PDLIM5 PDZ and LIM domain 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDLIM5provided by HGNC
Official Full Name: PDZ and LIM domain 5provided by HGNC
Primary source: HGNC:HGNC:17468
See related: Ensembl:ENSG00000163110 MIM:605904; AllianceGenome:HGNC:17468
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: L9; ENH; LIM; ENH1
Summary: This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Expression: Broad expression in heart (RPKM 70.2), prostate (RPKM 31.5) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q22.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (94451942..94668223)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (97767448..97983384)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (95373093..95589374)

Chromosome 4 - NC_000004.12 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
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?

Mechanical Sensing Element PDLIM5 Promotes Osteogenesis of Human Fibroblasts by Affecting the Activity of Microfilaments.
Title: Mechanical Sensing Element PDLIM5 Promotes Osteogenesis of Human Fibroblasts by Affecting the Activity of Microfilaments.
Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers.
Title: Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers.
PDLIM5 inhibits STUB1-mediated degradation of SMAD3 and promotes the migration and invasion of lung cancer cells.
Title: PDLIM5 inhibits STUB1-mediated degradation of SMAD3 and promotes the migration and invasion of lung cancer cells.
Novel polymorphisms in PDLIM3 and PDLIM5 gene encoding Z-line proteins increase risk of idiopathic dilated cardiomyopathy.
Title: Novel polymorphisms in PDLIM3 and PDLIM5 gene encoding Z-line proteins increase risk of idiopathic dilated cardiomyopathy.
Forces acting on integrins recruit Enigma family proteins (PDLIM5 AND PDLIM7) to trigger YAP activation during mechanotransduction.
Title: Enigma proteins regulate YAP mechanotransduction.
this study shows functional importance of PDLIM5 for proper kAE1 membrane residency, as a crucial linker between kidneyAE1 and actin cytoskeleton-associated proteins in polarized cells
Title: PDLIM5 links kidney anion exchanger 1 (kAE1) to ILK and is required for membrane targeting of kAE1.
PDLIM5 promotes papillary thyroid carcinoma via activation of the Ras-ERK pathway.
Title: PDLIM5 identified by label-free quantitative proteomics as a potential novel biomarker of papillary thyroid carcinoma.
PDLIM5 was strongly up-regulated during cardiomyogenesis and novel stage-specific isoforms were detected for PDLIM5
Title: Proteomic Analysis of Human Pluripotent Stem Cell Cardiomyogenesis Revealed Altered Expression of Metabolic Enzymes and PDLIM5 Isoforms.
Findings provide evidence of shared genetic variants in PDLIM5 gene influencing alcohol dependence, type 2 diabetes, and hypertension.
Title: Polymorphisms in PDLIM5 gene are associated with alcohol dependence, type 2 diabetes, and hypertension.
The study provides evidence of several genetic variants within the PDLIM5 gene and interactions between PDLIM5 and steroid use influencing cancer.
Title: Bayesian logistic regression in detection of gene-steroid interaction for cancer at PDLIM5 locus.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. 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

D11S2921 (e-PCR)
- UniSTS:152074

L17705 (e-PCR)
- UniSTS:66091

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-67607 (e-PCR)
- UniSTS:74556

SHGC-85116 (e-PCR)
- UniSTS:103489

D9S1746E (e-PCR)
- UniSTS:153922

D10S2448 (e-PCR)
- UniSTS:474444

L18426 (e-PCR)
- UniSTS:34648

RH91857 (e-PCR)
- UniSTS:88158

D4S964 (e-PCR)
- UniSTS:66400

RH36106 (e-PCR)
- UniSTS:1382

D4S2569E (e-PCR)
- UniSTS:19561

SHGC-63475 (e-PCR)
- UniSTS:5487

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

SHGC-59267 (e-PCR)
- UniSTS:57977

RH121053 (e-PCR)
- UniSTS:132274

SHGC-24108 (e-PCR)
- UniSTS:4790

SHGC-67609 (e-PCR)
- UniSTS:54969

D4S1159 (e-PCR)
- UniSTS:59834

STS-AA009657 (e-PCR)
- UniSTS:69085

SHGC-63474 (e-PCR)
- UniSTS:15587

RH91416 (e-PCR)
- UniSTS:88822

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 actinin 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 protein kinase C binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell growth involved in cardiac muscle cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation 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 regulation of dendritic spine morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synapse 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 actin cytoskeleton	IDA Inferred from Direct Assay more info
located_in adherens junction	HDA more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info
located_in presynapse	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 5

Names: enigma homolog; enigma-like LIM domain protein; enigma-like PDZ and LIM domains 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.

mRNA and Protein(s)

NM_001011513.4 → NP_001011513.4 PDZ and LIM domain protein 5 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.

