PDLIM1

PDZ and LIM domain 1, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 10:95237572-95291012

Previous symbols: [ "CLIM1" ]

Links

ENSG00000107438 ∙ NCBI:9124 ∙ OMIM:605900 ∙ HGNC:2067 ∙ Uniprot:O00151 ∙ 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 PDLIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in PDLIM1

This is a list of pathogenic ClinVar variants found in the PDLIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-95238017-A-C		not specified	Uncertain significance (Feb 14, 2023)
10-95238079-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-95238091-C-T		not specified	Uncertain significance (Jul 26, 2022)
10-95238092-G-A		not specified	Uncertain significance (Dec 13, 2023)
10-95238622-G-A		not specified	Uncertain significance (Nov 29, 2023)
10-95247235-A-G		not specified	Uncertain significance (Nov 29, 2021)
10-95247259-G-A		not specified	Uncertain significance (May 25, 2022)
10-95263876-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-95263883-C-T		not specified	Uncertain significance (Aug 12, 2021)
10-95263886-C-T		not specified	Uncertain significance (Mar 30, 2024)
10-95263960-T-C		not specified	Uncertain significance (Jun 28, 2023)
10-95263973-T-C		not specified	Uncertain significance (May 23, 2023)
10-95268779-T-C		not specified	Uncertain significance (Dec 14, 2022)
10-95268844-C-G		not specified	Uncertain significance (Aug 14, 2023)
10-95271765-G-A		not specified	Uncertain significance (Apr 25, 2023)
10-95290837-G-T		not specified	Uncertain significance (Mar 14, 2023)
10-95290884-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM1	protein_coding	protein_coding	ENST00000329399	7	53453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00147	0.970	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.763	161	191	0.844	0.0000103	2155
Missense in Polyphen		34	52.413	0.6487		674
Synonymous	-0.00167	74	74.0	1.00	0.00000419	636
Loss of Function	1.92	7	15.1	0.465	8.18e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000295	0.000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.000246	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000237
Middle Eastern	0.000246	0.000217
South Asian	0.000274	0.000261
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton (PubMed:10861853). Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts (By similarity). {ECO:0000250|UniProtKB:P52944, ECO:0000269|PubMed:10861853}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.547
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.771
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdlim1
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: response to hypoxia;regulation of transcription, DNA-templated;response to oxidative stress;cell-cell adhesion;positive regulation of nucleic acid-templated transcription
• Cellular component: transcription factor complex;cytoskeleton;cell-cell adherens junction;focal adhesion;Z disc
• Molecular function: transcription coactivator activity;metal ion binding;cadherin binding involved in cell-cell adhesion