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Aliases for PDLIM1 Gene

Aliases for PDLIM1 Gene

  • PDZ And LIM Domain 1 2 3 5
  • Elfin 2 3 4
  • Carboxyl Terminal LIM Domain Protein 1 2 3
  • LIM Domain Protein CLP-36 3 4
  • CLIM1 3 4
  • CLP36 3 4
  • Epididymis Secretory Protein Li 112 3
  • C-Terminal LIM Domain Protein 1 4
  • PDZ And LIM Domain 1 (Elfin) 2
  • PDZ And LIM Domain Protein 1 3
  • HEL-S-112 3
  • CLP-36 3
  • HCLIM1 3

External Ids for PDLIM1 Gene

Previous HGNC Symbols for PDLIM1 Gene

  • CLIM1

Previous GeneCards Identifiers for PDLIM1 Gene

  • GC10M095890
  • GC10M096230
  • GC10M097128
  • GC10M096661
  • GC10M096987
  • GC10M096997
  • GC10M090624

Summaries for PDLIM1 Gene

Entrez Gene Summary for PDLIM1 Gene

  • This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]

GeneCards Summary for PDLIM1 Gene

PDLIM1 (PDZ And LIM Domain 1) is a Protein Coding gene. Diseases associated with PDLIM1 include Supravalvar Aortic Stenosis and Hyperacusis. GO annotations related to this gene include transcription coactivator activity. An important paralog of this gene is PDLIM3.

UniProtKB/Swiss-Prot for PDLIM1 Gene

  • Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton.

Gene Wiki entry for PDLIM1 Gene

Additional gene information for PDLIM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM1 Gene

Genomics for PDLIM1 Gene

Regulatory Elements for PDLIM1 Gene

Enhancers for PDLIM1 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
GH10H095259 1.9 FANTOM5 Ensembl ENCODE dbSUPER 16.9 +26.6 26614 10.2 FOXA2 ATF1 ARNT TCF12 ZNF121 ZNF766 GLIS2 GATA2 ELK1 FOS PDLIM1 CYP2C8 ACSM6 GC10M095264 GC10M095235
GH10H095286 2 FANTOM5 Ensembl ENCODE dbSUPER 11.8 -1.1 -1067 11.8 HDGF PKNOX1 ARID4B SIN3A FEZF1 ZNF143 ZNF207 SP3 SP5 JUNB PDLIM1 TBC1D12 CYP2C8 ENTPD1 SORBS1 GC10M095392
GH10H095234 1.4 Ensembl ENCODE dbSUPER 11.3 +55.2 55160 2.2 PKNOX1 TBL1XR1 BMI1 BATF RFX5 ATF7 FOS ETV6 RUNX3 CREM ACSM6 PDLIM1 CYP2C8 TCTN3 GC10M095235 ENSG00000234026
GH10H095182 1.4 FANTOM5 ENCODE 10.6 +107.6 107565 1.5 ATF1 SIN3A ZNF2 YY1 ETS1 ZNF121 GLIS2 ZNF143 ZNF207 ATF7 ZNF518A TCTN3 CCNJ PDLIM1 HELLS CYP2C8 ACSM6 SORBS1 PAWRP1 ENSG00000274691
GH10H095332 1.3 Ensembl ENCODE dbSUPER 11.2 -43.8 -43822 4.3 FOXA2 MLX ARID4B RAD21 RARA FOS CREM NR2F2 TGIF2 NFIL3 PDLIM1 ACSM6 GC10M095392
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDLIM1 on UCSC Golden Path with GeneCards custom track

Promoters for PDLIM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000031912 448 1801 HDGF ARID4B SIN3A ZNF121 GLIS2 ZNF143 ZNF207 KLF7 RUNX3 SP3

Genomic Locations for PDLIM1 Gene

Genomic Locations for PDLIM1 Gene
53,581 bases
Minus strand

Genomic View for PDLIM1 Gene

Genes around PDLIM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM1 Gene

Proteins for PDLIM1 Gene

  • Protein details for PDLIM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PDZ and LIM domain protein 1
    Protein Accession:
    Secondary Accessions:
    • B2RBS6
    • Q5VZH5
    • Q9BPZ9

    Protein attributes for PDLIM1 Gene

    329 amino acids
    Molecular mass:
    36072 Da
    Quaternary structure:
    • Interacts with alpha-actinins 1, 2 and 4.

