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PDLIM2 PDZ and LIM domain 2 [ Homo sapiens (human) ]

Gene ID: 64236, updated on 2-Nov-2024

Summary

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Official Symbol
PDLIM2provided by HGNC
Official Full Name
PDZ and LIM domain 2provided by HGNC
Primary source
HGNC:HGNC:13992
See related
Ensembl:ENSG00000120913 MIM:609722; AllianceGenome:HGNC:13992
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLIM; MYSTIQUE
Summary
This gene encodes a member of the ALP subfamily of PDZ-LIM domain proteins. The encoded protein suppresses anchorage-dependent growth and promotes cell migration and adhesion through interactions with the actin cytoskeleton via the PDZ domain. The encoded protein is also a putative tumor suppressor protein, and decreased expression of this gene is associated with several malignancies including breast cancer and adult T-cell leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
Expression
Broad expression in spleen (RPKM 22.4), lung (RPKM 9.5) and 21 other tissues See more
Orthologs
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Genomic context

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See PDLIM2 in Genome Data Viewer
Location:
8p21.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (22578741..22598026)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (22852592..22871886)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22436254..22455539)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 3 catalytic subunit gamma Neighboring gene uncharacterized LOC124901905 Neighboring gene BTF3 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22406579-22407079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22408405-22409369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22409593-22410470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22410471-22411346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22413914-22414436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18990 Neighboring gene Sharpr-MPRA regulatory region 12029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22421349-22422242 Neighboring gene sorbin and SH3 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22429393-22430084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22430085-22430775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22431841-22432559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22435755-22436448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22439222-22439914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22442189-22442858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22447071-22448071 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22454615-22455362 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22455363-22456110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22458799-22459676 Neighboring gene uncharacterized LOC107986876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27082 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22462104-22462604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19003 Neighboring gene chromosome 8 open reading frame 58 Neighboring gene cell cycle and apoptosis regulator 2 Neighboring gene bridging integrator 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Tumor promoting effect of PDLIM2 downregulation involves mitochondrial ROS, oncometabolite accumulations and HIF-1alpha activation.
    Title: Tumor promoting effect of PDLIM2 downregulation involves mitochondrial ROS, oncometabolite accumulations and HIF-1α activation.
  2. PDLIM2 can inactivate the TGF-beta/Smad pathway to inhibit the malignant behavior of ovarian cancer cells.
    Title: PDLIM2 can inactivate the TGF-β/Smad pathway to inhibit the malignant behavior of ovarian cancer cells.
  3. High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration.
    Title: High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration.
  4. Kruppel like factor 10 up-regulates PDZ and LIM domain containing protein 2 via nuclear factor kappa-B pathway to inhibit proliferation and inflammatory of fibroblastoid synovial cell in rheumatoid arthritis.
    Title: Kruppel like factor 10 up-regulates PDZ and LIM domain containing protein 2 via nuclear factor kappa-B pathway to inhibit proliferation and inflammatory of fibroblastoid synovial cell in rheumatoid arthritis.
  5. Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types.
    Title: Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types.
  6. Central Nervous System-Infecting Pathogens Escherichia coli and Cryptococcus neoformans Exploit the Host Pdlim2 for Intracellular Traversal and Exocytosis in the Blood-Brain Barrier.
    Title: Central Nervous System-Infecting Pathogens Escherichia coli and Cryptococcus neoformans Exploit the Host Pdlim2 for Intracellular Traversal and Exocytosis in the Blood-Brain Barrier.
  7. PDLIM2 acts as a cancer suppressor gene in non-small cell lung cancer via the down regulation of NF-kappaB signaling.
    Title: PDLIM2 acts as a cancer suppressor gene in non-small cell lung cancer via the down regulation of NF-κB signaling.
  8. Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC).
    Title: Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC).
  9. Compared to normal lung tissues, the expression of PDLIM2 was significantly decreased in human lung cancers.
    Title: Causative role of PDLIM2 epigenetic repression in lung cancer and therapeutic resistance.
  10. study shows that PDLIM2 expression defines a subset of triple-negative breast cancer that may benefit from targeting the beta-catenin and adhesion signaling pathways
    Title: PDLIM2 Is a Marker of Adhesion and β-Catenin Activity in Triple-Negative Breast Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ34715

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables filamin binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables muscle alpha-actinin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables myosin heavy chain binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heart development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in muscle structure development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Z disc IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cortical actin cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
PDZ and LIM domain protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_030435.2 RefSeqGene

    Range
    6735..20558
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001368120.1 → NP_001355049.1  PDZ and LIM domain protein 2 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC037459
    Consensus CDS
    CCDS94264.1
    UniProtKB/Swiss-Prot
    D3DSR5, J3KNH4, Q7Z584, Q86WM8, Q8WZ29, Q96JY6, Q9H4L9, Q9H7I2
    Related
    ENSP00000387084.1, ENST00000409417.6

  2. NM_021630.6 → NP_067643.3  PDZ and LIM domain protein 2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC037459
    Consensus CDS
    CCDS6032.2
    UniProtKB/Swiss-Prot
    Q96JY6
    Related
    ENSP00000312634.7, ENST00000308354.11
    Conserved Domains (3) summary
    cd09449
    Location:536 → 588
    LIM_Mystique; The LIM domain of Mystique, a subfamily of ALP LIM domain proteins
    cd00992
    Location:259 → 330
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam15936
    Location:462 → 505
    DUF4749; Domain of unknown function (DUF4749)

  3. NM_176871.5 → NP_789847.1  PDZ and LIM domain protein 2 isoform 1

    See identical proteins and their annotated locations for NP_789847.1

    Status: REVIEWED

    Source sequence(s)
    AC037459
    Consensus CDS
    CCDS34860.1
    UniProtKB/Swiss-Prot
    Q96JY6
    Related
    ENSP00000265810.4, ENST00000265810.8
    Conserved Domains (3) summary
    cd09449
    Location:286 → 342
    LIM_Mystique; The LIM domain of Mystique, a subfamily of ALP LIM domain proteins
    cd00992
    Location:9 → 80
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam15936
    Location:212 → 255
    DUF4749; Domain of unknown function (DUF4749)

  4. NM_198042.4 → NP_932159.1  PDZ and LIM domain protein 2 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC037459
    Consensus CDS
    CCDS34861.1
    UniProtKB/TrEMBL
    C9JS55
    Related
    ENSP00000386868.1, ENST00000409141.5
    Conserved Domains (2) summary
    cd00992
    Location:9 → 80
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam15936
    Location:212 → 257
    DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    22578741..22598026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    22852592..22871886
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JY6.1 GenPept UniProtKB/Swiss-Prot:Q96JY6

Gene LinkOut

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Chemical Information
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