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PDLIM4 PDZ and LIM domain 4 [ Homo sapiens (human) ]

Gene ID: 8572, updated on 7-Apr-2024

Summary

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Official Symbol
PDLIM4provided by HGNC
Official Full Name
PDZ and LIM domain 4provided by HGNC
Primary source
HGNC:HGNC:16501
See related
Ensembl:ENSG00000131435 MIM:603422; AllianceGenome:HGNC:16501
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
RIL
Summary
Enables alpha-actinin binding activity; protein homodimerization activity; and protein phosphatase binding activity. Involved in actin cytoskeleton reorganization. Located in several cellular components, including lamellipodium; perinuclear region of cytoplasm; and stress fiber. Part of filamentous actin. Implicated in osteoporosis. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in endometrium (RPKM 8.6), prostate (RPKM 6.1) and 21 other tissues See more
Orthologs
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Genomic context

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Location:
5q31.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132257696..132273454)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132777576..132793334)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131593389..131609147)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:131520231-131520732 Neighboring gene Sharpr-MPRA regulatory region 7421 Neighboring gene P4HA2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543137-131543638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543639-131544138 Neighboring gene prolyl 4-hydroxylase subunit alpha 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16313 Neighboring gene microRNA 6830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131586685-131587186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131587187-131587686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131593943-131594732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23063 Neighboring gene VISTA enhancer hs1449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131603965-131604508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131605973-131606861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131607809-131608310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131608311-131608810 Neighboring gene Sharpr-MPRA regulatory region 4855 Neighboring gene uncharacterized LOC124901063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131613864-131614676 Neighboring gene CAGE-defined mid-level expression enhancer upstream of SLC22A4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16316 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131656893-131657393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131657550-131658068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131658069-131658587

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
  • 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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Related articles in PubMed

  1. Associations between polymorphisms of the PDLIM4 gene and susceptibility to osteoporotic fracture in an elderly population of Han Chinese. Chen J, et al. Biosci Rep, 2019 Jan 31. PMID 30578378, Free PMC Article
  2. RIL, a LIM gene on 5q31, is silenced by methylation in cancer and sensitizes cancer cells to apoptosis. Boumber YA, et al. Cancer Res, 2007 Mar 1. PMID 17332327
  3. Association of genetic variation of the RIL gene, encoding a PDZ-LIM domain protein and localized in 5q31.1, with low bone mineral density in adult Japanese women. Omasu F, et al. J Hum Genet, 2003. PMID 12908099
  4. The human RIL gene: mapping to human chromosome 5q31.1, genomic organization and alternative transcripts. Bashirova AA, et al. Gene, 1998 Apr 14. PMID 9573374
  5. PDZ and LIM domain protein 4 suppresses the growth and invasion of ovarian cancer cells via inactivation of STAT3 signaling. Jia Y, et al. Life Sci, 2019 Sep 15. PMID 31376371

