PLEK

pleckstrin, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:68365282-68397453

Links

ENSG00000115956 ∙ NCBI:5341 ∙ OMIM:173570 ∙ HGNC:9070 ∙ Uniprot:P08567 ∙ 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 PLEK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEK 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		2	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	14	0	2

Variants in PLEK

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

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

Position	Type	Phenotype	Significance	ClinVar
2-68380392-A-G		not specified	Uncertain significance (Sep 29, 2023)
2-68380742-C-T		not specified	Uncertain significance (May 26, 2024)
2-68380815-G-T			Benign (Nov 27, 2019)
2-68380833-T-G		not specified	Uncertain significance (Nov 22, 2021)
2-68380840-G-T		not specified	Uncertain significance (Jan 16, 2024)
2-68380867-A-G		not specified	Uncertain significance (Jun 11, 2021)
2-68380891-A-C		not specified	Uncertain significance (Apr 04, 2023)
2-68380895-T-C		not specified	Uncertain significance (May 09, 2023)
2-68386510-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-68386550-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-68388414-A-C			Benign (Jan 12, 2018)
2-68388442-A-G		not specified	Uncertain significance (Mar 22, 2023)
2-68388480-T-G		not specified	Uncertain significance (Jun 12, 2023)
2-68395703-C-G		not specified	Uncertain significance (Dec 19, 2023)
2-68395734-A-T		not specified	Uncertain significance (Jun 07, 2024)
2-68395766-C-T		not specified	Uncertain significance (Jul 07, 2022)
2-68395785-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEK	protein_coding	protein_coding	ENST00000234313	9	32281

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00107	0.989	125717	0	20	125737	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.211	178	186	0.956	0.00000905	2326
Missense in Polyphen		54	64.033	0.84332		835
Synonymous	-0.203	69	66.9	1.03	0.00000330	615
Loss of Function	2.27	8	18.6	0.431	8.50e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000273	0.000272
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major protein kinase C substrate of platelets.
• Pathway: Serotonin and anxiety;Serotonin and anxiety-related events;TYROBP Causal Network;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.352

Intolerance Scores

• loftool: 0.453
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.348
• hipred: Y
• hipred_score: 0.513
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;platelet degranulation;regulation of transcription by RNA polymerase II;vesicle docking involved in exocytosis;integrin-mediated signaling pathway;positive regulation of platelet activation;negative regulation of inositol phosphate biosynthetic process;positive regulation of inositol-polyphosphate 5-phosphatase activity;cell projection organization;positive regulation of actin filament depolymerization;phospholipase C-inhibiting G protein-coupled receptor signaling pathway;cortical actin cytoskeleton organization;ruffle organization;actin cytoskeleton reorganization;positive regulation of actin filament bundle assembly;positive regulation of integrin activation;negative regulation of G protein-coupled receptor signaling pathway;phosphatidylinositol metabolic process;negative regulation of calcium-mediated signaling;regulation of cell diameter;thrombin-activated receptor signaling pathway;platelet aggregation;protein kinase C signaling;protein secretion by platelet
• Cellular component: extracellular region;cytoplasm;cytosol;plasma membrane;membrane;ruffle membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein kinase C binding;protein binding;protein homodimerization activity;phosphatidylinositol-3,4-bisphosphate binding