PDLIM3

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

Basic information

Region (hg38): 4:185500660-185535507

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 (322 variants)
Hypertrophic_cardiomyopathy (321 variants)
not_specified (237 variants)
not_provided (78 variants)
PDLIM3-related_disorder (8 variants)
Cardiovascular_phenotype (4 variants)
Primary_familial_hypertrophic_cardiomyopathy (1 variants)
Cardiomyopathy (1 variants)
Familial_cardiomyopathy (1 variants)
Restrictive_cardiomyopathy (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. These statistics are base on transcript: NM_000014476.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	106 clinvar		108
missense			232 clinvar	13 clinvar		245
nonsense			4 clinvar			4
start loss			2			2
frameshift		1 clinvar	9 clinvar			10
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	1	255	119	0

Highest pathogenic variant AF is 0.0000034203797

Loading clinvar variants...

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