Source sequence(s)

AC093778, AC108067, AC109925

Consensus CDS

CCDS47102.1

UniProtKB/TrEMBL

B7Z8X5

Related

ENSP00000442187.2, ENST00000542407.5

Conserved Domains (6) summary

cd09453
Location:311 → 362

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

cd09459
Location:429 → 483

LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family

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) ...

pfam05109
Location:143 → 294

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

cl02475
Location:370 → 421

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:105 → 195

DUF4749; Domain of unknown function (DUF4749)
NM_001011515.3 → NP_001011515.1 PDZ and LIM domain protein 5 isoform d

See identical proteins and their annotated locations for NP_001011515.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) has multiple differences in the coding region, lacks several 3' exons but contains an alternate 3' exon, and it thus has an alternate 3' coding region and 3' UTR, compared to isoform a. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AA253314, AC093778, AL833151, DA895978

Consensus CDS

CCDS47103.1

UniProtKB/TrEMBL

H0YBI4

Related

ENSP00000369527.3, ENST00000380180.7

Conserved Domains (2) summary

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) ...

cl25776
Location:105 → 191

DUF4749; Domain of unknown function (DUF4749)
NM_001011516.3 → NP_001011516.1 PDZ and LIM domain protein 5 isoform e

See identical proteins and their annotated locations for NP_001011516.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) has multiple differences in the coding region, lacks several 3' exons but contains an alternate 3' exon, and it thus has an alternate 3' coding region and 3' UTR, compared to isoform a. The encoded isoform (e, also known as ENH4) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AA253314, AC093778, AK291898, BC017902

Consensus CDS

CCDS47104.1

UniProtKB/TrEMBL

H0YBI4

Related

ENSP00000322021.5, ENST00000318007.9

Conserved Domains (2) summary

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) ...

cl25776
Location:100 → 171

DUF4749; Domain of unknown function (DUF4749)
NM_001256425.2 → NP_001243354.2 PDZ and LIM domain protein 5 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.

Source sequence(s)

AC093778, AC108067, AC109925

Consensus CDS

CCDS75166.1

UniProtKB/TrEMBL

A0A0A0MSP3

Related

ENSP00000398469.2, ENST00000437932.5

Conserved Domains (2) summary

cd09453
Location:95 → 146

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

cl02475
Location:213 → 267

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001256426.2 → NP_001243355.2 PDZ and LIM domain protein 5 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region, and contains four additional in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (f) that is longer than isoform a.

Source sequence(s)

AC093778, AC108067, AC109925

Consensus CDS

CCDS58916.1

Related

ENSP00000480359.1, ENST00000615540.4

Conserved Domains (5) summary

cd09453
Location:449 → 500

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

cd09459
Location:567 → 621

LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family

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:105 → 201

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:508 → 559

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001256427.2 → NP_001243356.2 PDZ and LIM domain protein 5 isoform g

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, contains an additional in-frame exon in the central coding region, and uses alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (g) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC093778, AC108067, AC109925

Consensus CDS

CCDS58917.1

UniProtKB/TrEMBL

B7Z8X5

Related

ENSP00000424297.1, ENST00000503974.5

Conserved Domains (5) summary

cd09453
Location:317 → 368

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

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) ...

pfam05109
Location:149 → 300

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

cl02475
Location:376 → 427

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:105 → 201

DUF4749; Domain of unknown function (DUF4749)
NM_001256428.2 → NP_001243357.2 PDZ and LIM domain protein 5 isoform h

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks an alternate exon in the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (h) is shorter at the N-terminus, compared to isoform a.

Source sequence(s)

AC093778, AC108067, AC109925

UniProtKB/TrEMBL

B7Z481

Conserved Domains (4) summary

cd09453
Location:298 → 349

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

pfam05109
Location:7 → 277

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

cl02475
Location:416 → 470

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:92 → 182

DUF4749; Domain of unknown function (DUF4749)
NM_001256429.2 → NP_001243358.1 PDZ and LIM domain protein 5 isoform i

See identical proteins and their annotated locations for NP_001243358.1

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks several central and 3' exons but contains an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (i) has the same N-terminus but has a distinct and significantly shorter C-terminus, compared to isoform a.

Source sequence(s)

AA922628, AY345240

Consensus CDS

CCDS58915.1

UniProtKB/Swiss-Prot

Q96HC4

Related

ENSP00000352210.4, ENST00000359265.8
NM_006457.5 → NP_006448.5 PDZ and LIM domain protein 5 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform a (also known as ENH1).

Source sequence(s)

AC093778, AC108067, AC109925

Consensus CDS

CCDS3641.1

UniProtKB/Swiss-Prot

A8K6F9, D6RB78, E9PBF5, O60705, Q56VN4, Q5UW38, Q8WVK0, Q96HC4

UniProtKB/TrEMBL

B7Z8X5

Related

ENSP00000321746.4, ENST00000317968.9

Conserved Domains (6) summary

cd09453
Location:420 → 471

LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family

cd09459
Location:538 → 592

LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family

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) ...

pfam05109
Location:84 → 399

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam15936
Location:214 → 294

DUF4749; Domain of unknown function (DUF4749)

cl02475
Location:479 → 530

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

RNA

NR_046186.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks several exons in the central and 3' regions, but contains an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because it lacks the majority of the coding region, as found in variant 1, and it does not have any significant coding potential.

Source sequence(s)

AA922628, AC109925, DA381128