PDLIM3 PDZ and LIM domain 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDLIM3provided by HGNC
Official Full Name: PDZ and LIM domain 3provided by HGNC
Primary source: HGNC:HGNC:20767
See related: Ensembl:ENSG00000154553 MIM:605889; AllianceGenome:HGNC:20767
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: ALP
Summary: 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]
Expression: Broad expression in esophagus (RPKM 61.1), heart (RPKM 58.0) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q35.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (185500660..185535507, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (188844192..188876603, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (186421814..186456661, complement)

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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Comprehensive Analysis of PDLIM3 Expression Profile, Prognostic Value, and Correlations with Immune Infiltrates in Gastric Cancer.
Title: Comprehensive Analysis of PDLIM3 Expression Profile, Prognostic Value, and Correlations with Immune Infiltrates in Gastric Cancer.
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.
This study confirmed that PDLIM3 as genetic modifiers of age at onset of Alzheimer disease.
Title: Genetic Modifiers of Age at Onset in Carriers of the G206A Mutation in PSEN1 With Familial Alzheimer Disease Among Caribbean Hispanics.
two abnormal splicing events for actinin-associated LIM protein 3 (PDLIM3/ALP) and fibronectin 1 (FN1) in the skeletal muscles of myotonic dystrophy type 1 patients.
Title: Alternative splicing of PDLIM3/ALP, for α-actinin-associated LIM protein 3, is aberrant in persons with myotonic dystrophy.
mutations in PDLIM3 and MYPN are infrequent in hypertrophic cardiomyopathies
Title: Analysis of the Z-disc genes PDLIM3 and MYPN in patients with hypertrophic cardiomyopathy.
Observational study of gene-disease association. (HuGE Navigator)
Title: Coding sequence mutations identified in MYH7, TNNT2, SCN5A, CSRP3, LBD3, and TCAP from 313 patients with familial or idiopathic dilated cardiomyopathy.
Mutations in PDLIM3 and MYOZ1, encoding myocyte Z line proteins, do not play any significant role in the genetic etiology of idiopathic DCM.
Title: Mutations in PDLIM3 and MYOZ1 encoding myocyte Z line proteins are infrequently found in idiopathic dilated cardiomyopathy.
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
Title: 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.

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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

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

SHGC-59837 (e-PCR)
- UniSTS:70939

SHGC-67723 (e-PCR)
- UniSTS:15669

SHGC-152352 (e-PCR)
- UniSTS:177483

SHGC-67694 (e-PCR)
- UniSTS:30302

SHGC-58157 (e-PCR)
- UniSTS:73826

SHGC-59720 (e-PCR)
- UniSTS:17764

RH80030 (e-PCR)
- UniSTS:87680

D4S2924 (e-PCR), detects polymorphism
- UniSTS:63626

PDLIM3 (e-PCR)
- UniSTS:506256

SHGC-63497 (e-PCR)
- UniSTS:95396

D4S2474E (e-PCR)
- UniSTS:150952

RH94037 (e-PCR)
- UniSTS:87208

D4S2478E (e-PCR)
- UniSTS:150954

SHGC-63498 (e-PCR)
- UniSTS:82644

D4S475 (e-PCR)
- UniSTS:54775

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor 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 protein 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 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 cytosol	IDA Inferred from Direct Assay more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor 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 3

Names: alpha-actinin-2-associated LIM protein; enigma homolog

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

NG_032576.3 RefSeqGene

Range

5052..39899

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_752

mRNA and Protein(s)

NM_001114107.5 → NP_001107579.1 PDZ and LIM domain protein 3 isoform b

See identical proteins and their annotated locations for NP_001107579.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two consecutive exons in the coding region and contains an alternate coding exon, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AC106897, BC027870

Consensus CDS

CCDS47172.1

UniProtKB/Swiss-Prot

Q53GG5

Related

ENSP00000284771.6, ENST00000284771.7

Conserved Domains (3) summary

cd09450
Location:246 → 298

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

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:137 → 215

DUF4749; Domain of unknown function (DUF4749)
NM_001257962.2 → NP_001244891.1 PDZ and LIM domain protein 3 isoform c

See identical proteins and their annotated locations for NP_001244891.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC106897

Consensus CDS

CCDS75219.1

UniProtKB/TrEMBL

A0A087WYF8, A0A0A0MQY0

Related

ENSP00000481771.2, ENST00000620787.5

Conserved Domains (3) summary

cd09450
Location:206 → 258

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

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:132 → 175

DUF4749; Domain of unknown function (DUF4749)
NM_001257963.2 → NP_001244892.1 PDZ and LIM domain protein 3 isoform d

See identical proteins and their annotated locations for NP_001244892.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks three exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (d) is shorter than isoform a.

Source sequence(s)

AC106897

Consensus CDS

CCDS75218.1

UniProtKB/TrEMBL

A0A2U3TZH4

Related

ENSP00000284770.5, ENST00000284770.10

Conserved Domains (2) summary

cd09450
Location:127 → 179

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

pfam15936
Location:23 → 96

DUF4749; Domain of unknown function (DUF4749)
NM_014476.6 → NP_055291.2 PDZ and LIM domain protein 3 isoform a

See identical proteins and their annotated locations for NP_055291.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC106897, AK313253

Consensus CDS

CCDS3844.1

UniProtKB/Swiss-Prot

B2R866, O43590, O60439, O60440, Q53GG5, Q8N6Y6, Q9BVP4

Related

ENSP00000284767.8, ENST00000284767.12

Conserved Domains (3) summary

cd09450
Location:294 → 346

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

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:184 → 265

DUF4749; Domain of unknown function (DUF4749)

RNA

NR_047562.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two consecutive internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC106897