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Low expression of PDLIM4 is associated with growth and invasion of ovarian cancer.
    Title: PDZ and LIM domain protein 4 suppresses the growth and invasion of ovarian cancer cells via inactivation of STAT3 signaling.
  2. Our study provides supportive evidence for the contribution of PDLIM4 gene polymorphisms to the susceptibility to osteoporotic fracture and suggests that rs270611 and rs3900945 are genetic risk factors, while rs366512 might be a genetic protective factor against osteoporotic fracture in elderly Han individuals.
    Title: Associations between polymorphisms of the PDLIM4 gene and susceptibility to osteoporotic fracture in an elderly population of Han Chinese.
  3. The levels of the EDNRB, HJURP and p60/CAF-1 proteins were strongly associated with overall survival in high-grade gliomas patients (p<0.001, p<0.001 and p=0.002, respectively), whereas the one of PDLI4 was not (P=0.11).
    Title: Prognostic significance of EDN/RB, HJURP, p60/CAF-1 and PDLI4, four new markers in high-grade gliomas.
  4. Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancers was associated with clinical characteristics, but only RASSF1A methylation was associated with time to first recurrence and overall survival.
    Title: Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancer is associated with clinical characteristics, but only RASSF1A methylation is associated with outcome.
  5. Actin cytoskeleton remodeling by the alternatively spliced isoform of PDLIM4/RIL protein.
    Title: Actin cytoskeleton remodeling by the alternatively spliced isoform of PDLIM4/RIL protein.
  6. Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle.
    Title: Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle.
  7. PDLIM4 may function as a tumor suppressor, involved in the control of cell proliferation by associating with actin in prostate cancer cells.
    Title: PDLIM4, an actin binding protein, suppresses prostate cancer cell growth.
  8. several genes that are known to be regulated by DNA methylation were up-regulated dramatically by integrin alpha6beta4 expression, including S100A4, FST, PDLIM4, CAPG, and Nkx2.2.
    Title: Integrin alpha6beta4 controls the expression of genes associated with cell motility, invasion, and metastasis, including S100A4/metastasin.
  9. Results showed that the hypermethylation of PDLIM4 gene could be used as a sensitive molecular tool in detection of prostate.
    Title: PDLIM4 repression by hypermethylation as a potential biomarker for prostate cancer.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Osteoporosis
MedGen: C0029456 OMIM: 166710 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables alpha-actinin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein phosphatase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actin cytoskeleton organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in excitatory chemical synaptic transmission ISS
Inferred from Sequence or Structural Similarity
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
  
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 cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendritic spine ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in early endosome lumen ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in early endosome membrane IEA
Inferred from Electronic Annotation
more info
  
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of filamentous actin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lamellipodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in postsynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in recycling endosome lumen ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in recycling endosome membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in stress fiber IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
PDZ and LIM domain protein 4
Names
LIM domain protein
LIM protein RIL
enigma homolog
reversion-induced LIM protein

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_015836.2 RefSeqGene

    Range
    5039..20797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001131027.2 → NP_001124499.1  PDZ and LIM domain protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001124499.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a coding exon in the 3' region, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    AF153882, AW590987, BC003096, BC016765, BF689609, BF690514, DN997097
    Consensus CDS
    CCDS47261.1
    UniProtKB/TrEMBL
    A0A0S2Z4N4
    Related
    ENSP00000368303.3, ENST00000379018.7
    Conserved Domains (2) summary
    cd00992
    Location:2 → 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:148 → 230
    DUF4749; Domain of unknown function (DUF4749)

  2. NM_003687.4 → NP_003678.2  PDZ and LIM domain protein 4 isoform 1

    See identical proteins and their annotated locations for NP_003678.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF153882, AW590987, BC016765, BF689609, BF690514, DN997097
    Consensus CDS
    CCDS4152.1
    UniProtKB/Swiss-Prot
    B2R8U1, P50479, Q53Y39, Q96AT8, Q9BTW8, Q9Y292
    UniProtKB/TrEMBL
    A0A0S2Z4P0
    Related
    ENSP00000253754.3, ENST00000253754.8
    Conserved Domains (3) summary
    cd09451
    Location:255 → 307
    LIM_RIL; The LIM domain of RIL
    cd00992
    Location:2 → 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:148 → 220
    DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    132257696..132273454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417848.1 → XP_047273804.1  PDZ and LIM domain protein 4 isoform X1

  2. XM_047417850.1 → XP_047273806.1  PDZ and LIM domain protein 4 isoform X2

  3. XM_017010002.2 → XP_016865491.1  PDZ and LIM domain protein 4 isoform X3

  4. XM_047417851.1 → XP_047273807.1  PDZ and LIM domain protein 4 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132777576..132793334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353734.1 → XP_054209709.1  PDZ and LIM domain protein 4 isoform X1

  2. XM_054353735.1 → XP_054209710.1  PDZ and LIM domain protein 4 isoform X2

  3. XM_054353736.1 → XP_054209711.1  PDZ and LIM domain protein 4 isoform X3

  4. XM_054353737.1 → XP_054209712.1  PDZ and LIM domain protein 4 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P50479.2 GenPept UniProtKB/Swiss-Prot:P50479

Gene LinkOut

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