LDB3
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for LDB3
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat LDB3
      QuantiTect SYBR Green Assays in human, mouse, rat LDB3
      QuantiFast Probe-based Assays in human, mouse, rat LDB3

    Additional mRNA sequence: 

    AB014513.1 AF086263.1 AF276807.1 AF276809.1 AJ133766.1 AJ133767.1 AJ133768.1 AK294696.1 
    AK297871.1 AK300692.1 AK304760.1 AL359621.1 BC010929.2 

    22 DOTS entries:

    DT.121286610  DT.121286688  DT.100747087  DT.95269114  DT.115157  DT.121286569  DT.413708  DT.100018449 
    DT.121286559  DT.121286522  DT.115158  DT.121286621  DT.100674644  DT.100747088  DT.121286595  DT.121286611 
    DT.121286672  DT.91865560  DT.95265953  DT.100722552  DT.102835935  DT.91789178 

    Selected AceView cDNA sequences (see all 143):

    AI566346 AA884579 F26953 C05437 AI336399 BX499990 F33131 F27063 
    F36193 W67975 AI688502 AA425362 F31093 F36311 AL044762 BX094078 
    BX500170 AA425568 AB014513 NM_007078 AJ572188 AF086263 AI383171 BC023609 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for LDB3 (see all 12)    About this scheme

    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:              -     -     -     -     -                       -     -     -                                                                                 

    ExUns: 16
    SP1:      
    SP2:      
    SP3:      
    SP4:      
    SP5:      


    ECgene alternative splicing isoforms for LDB3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LDB3 expression in normal human tissues (normalized intensities)      LDB3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTTTTTTTT
    LDB3 Expression
    About this image


    LDB3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 18 entries
             Mononuclear Myocytes Hyoid Arch Muscles
     
     Limb (Muscoskeletal System)    fully expand to see all 4 entries
             Multinuclear Myocytes Forelimb Dorsal Muscles
     
     Heart (Cardiovascular System)    fully expand to see all 3 entries
             Primitive Heart Tube Cells Primitive Heart Tube
             Heart Tube
             Cardiomyocyte-like progenitor cells
     
     Dermis (Integumentary System)    fully expand to see all 2 entries
             Zigzag Dermal Papilla Cells Dermal Papilla
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
    LDB3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LDB3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.657271

    UniProtKB/Swiss-Prot: LDB3_HUMAN, O75112
    Tissue specificity: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain
    and placenta

        Custom PCR Arrays for LDB3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LDB3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for LDB3 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ldb31 , 5 LIM domain binding 31, 5 82.47(n)1
    86.53(a)1
      14 (20.83 cM)5
    241311  NM_001039072.21  NP_001034161.11 
     345266995 
    chicken
    (Gallus gallus)
    Aves LOC1017500261 LIM domain-binding protein 3-like 78.32(n)
    85.31(a)
      101750026  XM_004941945.1  XP_004942002.1 
    lizard
    (Anolis carolinensis)
    Reptilia LDB36
    LIM domain binding 3
    59(a)
    1 ↔ 1
    GL343199.1(4430792-4644175)
    African clawed frog
    (Xenopus laevis)
    Amphibia ldb3-prov2 LIM domain binding 3 77.96(n)    BC042340.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC045908.12   -- 78.5(n)    BC045908.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Zasp526
    Z band alternatively spliced PDZ-motif protein 52
    11(a)
    1 → many
    2R(11650070-11704509)
    worm
    (Caenorhabditis elegans)
    Secernentea alp-16
    Protein ALP-1, isoform d
    14(a)
    1 → many
    IV(8852500-8862487) WBGene00001132


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LDB3 gene
    LIMS12  PDLIM72  LIMS3L2  FHL32  FHL52  LPXN2  FHL12  ENSG000002572072  
    LIMS32  TGFB1I12  PDLIM52  PXN2  LIMS22  FHL22  
    7 SIMAP similar genes for LDB3 using alignment to 2 protein entries:     LDB3_HUMAN (see all proteins):
    LHx4    LIMS2    LIM    LMO3    FHL3    LMO1
    PDLIM5

    LDB3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for LDB3 (see all 1737)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs454876991,2,,4
    CCardiomyopathy, dilated 1C (CMD1C)4 pathogenic188813291(+) GGGCTC/TGAGCC 10 S L int1 mis17Minor allele frequency- T:0.00NS NA EU 5097
    rs455140021,2,,4
    CCardiomyopathy, dilated 1C (CMD1C)4 pathogenic188857773(+) GCTGCG/AATTTC 6 /N /D mis16Minor allele frequency- A:0.01NS NA EA 564
    VAR_0240104
    Cardiomyopathy, dilated 1C (CMD1C)4--see VAR_0240102 T I mis40--------
    VAR_0240114
    Cardiomyopathy, dilated 1C (CMD1C)4--see VAR_0240112 I M mis40--------
    rs455552401,2
    C,Fnon-pathogenic188838272(+) GCCTCC/AGCCTC 4 /S int1 syn17Minor allele frequency- A:0.06NS CSA WA NA 4848
    rs454594911,2
    C,Fnon-pathogenic188838305(+) CCTGCC/TGACAG 4 A int1 syn17Minor allele frequency- T:0.03NS NA EU 4345
    rs1219083381,2
    C,Fpathogenic188818684(+) GCGCCG/AACTAC 10 /N /D mis1 int11Minor allele frequency- A:0.01EU 713
    rs1219083351,2
    Cpathogenic188830921(+) AATTGC/TGCAAC 9 R C int1 mis10--------
    rs1219083361,2
    C,Fpathogenic188838266(+) GCCATC/G/TGCCTC 4 I M int1 mis11NA 4360
    rs455921391,2,,4
    C,Fprobable-non-pathogenic188811749(+) TCTGCC/TGGTGA 12 P L mis18Minor allele frequency- T:0.01NS NA WA EU 6457

