PLEKHA1

pleckstrin homology domain containing A1, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:122374695-122432354

Links

ENSG00000107679 ∙ NCBI:59338 ∙ OMIM:607772 ∙ HGNC:14335 ∙ Uniprot:Q9HB21 ∙ 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 PLEKHA1 gene.

• Inborn genetic diseases (19 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA1 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	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	18	2	1

Variants in PLEKHA1

This is a list of pathogenic ClinVar variants found in the PLEKHA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-122393318-G-A		not specified	Uncertain significance (Nov 12, 2021)
10-122397973-A-C		not specified	Uncertain significance (Nov 10, 2022)
10-122400343-G-A		not specified	Uncertain significance (Oct 03, 2022)
10-122406615-A-G		not specified	Uncertain significance (Feb 16, 2023)
10-122406620-C-G		not specified	Uncertain significance (Jul 26, 2022)
10-122407996-C-T			Benign (Feb 18, 2020)
10-122412947-A-C		not specified	Likely benign (May 25, 2022)
10-122412958-C-A		not specified	Uncertain significance (Dec 28, 2022)
10-122412965-C-G		not specified	Uncertain significance (Nov 01, 2022)
10-122412965-C-T		not specified	Uncertain significance (Nov 03, 2022)
10-122412988-G-C		not specified	Uncertain significance (Nov 30, 2022)
10-122413044-A-G			Uncertain significance (Jan 01, 2023)
10-122417921-T-C		not specified	Uncertain significance (May 24, 2023)
10-122424194-G-T			Benign (Dec 31, 2019)
10-122424214-C-G		not specified	Uncertain significance (Dec 05, 2022)
10-122424937-C-T		not specified	Uncertain significance (Nov 22, 2021)
10-122426942-G-T		not specified	Uncertain significance (Oct 04, 2022)
10-122427014-G-A		not specified	Uncertain significance (Mar 14, 2023)
10-122427029-T-G		not specified	Uncertain significance (Nov 27, 2023)
10-122429654-C-T		not specified	Uncertain significance (Jul 13, 2021)
10-122429664-G-A		not specified	Uncertain significance (Feb 28, 2024)
10-122429673-A-G		not specified	Likely benign (May 11, 2022)
10-122429722-G-T		not specified	Uncertain significance (Apr 05, 2023)
10-122429908-C-G		not specified	Uncertain significance (Jan 12, 2024)
10-122429909-G-A		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA1	protein_coding	protein_coding	ENST00000368990	11	57656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000235	0.996	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	207	235	0.880	0.0000133	2663
Missense in Polyphen		81	105.66	0.76662		1261
Synonymous	0.0292	82	82.3	0.996	0.00000504	750
Loss of Function	2.55	10	23.3	0.429	0.00000120	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000218	0.000217
South Asian	0.000622	0.000621
Other	0.000163	0.000163

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. {ECO:0000269|PubMed:11001876, ECO:0000269|PubMed:11513726, ECO:0000269|PubMed:14516276}.
• 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: 0.165

Intolerance Scores

• loftool: 0.845
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.589
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); digestive/alimentary phenotype

Gene ontology

• Biological process: luteinization;phosphatidylinositol biosynthetic process;spermatogenesis;androgen metabolic process;estrogen metabolic process;post-embryonic development;phosphatidylinositol 3-kinase signaling;ruffle organization;Leydig cell differentiation;multicellular organism growth;establishment of protein localization;platelet-derived growth factor receptor signaling pathway;skeletal system morphogenesis;B cell receptor signaling pathway;negative regulation of protein kinase B signaling;roof of mouth development;face morphogenesis;cellular response to hydrogen peroxide
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;membrane;ruffle membrane;extracellular exosome
• Molecular function: protein binding;PDZ domain binding;phosphatidylinositol-3,4-bisphosphate binding