PDLIM1 PDZ and LIM domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDLIM1provided by HGNC
Official Full Name: PDZ and LIM domain 1provided by HGNC
Primary source: HGNC:HGNC:2067
See related: Ensembl:ENSG00000107438 MIM:605900; AllianceGenome:HGNC:2067
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: CLIM1; CLP36; CLP-36; hCLIM1; HEL-S-112
Summary: 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]
Expression: Ubiquitous expression in small intestine (RPKM 111.6), colon (RPKM 111.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q23.33

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (95237572..95291003, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (96116721..96170181, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (96997329..97050760, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

PDLIM1 interacts with HK2 to promote gastric cancer progression through enhancing the Warburg effect via Wnt/beta-catenin signaling.
Title: PDLIM1 interacts with HK2 to promote gastric cancer progression through enhancing the Warburg effect via Wnt/β-catenin signaling.
Distribution of PDLIM1 at actin-rich structures generated by invasive and adherent bacterial pathogens.
Title: Distribution of PDLIM1 at actin-rich structures generated by invasive and adherent bacterial pathogens.
PDLIM1 Inhibits Tumor Metastasis Through Activating Hippo Signaling in Hepatocellular Carcinoma.
Title: PDLIM1 Inhibits Tumor Metastasis Through Activating Hippo Signaling in Hepatocellular Carcinoma.
Hyperprogression on immunotherapy with complete response to chemotherapy in a NSCLC patient with high PD-L1 and STK11: A case report.
Title: Hyperprogression on immunotherapy with complete response to chemotherapy in a NSCLC patient with high PD-L1 and STK11: A case report.
MicroRNA-370-3p inhibits cell proliferation and induces chronic myelogenous leukaemia cell apoptosis by suppressing PDLIM1/Wnt/beta-catenin signaling.
Title: MicroRNA-370-3p inhibits cell proliferation and induces chronic myelogenous leukaemia cell apoptosis by suppressing PDLIM1/Wnt/β-catenin signaling.
High titers of both TYMS and PDLIM1 serum autoantibodies were significantly more prevalent in breast cancer cases than in controls.
Title: Autoantibodies against TYMS and PDLIM1 proteins detected as circulatory signatures in Indian breast cancer patients.
PDLIM1 was shown to interact with p75(NTR) in highly invasive patient-derived glioma stem cells/tumor-initiating cells and shRNA knockdown of PDLIM1 in vitro and in vivo results in complete ablation of p75(NTR)-mediated invasion.
Title: Glioma invasion mediated by the p75 neurotrophin receptor (p75(NTR)/CD271) requires regulated interaction with PDLIM1.
downregulation of PDLIM1 in colorectal cancer samples correlated with reduced E-cadherin and membrane beta-catenin levels
Title: PDLIM1 Stabilizes the E-Cadherin/β-Catenin Complex to Prevent Epithelial-Mesenchymal Transition and Metastatic Potential of Colorectal Cancer Cells.
Our results identify CLP36 as an important regulator of breast cancer cell migration and metastasis, and shed light on how increased CLP36 expression contributes to the progression of breast cancer.
Title: PDZ and LIM domain protein 1(PDLIM1)/CLP36 promotes breast cancer cell migration, invasion and metastasis through interaction with α-actinin.
Femtomolar Zn2+ affinity of LIM domain of PDLIM1 protein uncovers crucial contribution of protein-protein interactions to protein stability.
Title: Femtomolar Zn2+ affinity of LIM domain of PDLIM1 protein uncovers crucial contribution of protein-protein interactions to protein stability.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of suicide attempts in mood disorder patients. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

A002E05 (e-PCR)
- UniSTS:37458

G44727 (e-PCR)
- UniSTS:95202

D10S181E (e-PCR)
- UniSTS:147174

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin binding	ISS Inferred from Sequence or Structural Similarity more info
enables cadherin binding involved in cell-cell adhesion	HDA 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 transcription coactivator activity	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 actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in establishment or maintenance of actin cytoskeleton polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in fibroblast migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in maintenance of cell polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in response to hypoxia	IEA Inferred from Electronic Annotation more info
involved_in response to oxidative stress	TAS Traceable Author Statement more info	PubMed
involved_in stress fiber assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
located_in adherens junction	HDA more info	PubMed
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
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	HDA more info	PubMed
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
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PDZ and LIM domain protein 1

Names: LIM domain protein CLP-36; carboxyl terminal LIM domain protein 1; elfin; epididymis secretory protein Li 112

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.

mRNA and Protein(s)

NM_020992.4 → NP_066272.1 PDZ and LIM domain protein 1

See identical proteins and their annotated locations for NP_066272.1

Status: REVIEWED

Source sequence(s)

AL160288, BC000915

Consensus CDS

CCDS7441.1

UniProtKB/Swiss-Prot

B2RBS6, O00151, Q5VZH5, Q9BPZ9

UniProtKB/TrEMBL

V9HW92

Related

ENSP00000360305.3, ENST00000329399.7

Conserved Domains (3) summary

cd09448
Location:260 → 311

LIM_CLP36; This family represents the LIM domain of CLP36

cd00992
Location:10 → 82

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:138 → 230

DUF4749; Domain of unknown function (DUF4749)