This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory s... See more...

Aliases for PDLIM5 Gene

Aliases for PDLIM5 Gene

  • PDZ And LIM Domain 5 2 3 5
  • Enigma-Like PDZ And LIM Domains Protein 3 4
  • PDZ And LIM Domain Protein 5 3 4
  • Enigma Homolog 3 4
  • ENH 3 4
  • Enigma-Like LIM Domain Protein 3
  • ENH1 3
  • LIM 3
  • L9 3

External Ids for PDLIM5 Gene

Previous GeneCards Identifiers for PDLIM5 Gene

  • GC04P095731
  • GC04P095592
  • GC04P095373
  • GC04P091110

Summaries for PDLIM5 Gene

Entrez Gene Summary for PDLIM5 Gene

  • This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

GeneCards Summary for PDLIM5 Gene

PDLIM5 (PDZ And LIM Domain 5) is a Protein Coding gene. Diseases associated with PDLIM5 include Nail-Patella Syndrome and Bipolar Disorder. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. Gene Ontology (GO) annotations related to this gene include actin binding and protein kinase C binding. An important paralog of this gene is LDB3.

UniProtKB/Swiss-Prot Summary for PDLIM5 Gene

  • May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Overexpression promotes the development of heart hypertrophy. Contributes to the regulation of dendritic spine morphogenesis in neurons. May restrain postsynaptic growth of excitatory synapses (By similarity).

Gene Wiki entry for PDLIM5 Gene

Additional gene information for PDLIM5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDLIM5 Gene

Genomics for PDLIM5 Gene

GeneHancer (GH) Regulatory Elements for PDLIM5 Gene

Promoters and enhancers for PDLIM5 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
GH04J094450 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 507.4 +1.4 1444 6.2 HNRNPK ZSCAN5C SIN3A NRF1 POLR2G NCOR1 FOS POLR2A CLOCK TCF7 PDLIM5 NONHSAG038451.2 lnc-HPGDS-4 lnc-SMARCAD1-3
GH04J094558 Enhancer 1.3 Ensembl ENCODE dbSUPER 22.2 +110.2 110155 8.4 EP300 NCOR1 KDM6A TCF7 TRIM28 CTBP1 SMARCC2 SKI TEAD1 TBX3 PDLIM5 L13714-348 MF281438-018 NONHSAG038451.2
GH04J094484 Enhancer 1.2 Ensembl ENCODE dbSUPER 18.6 +36.3 36344 8.8 TCF12 USF1 POLR2A REST USF2 TOE1 EP300 MYC ATF2 OSR2 RF00017-4365 PDLIM5 MF281438-018 NONHSAG038451.2
GH04J094515 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 17.5 +65.0 65048 3.2 ZNF10 POLR2A EP300 OSR2 ZNF316 TCF7L2 MAFF FOS FOSL2 MAFK PDLIM5 MF281438-018 L13714-348 NONHSAG038451.2
GH04J094542 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 14.1 +96.2 96243 10.6 TCF12 JUND ZBTB5 POLR2A CLOCK RFX1 HES1 MYC EP300 ATF2 PDLIM5 HPGDS L13714-348 MF281438-018 NONHSAG038451.2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDLIM5 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDLIM5

Top Transcription factor binding sites by QIAGEN in the PDLIM5 gene promoter:
  • SRF
  • SRF (504 AA)

Genomic Locations for PDLIM5 Gene

Genomic Locations for PDLIM5 Gene
chr4:94,451,857-94,668,227
(GRCh38/hg38)
Size:
216,371 bases
Orientation:
Plus strand
chr4:95,373,037-95,589,377
(GRCh37/hg19)
Size:
216,341 bases
Orientation:
Plus strand

Genomic View for PDLIM5 Gene

Genes around PDLIM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM5 Gene

Proteins for PDLIM5 Gene

  • Protein details for PDLIM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96HC4-PDLI5_HUMAN
    Recommended name:
    PDZ and LIM domain protein 5
    Protein Accession:
    Q96HC4
    Secondary Accessions:
    • A8K6F9
    • D6RB78
    • E9PBF5
    • O60705
    • Q56VN4
    • Q5UW38
    • Q8WVK0

    Protein attributes for PDLIM5 Gene

    Size:
    596 amino acids
    Molecular mass:
    63945 Da
    Quaternary structure:
    • Interacts with various PKC isoforms through the LIM domains. Interacts (via LIM domains) with SIPA1L1. Interacts (via PDZ domain) with actin and ACTN1 (By similarity).

