PLEK2

pleckstrin 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 14:67386984-67412167

Links

ENSG00000100558 ∙ NCBI:26499 ∙ OMIM:608007 ∙ HGNC:19238 ∙ Uniprot:Q9NYT0 ∙ 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 PLEK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEK2 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in PLEK2

This is a list of pathogenic ClinVar variants found in the PLEK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-67387361-C-T		not specified	Uncertain significance (Jun 04, 2024)
14-67387382-T-A		not specified	Uncertain significance (Jun 18, 2021)
14-67387385-C-T		not specified	Uncertain significance (Dec 02, 2024)
14-67388242-C-T		not specified	Uncertain significance (Oct 27, 2023)
14-67388256-A-G		not specified	Uncertain significance (Nov 17, 2022)
14-67388257-C-A		not specified	Uncertain significance (Sep 03, 2024)
14-67388269-G-A		not specified	Uncertain significance (May 04, 2023)
14-67388292-C-T		not specified	Uncertain significance (Feb 12, 2024)
14-67390719-G-A		not specified	Uncertain significance (Mar 20, 2023)
14-67392357-G-A		not specified	Likely benign (Oct 06, 2021)
14-67392372-A-C		not specified	Uncertain significance (Mar 01, 2024)
14-67392391-C-T		not specified	Uncertain significance (Aug 20, 2024)
14-67392673-G-C		not specified	Uncertain significance (Mar 31, 2022)
14-67392679-T-A		not specified	Uncertain significance (Aug 02, 2021)
14-67392683-G-C		not specified	Uncertain significance (Aug 10, 2021)
14-67392735-C-T		not specified	Uncertain significance (Nov 17, 2023)
14-67392775-T-G		not specified	Uncertain significance (Apr 18, 2023)
14-67393152-A-C		not specified	Uncertain significance (Nov 21, 2022)
14-67393185-A-G		not specified	Uncertain significance (Feb 06, 2023)
14-67393188-T-C		not specified	Uncertain significance (Feb 26, 2024)
14-67393201-G-A		not specified	Uncertain significance (Mar 01, 2024)
14-67393219-C-T		not specified	Uncertain significance (Nov 11, 2024)
14-67393231-C-T		not specified	Uncertain significance (Oct 10, 2023)
14-67395426-T-C		not specified	Uncertain significance (Oct 08, 2024)
14-67395477-G-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEK2	protein_coding	protein_coding	ENST00000216446	9	25218

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.29e-9	0.397	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.824	175	208	0.839	0.0000123	2301
Missense in Polyphen		69	87.724	0.78655		983
Synonymous	0.00134	82	82.0	1.00	0.00000481	691
Loss of Function	0.888	15	19.2	0.781	0.00000110	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000914	0.000911
Ashkenazi Jewish	0.00100	0.000993
East Asian	0.00131	0.00131
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.00131	0.00131
South Asian	0.000198	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May help orchestrate cytoskeletal arrangement. Contribute to lamellipodia formation.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.350
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.322

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plek2

Gene ontology

• Biological process: actin cytoskeleton reorganization;intracellular signal transduction;positive regulation of plasma membrane bounded cell projection assembly
• Cellular component: cytoplasm;cytoskeleton;plasma membrane;lamellipodium membrane
• Molecular function: phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-3,5-bisphosphate binding