    Three dimensional structures from OCA and Proteopedia for PDLIM1 Gene

neXtProt entry for PDLIM1 Gene

Post-translational modifications for PDLIM1 Gene

  • Ubiquitination at Lys22
  • Modification sites at PhosphoSitePlus

Other Protein References for PDLIM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PDLIM1 Gene

Domains & Families for PDLIM1 Gene

Gene Families for PDLIM1 Gene

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

Protein Domains for PDLIM1 Gene

Suggested Antigen Peptide Sequences for PDLIM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDLIM1: view

No data available for UniProtKB/Swiss-Prot for PDLIM1 Gene

Function for PDLIM1 Gene

Molecular function for PDLIM1 Gene

UniProtKB/Swiss-Prot Function:
Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton.

Phenotypes From GWAS Catalog for PDLIM1 Gene

Gene Ontology (GO) - Molecular Function for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IEA --
GO:0046872 metal ion binding IEA --
GO:0098641 cadherin binding involved in cell-cell adhesion IDA 25468996
genes like me logo Genes that share ontologies with PDLIM1: view
genes like me logo Genes that share phenotypes with PDLIM1: view

Animal Model Products

miRNA for PDLIM1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDLIM1 Gene

Localization for PDLIM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM1 Gene

Cytoplasm. Cytoplasm, cytoskeleton. Note=Associates with the actin stress fibers. {ECO:0000250}.

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 PDLIM1 gene
Compartment Confidence
cytoskeleton 4
cytosol 3
nucleus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (3)
  • Cell Junctions (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005667 transcription factor complex IEA --
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005913 cell-cell adherens junction IDA 25468996
GO:0005925 focal adhesion IDA 21423176
genes like me logo Genes that share ontologies with PDLIM1: view

Pathways & Interactions for PDLIM1 Gene

SuperPathways for PDLIM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006979 response to oxidative stress TAS 8522188
GO:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with PDLIM1: view

No data available for Pathways by source and SIGNOR curated interactions for PDLIM1 Gene

Drugs & Compounds for PDLIM1 Gene

(1) Drugs for PDLIM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDLIM1: view

Transcripts for PDLIM1 Gene

Unigene Clusters for PDLIM1 Gene

PDZ and LIM domain 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c · 9d
SP1: - - -
SP2: - - - - -
SP3: - - -
SP4: - -
SP5: - - - - - - - -
SP6: -
SP7: - - - - - -

Relevant External Links for PDLIM1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDLIM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDLIM1 Gene

This gene is overexpressed in Muscle - Skeletal (x5.4).

Protein differential expression in normal tissues from HIPED for PDLIM1 Gene

This gene is overexpressed in Platelet (19.2), Bone marrow stromal cell (6.8), and Peripheral blood mononuclear cells (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM1 Gene

Protein tissue co-expression partners for PDLIM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM1 Gene:


SOURCE GeneReport for Unigene cluster for PDLIM1 Gene:


mRNA Expression by UniProt/SwissProt for PDLIM1 Gene:

Tissue specificity: Strongly expressed in the heart and skeletal muscle, moderately expressed in the spleen, small intestine, colon, placenta, and lung. A lower level expression is seen in liver, thymus, kidney, prostate and pancreas and is not found in the brain, testis, ovary, and peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for PDLIM1 Gene

  • Heart(4.6)
  • Pancreas(4.6)
  • Liver(4.5)
  • Blood(4.4)
  • Lung(3.9)
  • Nervous system(3.7)
  • Intestine(3.5)
  • Muscle(3)
  • Skin(2.3)
  • Eye(2.2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with PDLIM1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM1 Gene

