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Aliases for PDLIM3 Gene

Aliases for PDLIM3 Gene

  • PDZ And LIM Domain 3 2 3 5
  • Alpha-Actinin-2-Associated LIM Protein 3 4
  • ALP 3 4
  • Actinin-Associated LIM Protein 4
  • PDZ And LIM Domain Protein 3 3
  • Enigma Homolog 3

External Ids for PDLIM3 Gene

Previous GeneCards Identifiers for PDLIM3 Gene

  • GC04M187118
  • GC04M186798
  • GC04M186659
  • GC04M186422
  • GC04M182175

Summaries for PDLIM3 Gene

Entrez Gene Summary for PDLIM3 Gene

  • The protein encoded by this gene contains a PDZ domain and a LIM domain, indicating that it may be involved in cytoskeletal assembly. In support of this, the encoded protein has been shown to bind the spectrin-like repeats of alpha-actinin-2 and to colocalize with alpha-actinin-2 at the Z lines of skeletal muscle. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Aberrant alternative splicing of this gene may play a role in myotonic dystrophy. [provided by RefSeq, Apr 2012]

GeneCards Summary for PDLIM3 Gene

PDLIM3 (PDZ And LIM Domain 3) is a Protein Coding gene. Diseases associated with PDLIM3 include Facioscapulohumeral Muscular Dystrophy 1 and Myotonic Dystrophy. GO annotations related to this gene include cytoskeletal protein binding and structural constituent of muscle. An important paralog of this gene is PDLIM1.

UniProtKB/Swiss-Prot for PDLIM3 Gene

  • May play a role in the organization of actin filament arrays within muscle cells.

Gene Wiki entry for PDLIM3 Gene

Additional gene information for PDLIM3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM3 Gene

Genomics for PDLIM3 Gene

Regulatory Elements for PDLIM3 Gene

Enhancers for PDLIM3 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
GH04H185565 1.7 FANTOM5 Ensembl ENCODE dbSUPER 21.2 -32.8 -32778 5.4 ELF3 TBP FOXA2 ATF1 ARID4B DMAP1 BATF YY1 ATF7 ETV6 PDLIM3 UFSP2 ENSG00000233110
GH04H185573 1.8 FANTOM5 Ensembl ENCODE dbSUPER 19.9 -38.3 -38313 1.7 PKNOX1 FOS ATF7 ZNF518A ZNF592 MAFF SMARCA4 NR2C1 SETDB1 SP7 PDLIM3 ENSG00000233110
GH04H185503 1.5 Ensembl ENCODE dbSUPER 16.8 +30.6 30587 2.4 PKNOX1 FOXA2 ATF1 ARID4B DMAP1 YY1 ELK1 ATF7 SP5 ZHX2 PDLIM3 GC04M185529 CCDC110
GH04H185559 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -24.4 -24361 1.7 ELF3 FOXA2 KLF17 DMAP1 GLIS2 FOS EGR2 SP3 REST ZNF398 PDLIM3 ENSG00000233110
GH04H185343 1.2 Ensembl ENCODE dbSUPER 11.8 +190.8 190775 2.4 SRF ZNF687 TBL1XR1 JUNB ELF1 BATF JUND HDAC2 POLR2A EED LRP2BP PDLIM3 UFSP2 LOC105377591 CFAP97
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDLIM3 on UCSC Golden Path with GeneCards custom track

Promoters for PDLIM3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000177061 411 1600 ATF1 ATF7 EGR2 SP3 ZNF174 ZEB2 SSRP1 CBX8 ZNF341 GLIS1

Genomic Locations for PDLIM3 Gene

Genomic Locations for PDLIM3 Gene
34,953 bases
Minus strand

Genomic View for PDLIM3 Gene

Genes around PDLIM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM3 Gene

Proteins for PDLIM3 Gene

  • Protein details for PDLIM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PDZ and LIM domain protein 3
    Protein Accession:
    Secondary Accessions:
    • B2R866
    • O43590
    • O60439
    • O60440
    • Q8N6Y6
    • Q9BVP4

    Protein attributes for PDLIM3 Gene

    364 amino acids
    Molecular mass:
    39232 Da
    Quaternary structure:
    • Interacts with ACTN2.

