PDLIM4

PDZ and LIM domain 4, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 5:132257696-132273454

Links

ENSG00000131435 ∙ NCBI:8572 ∙ OMIM:603422 ∙ HGNC:16501 ∙ Uniprot:P50479 ∙ 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 PDLIM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM4 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						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	14	1	0

Variants in PDLIM4

This is a list of pathogenic ClinVar variants found in the PDLIM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132257745-C-T		not specified	Uncertain significance (Nov 13, 2024)
5-132257795-C-T			Uncertain significance (May 01, 2024)
5-132262739-A-G		not specified	Uncertain significance (Aug 21, 2024)
5-132262764-T-C			Likely benign (Mar 01, 2022)
5-132266520-G-C		not specified	Uncertain significance (Mar 05, 2025)
5-132270925-C-G		not specified	Uncertain significance (Oct 12, 2021)
5-132270943-C-T		not specified	Uncertain significance (Aug 08, 2022)
5-132271006-C-T		not specified	Uncertain significance (Jan 09, 2024)
5-132271009-C-G		not specified	Uncertain significance (Mar 22, 2023)
5-132271041-G-A		not specified	Uncertain significance (Jun 10, 2022)
5-132271060-A-T		not specified	Uncertain significance (Jan 01, 2025)
5-132271370-A-T		not specified	Uncertain significance (May 20, 2024)
5-132271430-C-G		not specified	Uncertain significance (Dec 10, 2024)
5-132271457-G-T		not specified	Uncertain significance (Nov 17, 2022)
5-132272041-G-T		not specified	Uncertain significance (Jan 19, 2025)
5-132272042-C-T		not specified	Uncertain significance (Nov 25, 2024)
5-132272091-C-T		not specified	Likely benign (Dec 15, 2023)
5-132272159-C-T		not specified	Uncertain significance (Oct 22, 2024)
5-132272224-G-T		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM4	protein_coding	protein_coding	ENST00000253754	7	15784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0172	125673	0	7	125680	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.715	186	216	0.863	0.0000149	2104
Missense in Polyphen		67	85.671	0.78206		888
Synonymous	0.530	86	92.5	0.930	0.00000699	684
Loss of Function	3.26	0	12.4	0.00	5.27e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000460	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Suppresses SRC activation by recognizing and binding to active SRC and facilitating PTPN13-mediated dephosphorylation of SRC 'Tyr-419' leading to its inactivation. Inactivated SRC dissociates from this protein allowing the initiation of a new SRC inactivation cycle (PubMed:19307596). Involved in reorganization of the actin cytoskeleton (PubMed:21636573). In nonmuscle cells, binds to ACTN1 (alpha- actinin-1), increases the affinity of ACTN1 to F-actin (filamentous actin), and promotes formation of actin stress fibers. Involved in regulation of the synaptic AMPA receptor transport in dendritic spines of hippocampal pyramidal neurons directing the receptors toward an insertion at the postsynaptic membrane. Links endosomal surface-internalized GRIA1-containing AMPA receptors to the alpha-actinin/actin cytoskeleton. Increases AMPA receptor-mediated excitatory postsynaptic currents in neurons (By similarity). {ECO:0000250|UniProtKB:P36202, ECO:0000269|PubMed:19307596, ECO:0000269|PubMed:21636573}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.312

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.729
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdlim4

Gene ontology

• Biological process: actin cytoskeleton reorganization;excitatory chemical synaptic transmission
• Cellular component: stress fiber;nucleus;cytoplasm;cytoskeleton;lamellipodium;cell junction;early endosome membrane;early endosome lumen;filamentous actin;recycling endosome lumen;dendritic spine;postsynaptic membrane;perinuclear region of cytoplasm;recycling endosome membrane
• Molecular function: protein binding;protein phosphatase binding;protein homodimerization activity;metal ion binding;alpha-actinin binding