Orthologs for PDLIM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDLIM1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDLIM1 33 34
  • 99.5 (n)
(Bos Taurus)
Mammalia PDLIM1 33 34
  • 91.16 (n)
(Canis familiaris)
Mammalia PDLIM1 33 34
  • 88.55 (n)
(Mus musculus)
Mammalia Pdlim1 33 16 34
  • 87.38 (n)
(Monodelphis domestica)
Mammalia PDLIM1 34
  • 87 (a)
(Rattus norvegicus)
Mammalia Pdlim1 33
  • 86.44 (n)
(Ornithorhynchus anatinus)
Mammalia PDLIM1 34
  • 70 (a)
(Gallus gallus)
Aves PDLIM1 33 34
  • 73.5 (n)
(Anolis carolinensis)
Reptilia PDLIM1 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdlim1 33
  • 71.08 (n)
MGC76041 33
(Danio rerio)
Actinopterygii pdlim1 33 34
  • 68.03 (n)
Dr.23376 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10330 33
Species where no ortholog for PDLIM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PDLIM1 Gene

Gene Tree for PDLIM1 (if available)
Gene Tree for PDLIM1 (if available)

Paralogs for PDLIM1 Gene

Paralogs for PDLIM1 Gene

(3) SIMAP similar genes for PDLIM1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PDLIM1: view

Variants for PDLIM1 Gene

Sequence variations from dbSNP and Humsavar for PDLIM1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs1000035864 -- 95,271,695(+) AAGTG(C/T)GTCAT intron-variant, reference, synonymous-codon
rs1000083911 -- 95,281,062(+) AACAC(C/T)AAGAG intron-variant
rs1000268790 -- 95,246,991(+) GCCAG(G/T)CCTGG intron-variant
rs1000339445 -- 95,261,283(+) TTCAA(C/T)TAAGG intron-variant
rs1000359280 -- 95,241,049(+) GACAA(A/G)AGCAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDLIM1 Gene

Variant ID Type Subtype PubMed ID
nsv1113331 CNV deletion 24896259
nsv1110852 OTHER inversion 24896259
nsv1069957 CNV deletion 25765185
esv22688 CNV gain+loss 19812545

Variation tolerance for PDLIM1 Gene

Residual Variation Intolerance Score: 27.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.06; 21.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDLIM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM1 Gene

Disorders for PDLIM1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for PDLIM1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
supravalvar aortic stenosis
  • supravalvular aortic stenosis
  • low tolerance to sound
williams-beuren syndrome
  • fanconi schlesinger syndrome
  • susceptibility to strabismus
aortic valve disease 2
  • aortic valve stenosis
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PDLIM1

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 PDLIM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM1 Gene

Publications for PDLIM1 Gene

  1. Interaction of hCLIM1, an enigma family protein, with alpha-actinin 2. (PMID: 10861853) Kotaka M … Waye MM (Journal of cellular biochemistry 2000) 2 3 4 22 60
  2. CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4. (PMID: 10753915) Vallenius T … Mäkelä TP (The Journal of biological chemistry 2000) 3 4 22 60
  3. Human CLP36, a PDZ-domain and LIM-domain protein, binds to alpha-actinin-1 and associates with actin filaments and stress fibers in activated platelets and endothelial cells. (PMID: 11110697) Bauer K … Siess W (Blood 2000) 3 4 22 60
  4. Characterization of the human 36-kDa carboxyl terminal LIM domain protein (hCLIM1). (PMID: 10022510) Kotaka M … Waye MM (Journal of cellular biochemistry 1999) 3 4 22 60
  5. Refined genomic localization and ethnic differences observed for the IBD5 association with Crohn's disease. (PMID: 17213842) Silverberg MS … NIDDK IBD Genetics Consortium (European journal of human genetics : EJHG 2007) 3 45 60

Products for PDLIM1 Gene

Sources for PDLIM1 Gene

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