    Alternative splice isoforms for PDLIM3 Gene


neXtProt entry for PDLIM3 Gene

Post-translational modifications for PDLIM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDLIM3 Gene

Domains & Families for PDLIM3 Gene

Gene Families for PDLIM3 Gene

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

Protein Domains for PDLIM3 Gene

Suggested Antigen Peptide Sequences for PDLIM3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDLIM3: view

No data available for UniProtKB/Swiss-Prot for PDLIM3 Gene

Function for PDLIM3 Gene

Molecular function for PDLIM3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the organization of actin filament arrays within muscle cells.

Gene Ontology (GO) - Molecular Function for PDLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 23414517
GO:0008092 cytoskeletal protein binding IEA --
GO:0008307 structural constituent of muscle IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDLIM3: view
genes like me logo Genes that share phenotypes with PDLIM3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDLIM3 Gene

Localization for PDLIM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM3 Gene

Cytoplasm, myofibril, sarcomere, Z line. Note=Localizes to myofiber Z-lines.

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 PDLIM3 gene
Compartment Confidence
cytosol 5
cytoskeleton 3
nucleus 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0015629 actin cytoskeleton IEA --
GO:0030018 Z disc IEA --
genes like me logo Genes that share ontologies with PDLIM3: view

Pathways & Interactions for PDLIM3 Gene

SuperPathways for PDLIM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDLIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with PDLIM3: view

No data available for Pathways by source and SIGNOR curated interactions for PDLIM3 Gene

Drugs & Compounds for PDLIM3 Gene

(2) Drugs for PDLIM3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDLIM3: view

Transcripts for PDLIM3 Gene

Unigene Clusters for PDLIM3 Gene

PDZ and LIM domain 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM3 Gene

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

Relevant External Links for PDLIM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDLIM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM3 Gene

mRNA differential expression in normal tissues according to GTEx for PDLIM3 Gene

This gene is overexpressed in Muscle - Skeletal (x20.2).

Protein differential expression in normal tissues from HIPED for PDLIM3 Gene

This gene is overexpressed in Cardia (11.9), Prostate (7.2), and Rectum (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM3 Gene

Protein tissue co-expression partners for PDLIM3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM3 Gene:


SOURCE GeneReport for Unigene cluster for PDLIM3 Gene:


mRNA Expression by UniProt/SwissProt for PDLIM3 Gene:

Tissue specificity: Isoform 1 is highly expressed in differentiated skeletal muscle. Isoform 2 is heart-specific.

Evidence on tissue expression from TISSUES for PDLIM3 Gene

  • Heart(4.9)
  • Muscle(4.9)
  • Lung(4.3)
  • Liver(4.2)
  • Skin(4)
  • Nervous system(3.9)
  • Stomach(2.8)
  • Intestine(2.4)
genes like me logo Genes that share expression patterns with PDLIM3: 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 PDLIM3 Gene

Orthologs for PDLIM3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDLIM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDLIM3 33 34
  • 99.36 (n)
(Canis familiaris)
Mammalia PDLIM3 33 34
  • 91.03 (n)
(Monodelphis domestica)
Mammalia PDLIM3 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Pdlim3 33
  • 86.56 (n)
(Bos Taurus)
Mammalia PDLIM3 34
  • 81 (a)
(Mus musculus)
Mammalia Pdlim3 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia PDLIM3 34
  • 57 (a)
(Gallus gallus)
Aves PDLIM3 34
  • 68 (a)
(Anolis carolinensis)
Reptilia PDLIM3 34
  • 79 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13894 33
(Danio rerio)
Actinopterygii pdlim3b 34
  • 58 (a)
pdlim3a 34
  • 52 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7312 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3882 34
  • 20 (a)
Species where no ortholog for PDLIM3 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)
  • 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 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PDLIM3 Gene

Gene Tree for PDLIM3 (if available)
Gene Tree for PDLIM3 (if available)

Paralogs for PDLIM3 Gene

Paralogs for PDLIM3 Gene

(6) SIMAP similar genes for PDLIM3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with PDLIM3: view

