PLEKHA2

pleckstrin homology domain containing A2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 8:38901235-38973912

Links

ENSG00000169499 ∙ NCBI:59339 ∙ OMIM:607773 ∙ HGNC:14336 ∙ Uniprot:Q9HB19 ∙ 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 PLEKHA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in PLEKHA2

This is a list of pathogenic ClinVar variants found in the PLEKHA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-38917982-A-G		not specified	Uncertain significance (Jan 10, 2023)
8-38917996-G-A		not specified	Uncertain significance (Sep 14, 2022)
8-38946130-A-G		not specified	Uncertain significance (Feb 16, 2023)
8-38946163-A-G		not specified	Uncertain significance (Dec 07, 2021)
8-38950872-C-T		not specified	Uncertain significance (May 21, 2024)
8-38950956-T-C		not specified	Uncertain significance (Mar 22, 2023)
8-38950965-T-C		not specified	Uncertain significance (Aug 27, 2024)
8-38950977-C-T		not specified	Uncertain significance (Apr 09, 2024)
8-38950986-G-A		not specified	Likely benign (Nov 11, 2024)
8-38952253-C-G		not specified	Uncertain significance (Feb 23, 2023)
8-38952281-A-G		not specified	Uncertain significance (Oct 03, 2022)
8-38953341-G-T		not specified	Uncertain significance (Nov 03, 2022)
8-38953346-A-G		not specified	Uncertain significance (Mar 04, 2024)
8-38957365-C-A		not specified	Uncertain significance (Nov 14, 2023)
8-38968595-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-38969470-G-C		not specified	Uncertain significance (Jun 29, 2023)
8-38969472-C-G		not specified	Uncertain significance (Aug 26, 2024)
8-38969484-C-T		not specified	Uncertain significance (Nov 17, 2022)
8-38969493-A-G		not specified	Likely benign (Nov 15, 2024)
8-38969508-C-T		not specified	Uncertain significance (Jun 21, 2021)
8-38969539-G-A		not specified	Uncertain significance (Oct 04, 2024)
8-38969596-G-T		not specified	Uncertain significance (Mar 07, 2024)
8-38969610-C-T		not specified	Uncertain significance (Jun 22, 2023)
8-38969644-C-T		not specified	Likely benign (Sep 05, 2024)
8-38969649-C-T		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA2	protein_coding	protein_coding	ENST00000420274	12	72676

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.838	0.162	21281	103358	7	124646	0.587

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	156	248	0.629	0.0000140	2768
Missense in Polyphen		65	116.44	0.55823		1289
Synonymous	-0.347	95	90.8	1.05	0.00000505	818
Loss of Function	3.74	4	23.6	0.170	0.00000126	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.49
Ashkenazi Jewish	1.00	0.711
East Asian	1.00	0.582
Finnish	1.00	0.656
European (Non-Finnish)	1.00	0.558
Middle Eastern	1.00	0.582
South Asian	1.00	0.625
Other	1.00	0.639

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds specifically to phosphatidylinositol 3,4- diphosphate (PtdIns3,4P2), but not to other phosphoinositides. May recruit other proteins to the plasma membrane (By similarity). {ECO:0000250}.
• Pathway: Metabolism of lipids;Metabolism;BCR;Synthesis of PIPs at the plasma membrane;Class I PI3K signaling events;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0962

Haploinsufficiency Scores

• pHI: 0.103
• hipred: Y
• hipred_score: 0.605
• ghis: 0.560

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha2
• Phenotype: normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: positive regulation of cell-matrix adhesion;phosphatidylinositol biosynthetic process
• Cellular component: nucleus;cytoplasm;plasma membrane;membrane;protein-containing complex
• Molecular function: fibronectin binding;protein binding;PDZ domain binding;laminin binding;phosphatidylinositol-3,4-bisphosphate binding