    Three dimensional structures from OCA and Proteopedia for PDLIM5 Gene

    Alternative splice isoforms for PDLIM5 Gene

neXtProt entry for PDLIM5 Gene

Post-translational modifications for PDLIM5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDLIM5 Gene

Domains & Families for PDLIM5 Gene

Gene Families for PDLIM5 Gene

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

Protein Domains for PDLIM5 Gene

Blocks:
  • Zn-binding protein, LIM
  • PDZ/DHR/GLGF domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PDLIM5 Gene

GenScript: Design optimal peptide antigens:
  • Enigma-like PDZ and LIM domains protein (PDLI5_HUMAN)
genes like me logo Genes that share domains with PDLIM5: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PDLIM5 Gene

Function for PDLIM5 Gene

Molecular function for PDLIM5 Gene

UniProtKB/Swiss-Prot Function:
May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Overexpression promotes the development of heart hypertrophy. Contributes to the regulation of dendritic spine morphogenesis in neurons. May restrain postsynaptic growth of excitatory synapses (By similarity).

Phenotypes From GWAS Catalog for PDLIM5 Gene

Gene Ontology (GO) - Molecular Function for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding ISS,IEA --
GO:0005080 protein kinase C binding IEA,ISS --
GO:0005515 protein binding IPI,IEA 16549780
GO:0042805 actinin binding IEA,ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDLIM5: view
genes like me logo Genes that share phenotypes with PDLIM5: view

Animal Models for PDLIM5 Gene

MGI Knock Outs for PDLIM5:

Animal Model Products

CRISPR Products

miRNA for PDLIM5 Gene

miRTarBase miRNAs that target PDLIM5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDLIM5

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDLIM5 Gene

Localization for PDLIM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM5 Gene

Cell junction, synapse, postsynaptic density. Cell junction, synapse, presynapse. Cell junction, synapse, postsynapse. Cytoplasm, cytosol. Note=Detected both at presynaptic and postsynaptic sites, exclusively at excitatory synapses, but not inhibitory synapses, in hippocampal neurons. {ECO:0000250 UniProtKB:Q62920}.

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 PDLIM5 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
plasma membrane 4
nucleus 4
extracellular 2
mitochondrion 2
golgi apparatus 2
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA,ISS --
GO:0005886 plasma membrane IEA --
GO:0005913 cell-cell adherens junction IBA,HDA 21873635
genes like me logo Genes that share ontologies with PDLIM5: view

Pathways & Interactions for PDLIM5 Gene

genes like me logo Genes that share pathways with PDLIM5: view

Pathways by source for PDLIM5 Gene

Gene Ontology (GO) - Biological Process for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007507 heart development IBA 21873635
GO:0030036 actin cytoskeleton organization IBA 21873635
GO:0051963 regulation of synapse assembly IEA,ISS --
GO:0061001 regulation of dendritic spine morphogenesis IEA,ISS --
GO:0061049 cell growth involved in cardiac muscle cell development ISS,IEA --
genes like me logo Genes that share ontologies with PDLIM5: view

No data available for SIGNOR curated interactions for PDLIM5 Gene

Drugs & Compounds for PDLIM5 Gene

(7) Drugs for PDLIM5 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDLIM5: view

Transcripts for PDLIM5 Gene

mRNA/cDNA for PDLIM5 Gene

9 REFSEQ mRNAs :
34 NCBI additional mRNA sequence :
23 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDLIM5

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM5 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2: -
SP3: - -
SP4: - -
SP5:
SP6: - - -

Relevant External Links for PDLIM5 Gene

GeneLoc Exon Structure for
PDLIM5

Expression for PDLIM5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDLIM5 Gene

mRNA differential expression in normal tissues according to GTEx for PDLIM5 Gene

This gene is overexpressed in Heart - Left Ventricle (x7.6), Muscle - Skeletal (x7.4), and Heart - Atrial Appendage (x4.3).

Protein differential expression in normal tissues from HIPED for PDLIM5 Gene

This gene is overexpressed in Bone marrow stromal cell (22.6), Heart (9.7), and Uterus (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDLIM5 Gene



Protein tissue co-expression partners for PDLIM5 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDLIM5

SOURCE GeneReport for Unigene cluster for PDLIM5 Gene:

Hs.480311

mRNA Expression by UniProt/SwissProt for PDLIM5 Gene:

Q96HC4-PDLI5_HUMAN
Tissue specificity: Heart and skeletal muscle specific. Expression is commonly increased in the brain of patients with bipolar disorder, schizophrenia, and major depression.