Variants for PDLIM3 Gene

Sequence variations from dbSNP and Humsavar for PDLIM3 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs143812960 Likely benign 185,504,484(+) TGCCA(C/T)TCCCA nc-transcript-variant, reference, missense
rs146768859 Likely benign 185,535,406(+) GCGCA(A/G)GGCCC nc-transcript-variant, reference, missense
rs148256486 Likely benign 185,506,619(+) TACAC(A/C/G)TCCGA nc-transcript-variant, reference, synonymous-codon, missense
rs148570356 Likely benign 185,525,070(+) TCCTG(C/T)GCATC intron-variant, nc-transcript-variant, reference, synonymous-codon
rs776361335 Likely benign 185,508,394(+) TTAAA(C/T)TGAGC intron-variant, nc-transcript-variant, reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for PDLIM3 Gene

Variant ID Type Subtype PubMed ID
nsv830169 CNV gain+loss 17160897
nsv821047 CNV deletion 20802225
nsv596382 CNV loss 21841781
nsv596381 CNV loss 21841781
nsv596379 CNV loss 21841781
nsv596378 CNV gain+loss 21841781
nsv596375 CNV gain+loss 21841781
nsv596374 CNV gain 21841781
nsv596373 CNV gain 21841781
nsv527026 CNV gain 19592680
nsv517035 CNV gain+loss 19592680
nsv513187 CNV loss 21212237
nsv511267 CNV loss 21212237
nsv508339 CNV deletion 20534489
nsv499814 CNV loss 21111241
nsv4639 CNV deletion 18451855
nsv1149972 CNV deletion 26484159
nsv1135630 CNV deletion 24896259
nsv1111817 CNV deletion 24896259
nsv1072470 CNV deletion 25765185
nsv10624 CNV gain 18304495
nsv1029738 CNV gain 25217958
esv9232 CNV loss 19470904
esv4371 CNV loss 18987735
esv3894088 CNV gain 25118596
esv3603506 CNV gain 21293372
esv3603505 CNV loss 21293372
esv3603504 CNV gain 21293372
esv3603500 CNV gain 21293372
esv3603499 CNV loss 21293372
esv3603496 CNV gain 21293372
esv3565187 CNV deletion 23714750
esv3565185 CNV deletion 23714750
esv3296495 CNV deletion 24192839
esv28251 CNV gain 19812545
esv2759309 CNV loss 17122850
esv2728910 CNV deletion 23290073
esv2657042 CNV deletion 23128226
esv2430031 CNV deletion 19546169
esv2068423 CNV deletion 18987734
dgv9425n54 CNV gain 21841781
dgv9424n54 CNV loss 21841781
dgv9423n54 CNV gain 21841781
dgv915n67 CNV loss 20364138
dgv5493n100 CNV gain 25217958
dgv159n73 CNV deletion 24416366
dgv134e180 CNV deletion 20482838

Variation tolerance for PDLIM3 Gene

Residual Variation Intolerance Score: 36.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.62; 56.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDLIM3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM3 Gene

Disorders for PDLIM3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PDLIM3 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
facioscapulohumeral muscular dystrophy 1
  • facioscapulohumeral muscular dystrophy
myotonic dystrophy
  • myotonic dystrophy 1
osteitis fibrosa
  • hyperparathyroid bone disease
mitochondrial dna depletion syndrome 7
  • spinocerebellar ataxia 8
malignant histiocytosis
  • histiocytic medullary reticulosis [obs]
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PDLIM3

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 PDLIM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM3 Gene

Publications for PDLIM3 Gene

  1. Exclusion of muscle specific actinin-associated LIM protein (ALP) gene from 4q35 facioscapulohumeral muscular dystrophy (FSHD) candidate genes. (PMID: 10063829) Bouju S … Dechesne CA (Neuromuscular disorders : NMD 1999) 2 3 4 22 60
  2. Coding sequence mutations identified in MYH7, TNNT2, SCN5A, CSRP3, LBD3, and TCAP from 313 patients with familial or idiopathic dilated cardiomyopathy. (PMID: 19412328) Hershberger RE … Litt M (Clinical and translational science 2008) 3 45 60
  3. The ZASP-like motif in actinin-associated LIM protein is required for interaction with the alpha-actinin rod and for targeting to the muscle Z-line. (PMID: 15084604) Klaavuniemi T … Ylänne J (The Journal of biological chemistry 2004) 3 22 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. Actinin-associated LIM protein: identification of a domain interaction between PDZ and spectrin-like repeat motifs. (PMID: 9334352) Xia H … Bredt DS (The Journal of cell biology 1997) 3 4 60

Products for PDLIM3 Gene

Sources for PDLIM3 Gene

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