PDLIM5

PDZ and LIM domain 5, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 4:94451857-94668227

Links

ENSG00000163110 ∙ NCBI:10611 ∙ OMIM:605904 ∙ HGNC:17468 ∙ Uniprot:Q96HC4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDLIM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	31	3	2

Variants in PDLIM5

This is a list of pathogenic ClinVar variants found in the PDLIM5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-94456255-G-A			Likely benign (Oct 01, 2023)
4-94523730-G-A		not specified	Uncertain significance (Aug 16, 2022)
4-94523736-G-A		not specified	Uncertain significance (Apr 18, 2023)
4-94523769-G-A		not specified	Uncertain significance (Aug 08, 2023)
4-94523850-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-94573370-C-T		not specified	Uncertain significance (Sep 25, 2023)
4-94575693-G-C		not specified	Uncertain significance (Jan 30, 2024)
4-94575713-G-A		not specified	Uncertain significance (Aug 28, 2023)
4-94575713-G-T		not specified	Uncertain significance (Nov 18, 2022)
4-94575715-C-A		not specified	Uncertain significance (Dec 26, 2023)
4-94575730-T-G		not specified	Uncertain significance (Jul 05, 2023)
4-94575764-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-94575767-C-G		not specified	Uncertain significance (Sep 28, 2021)
4-94575788-C-T		not specified	Uncertain significance (Aug 08, 2023)
4-94575789-G-A			Benign (Jul 11, 2018)
4-94575829-G-A		not specified	Uncertain significance (Jan 11, 2023)
4-94575910-G-A		not specified	Uncertain significance (Apr 19, 2024)
4-94575923-C-A		not specified	Uncertain significance (Jun 29, 2022)
4-94585582-T-C		not specified	Uncertain significance (Mar 16, 2022)
4-94585590-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-94585606-A-G		not specified	Uncertain significance (Jan 23, 2024)
4-94585621-A-G		not specified	Uncertain significance (Dec 18, 2023)
4-94585669-G-A		not specified	Uncertain significance (Apr 18, 2023)
4-94585671-C-A		not specified	Uncertain significance (Aug 22, 2023)
4-94618024-C-T		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM5	protein_coding	protein_coding	ENST00000514743	16	216341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00168	0.998	125718	0	27	125745	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	294	329	0.895	0.0000168	4043
Missense in Polyphen		101	132.68	0.76123		1653
Synonymous	1.12	102	117	0.868	0.00000626	1222
Loss of Function	3.55	11	33.0	0.334	0.00000164	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000262	0.000262
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000164	0.000163
South Asian	0.000134	0.000131
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Overexpression promotes the development of heart hypertrophy. Contributes to the regulation of dendritic spine morphogenesis in neurons. May restrain postsynaptic growth of excitatory synapses (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.852

Intolerance Scores

• loftool: 0.681
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.25

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.306
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.546

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdlim5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype

Gene ontology

• Biological process: regulation of synapse assembly;regulation of dendritic spine morphogenesis;cell growth involved in cardiac muscle cell development;cell-cell adhesion
• Cellular component: cytosol;cell-cell adherens junction;postsynaptic density;actin cytoskeleton;membrane;neuron projection;postsynaptic membrane
• Molecular function: actin binding;protein kinase C binding;protein binding;actinin binding;metal ion binding;protein N-terminus binding;cadherin binding involved in cell-cell adhesion