    HapMap Linkage Disequilibrium report for LDB3 (88428206 - 88495825 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for LDB3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv470968CNV Loss18288195
    nsv519805CNV Loss19592680
    nsv895836CNV Loss21882294
    dgv116n27CNV Loss19166990
    nsv895857CNV Loss21882294
    nsv467411CNV Loss19166990
    nsv524269CNV Loss19592680
    nsv520811CNV Loss19592680
    dgv793n71CNV Gain21882294
    nsv517139CNV Gain+Loss19592680

    Human Gene Mutation Database (HGMD): LDB3
    Locus Specific Mutation Databases (LSDB): LDB3

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LDB3
    DNA2.0 Custom Variant and Variant Library Synthesis for LDB3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605906   
    OMIM disorders: 609452  601493  
    UniProtKB/Swiss-Prot: LDB3_HUMAN, O75112
  • Cardiomyopathy, dilated 1C (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. 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

  • Selected diseases for LDB3 (see all 28):    About MalaCards
    left ventricular noncompaction 3, with or without dilated cardiomyopathy    zaspopathy    myopathy, myofibrillar, 4    cardiomyopathy, dilated 1c
    ldb3-related dilated cardiomyopathy    myofibrillar myopathy    coronary aneurysm    left ventricular noncompaction
    cardiomyopathy, dilated, 1w    dilated cardiomyopathy    left ventricular noncompaction 1, with or without congenital heart defects    barth syndrome
    myopathy    arrhythmogenic right ventricular dysplasia    inclusion body myositis    myositis
    limb-girdle muscular dystrophy    myotonic dystrophy    congestive heart failure    hypertrophic cardiomyopathy

    4 diseases from the University of Copenhagen DISEASES database for LDB3:
    Myocardial infarction     Coronary aneurysm     Coronary heart disease     Barth syndrome

    LDB3 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    1 Novoseek inferred disease relationship for LDB3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    myopathy 75.1 4 19047374 (1), 17337483 (1), 19181098 (1), 19050726 (1)

    GeneTests: LDB3
    GeneReviews: LDB3
    Genetic Association Database (GAD): LDB3
    Human Genome Epidemiology (HuGE) Navigator: LDB3 (6 documents)

    Export disorders for LDB3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LDB3 gene, integrated from 10 sources (see all 44):
    (articles sorted by number of sources associating them with LDB3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in Cypher/ZASP in patients with dilated cardiomyopathy and left ventricular non-compaction. (PubMed id 14662268)1, 2, 3 Vatta M.... Towbin J.A. (J. Am. Coll. Cardiol. 2003)
    2. ZASP: a new Z-band alternatively spliced PDZ-motif protein. (PubMed id 10427098)1, 2, 3 Faulkner G.... Lanfranchi G. (J. Cell Biol. 1999)
    3. Cypher/ZASP is a novel A-kinase anchoring protein. (PubMed id 23996002)1, 3 Lin C....Cheng H. (J. Biol. Chem. 2013)
    4. Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked I^-N-acetylglucosamine-substituted protein in human heart myofibrils. (PubMed id 23271734)1, 3 Leung M.C....Marston S.B. (J. Biol. Chem. 2013)
    5. A novel custom resequencing array for dilated cardiomyopathy. (PubMed id 20474083)1, 4 Zimmerman R.S....Funke B.H. (Genet. Med. 2010)
    6. Common susceptibility variants examined for association with dilated cardiomyopathy. (PubMed id 20201937)1, 4 Rampersaud E....Martin E.R. (Ann. Hum. Genet. 2010)
    7. Candidate-gene testing for orphan limb-girdle muscular dystrophies. (PubMed id 19472918)1, 4 Aurino S....Nigro V. (Acta Myol 2008)
    8. Relationship between sex, shape, and substrate in hypertrophic cardiomyopathy. (PubMed id 18513529)1, 4 Bos J.M....Ackerman M.J. (Am. Heart J. 2008)
    9. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 11155 HGNC: 15710 AceView: LDB3 Ensembl:ENSG00000122367 euGenes: HUgn11155
    ECgene: LDB3 H-InvDB: LDB3

    (According to HUGE)
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    HUGE: KIAA0613 KIAA01613

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LDB3 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=LDB3[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LDB3 gene:
    Search GeneIP for patents involving LDB3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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