PDLIM3

PDZ and LIM domain 3, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 4:185500659-185535507

Links

ENSG00000154553 ∙ NCBI:27295 ∙ OMIM:605889 ∙ HGNC:20767 ∙ Uniprot:Q53GG5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypertrophic cardiomyopathy (Limited), mode of inheritance: AD
• dilated cardiomyopathy (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDLIM3 gene.

• Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy (163 variants)
• Inborn genetic diseases (119 variants)
• not provided (94 variants)
• Hypertrophic cardiomyopathy;Primary dilated cardiomyopathy (73 variants)
• not specified (42 variants)
• Cardiovascular phenotype (5 variants)
• Cardiomyopathy (1 variants)
• Hypertrophic cardiomyopathy (1 variants)
• Restrictive cardiomyopathy (1 variants)
• Primary dilated cardiomyopathy (1 variants)
• Familial cardiomyopathy (1 variants)
• PDLIM3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM3 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			3	75		78
missense			160	4		164
nonsense			2			2
start loss						0
frameshift		1	6			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)			4			4
splice region			6	5	3	14
non coding			1	44	36	81
Total	0	1	177	123	36

Variants in PDLIM3

This is a list of pathogenic ClinVar variants found in the PDLIM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-185502105-G-GT			Likely benign (Jun 18, 2018)
4-185502168-GTCTAAAGCCTTGACTTTAGATTTGGAGTTGACAA-G			Benign (Jul 06, 2018)
4-185502205-T-C			Likely benign (Jun 16, 2018)
4-185502275-G-A			Benign (Feb 13, 2017)
4-185502282-G-A		not specified	Benign (Apr 04, 2023)
4-185502294-T-C		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Conflicting classifications of pathogenicity (Dec 14, 2022)
4-185502307-T-C		Hypertrophic cardiomyopathy;Primary dilated cardiomyopathy	Uncertain significance (Feb 24, 2022)
4-185502309-C-G			Uncertain significance (Feb 20, 2015)
4-185502311-G-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Likely benign (Oct 03, 2023)
4-185502315-G-T		not specified	Likely benign (Apr 30, 2014)
4-185502317-C-T		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Sep 19, 2022)
4-185502318-C-T		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Likely benign (Jan 16, 2023)
4-185502319-G-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Uncertain significance (Jul 16, 2023)
4-185502320-T-C		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Apr 03, 2022)
4-185502325-T-C		not specified	Uncertain significance (Oct 29, 2023)
4-185502326-A-G		Hypertrophic cardiomyopathy;Primary dilated cardiomyopathy	Uncertain significance (Sep 21, 2022)
4-185502329-C-T		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Mar 09, 2021)
4-185502336-G-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Likely benign (Feb 22, 2023)
4-185502346-C-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Sep 11, 2023)
4-185502346-C-T		Hypertrophic cardiomyopathy;Primary dilated cardiomyopathy	Uncertain significance (Feb 04, 2022)
4-185502347-G-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Nov 01, 2021)
4-185502349-G-A		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Dec 22, 2021)
4-185502352-C-T		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy • not specified	Uncertain significance (Jul 29, 2023)
4-185502354-T-C		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Likely benign (Nov 04, 2022)
4-185502356-C-G		Primary dilated cardiomyopathy;Hypertrophic cardiomyopathy	Uncertain significance (Aug 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM3	protein_coding	protein_coding	ENST00000284770	8	33916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-7	0.541	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0223	224	223	1.00	0.0000139	2374
Missense in Polyphen		95	84.968	1.1181		858
Synonymous	-0.492	92	86.2	1.07	0.00000587	732
Loss of Function	0.922	12	16.0	0.751	7.72e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000503	0.000503
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the organization of actin filament arrays within muscle cells. {ECO:0000250}.
• Pathway: Fibroblast growth factor-1 (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.556
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.232
• hipred: N
• hipred_score: 0.365
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.347

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdlim3
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; 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); normal phenotype; 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)

Gene ontology

• Biological process: actin filament organization;heart development
• Cellular component: actin cytoskeleton;Z disc
• Molecular function: protein binding;cytoskeletal protein binding;structural constituent of muscle;metal ion binding