Evidence on tissue expression from TISSUES for PDLIM5 Gene

  • Heart(4.8)
  • Blood(4.5)
  • Liver(4.5)
  • Muscle(4.5)
  • Nervous system(4.4)
  • Skin(4.3)
  • Kidney(2.9)
  • Lung(2.7)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with PDLIM5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM5 Gene

Orthologs for PDLIM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDLIM5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDLIM5 31 30
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PDLIM5 31 30
  • 92 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdlim5 30
  • 86.35 (n)
mouse
(Mus musculus)
Mammalia Pdlim5 17 31 30
  • 86.24 (n)
cow
(Bos Taurus)
Mammalia PDLIM5 31
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDLIM5 31
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDLIM5 31
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDLIM5 31 30
  • 75.18 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDLIM5 31
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdlim5 30
  • 70.18 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2356 30
zebrafish
(Danio rerio)
Actinopterygii pdlim5a 31 30
  • 62.09 (n)
OneToMany
pdlim5b 31
  • 46 (a)
OneToMany
zgc56116 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7740 30
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 31
  • 9 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea alp-1 31
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 36 (a)
ManyToMany
-- 31
  • 34 (a)
ManyToMany
Species where no ortholog for PDLIM5 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)
  • 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 PDLIM5 Gene

ENSEMBL:
Gene Tree for PDLIM5 (if available)
TreeFam:
Gene Tree for PDLIM5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDLIM5: view image

Paralogs for PDLIM5 Gene

(21) SIMAP similar genes for PDLIM5 Gene using alignment to 9 proteins:

  • PDLI5_HUMAN
  • D3YTJ1_HUMAN
  • D6RAA1_HUMAN
  • D6RGG6_HUMAN
  • F5H0X8_HUMAN
  • F5H7Y0_HUMAN
  • H0Y8Y3_HUMAN
  • H0Y929_HUMAN
  • H0YBI4_HUMAN
genes like me logo Genes that share paralogs with PDLIM5: view

Variants for PDLIM5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDLIM5 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
760601 Likely Benign: not provided 94,640,394(+) G/A SYNONYMOUS_VARIANT
773710 Benign: not provided 94,618,116(+) G/. MISSENSE_VARIANT,NO_SEQUENCE_ALTERATION
777394 Benign: not provided 94,575,789(+) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
789175 Likely Benign: not provided 94,662,506(+) A/G MISSENSE_VARIANT
rs1064238 - p.Ser319Leu

Additional dbSNP identifiers (rs#s) for PDLIM5 Gene

Structural Variations from Database of Genomic Variants (DGV) for PDLIM5 Gene

Variant ID Type Subtype PubMed ID
dgv2855n106 CNV deletion 24896259
esv1135092 CNV deletion 17803354
esv2304226 CNV deletion 18987734
esv2451649 CNV deletion 19546169
esv2492606 CNV deletion 19546169
esv2727990 CNV deletion 23290073
esv3310128 CNV mobile element insertion 20981092
esv3326324 CNV insertion 20981092
esv3349257 CNV insertion 20981092
esv3422122 CNV insertion 20981092
esv3449928 CNV insertion 20981092
esv3564279 CNV deletion 23714750
esv4831 CNV loss 18987735
esv6075 CNV loss 19470904
esv991897 CNV deletion 20482838
nsv1074199 CNV deletion 25765185
nsv1141989 OTHER inversion 24896259
nsv477201 CNV novel sequence insertion 20440878
nsv594901 CNV gain 21841781
nsv956329 CNV deletion 24416366

Variation tolerance for PDLIM5 Gene

Residual Variation Intolerance Score: 47.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.21; 52.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDLIM5 Gene

Human Gene Mutation Database (HGMD)
PDLIM5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDLIM5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM5 Gene

Disorders for PDLIM5 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PDLIM5 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
nail-patella syndrome
  • nps
bipolar disorder
  • major affective disorder 1
depression
  • major depressive disorder
schizophrenia
  • sczd
left ventricular noncompaction
  • left ventricular hypertrabeculation
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDLIM5

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 PDLIM5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM5 Gene

Publications for PDLIM5 Gene

  1. Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia. (PMID: 16044170) Kato T … Yoshikawa T (Molecular psychiatry 2005) 3 4 23 41 54
  2. Positive association between the PDLIM5 gene and bipolar disorder in the Chinese Han population. (PMID: 19448850) Zhao T … Yu L (Journal of psychiatry & neuroscience : JPN 2009) 3 23 41 54
  3. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample. (PMID: 18496210) Squassina A … Del Zompo M (Psychiatric genetics 2008) 3 23 41 54
  4. The PDLIM5 gene and lithium prophylaxis: an association and gene expression analysis in Sardinian patients with bipolar disorder. (PMID: 18456508) Squassina A … Zompo MD (Pharmacological research 2008) 3 23 41 54
  5. A major single nucleotide polymorphism of the PDLIM5 gene associated with recurrent major depressive disorder. (PMID: 18197271) Liu Z … Li W (Journal of psychiatry & neuroscience : JPN 2008) 3 23 41 54

Products for PDLIM5 Gene

Sources for PDLIM5 Gene