PDLIM2

PDZ and LIM domain 2, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 8:22578278-22598025

Links

ENSG00000120913 ∙ NCBI:64236 ∙ OMIM:609722 ∙ HGNC:13992 ∙ Uniprot:Q96JY6 ∙ 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 PDLIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM2 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			58	4		62
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	59	4	0

Variants in PDLIM2

This is a list of pathogenic ClinVar variants found in the PDLIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22578802-C-T		not specified	Uncertain significance (Sep 26, 2023)
8-22578835-G-A		not specified	Likely benign (Feb 23, 2023)
8-22578862-A-G		not specified	Uncertain significance (Mar 01, 2023)
8-22578889-C-G		not specified	Uncertain significance (Jun 21, 2023)
8-22578891-G-T		not specified	Uncertain significance (Sep 14, 2022)
8-22578894-A-T		not specified	Uncertain significance (Feb 15, 2023)
8-22578927-C-G		not specified	Uncertain significance (Dec 21, 2022)
8-22578928-G-A		not specified	Uncertain significance (Nov 10, 2022)
8-22578963-G-A		not specified	Likely benign (Apr 04, 2024)
8-22579003-G-C		not specified	Uncertain significance (Aug 11, 2022)
8-22579029-C-G		not specified	Uncertain significance (Apr 04, 2024)
8-22579102-G-C		not specified	Uncertain significance (Aug 12, 2021)
8-22579186-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-22579216-G-T		not specified	Uncertain significance (May 20, 2024)
8-22579219-A-G		not specified	Uncertain significance (Jun 02, 2023)
8-22579303-G-C		not specified	Likely benign (Jul 05, 2023)
8-22579374-C-A		not specified	Uncertain significance (Apr 05, 2023)
8-22579381-C-T		not specified	Uncertain significance (Jan 02, 2024)
8-22579392-C-T		not specified	Uncertain significance (May 31, 2023)
8-22579443-G-A		not specified	Uncertain significance (Dec 28, 2023)
8-22579503-G-C		not specified	Uncertain significance (Mar 25, 2024)
8-22579504-C-T		not specified	Uncertain significance (Apr 12, 2022)
8-22579515-G-A		not specified	Uncertain significance (Dec 28, 2023)
8-22580620-G-C		not specified	Uncertain significance (Jul 14, 2023)
8-22580629-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM2	protein_coding	protein_coding	ENST00000308354	10	19747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000221	0.981	125716	0	12	125728	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0866	259	263	0.985	0.0000166	3698
Missense in Polyphen		87	90.873	0.95738		1073
Synonymous	-0.668	121	112	1.08	0.00000716	1381
Loss of Function	2.09	9	18.8	0.479	0.00000103	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000815	0.0000791
Middle Eastern	0.000111	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable adapter protein located at the actin cytoskeleton that promotes cell attachment. Necessary for the migratory capacity of epithelial cells. Overexpression enhances cell adhesion to collagen and fibronectin and suppresses anchorage independent growth. May contribute to tumor cell migratory capacity. {ECO:0000269|PubMed:15659642}.

Recessive Scores

• pRec: 0.181

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: Y
• hipred_score: 0.508
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.679

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdlim2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: nucleus;cytoplasm;cytoskeleton
• Molecular function: protein binding;metal ion binding