PLEKHA5

pleckstrin homology domain containing A5, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 12:19129668-19376400

Links

ENSG00000052126 ∙ NCBI:54477 ∙ OMIM:607770 ∙ HGNC:30036 ∙ Uniprot:Q9HAU0 ∙ 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 PLEKHA5 gene.

• Inborn genetic diseases (33 variants)
• not provided (4 variants)
• Bilateral cleft lip (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA5 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				3	1	4
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	5	1

Variants in PLEKHA5

This is a list of pathogenic ClinVar variants found in the PLEKHA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-19129809-G-A		PLEKHA5-related disorder	Likely benign (Nov 03, 2023)
12-19129829-C-T		PLEKHA5-related disorder	Likely benign (Jul 01, 2022)
12-19129884-A-G		not specified	Uncertain significance (Dec 21, 2022)
12-19130072-C-T		PLEKHA5-related disorder	Likely benign (Mar 21, 2023)
12-19255143-A-G		not specified	Uncertain significance (Dec 19, 2022)
12-19257427-A-G		PLEKHA5-related disorder	Benign (Aug 28, 2019)
12-19257442-G-C		not specified	Uncertain significance (Apr 11, 2023)
12-19257457-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-19265783-T-A		not specified	Uncertain significance (Oct 25, 2022)
12-19274530-C-T		not specified	Uncertain significance (Nov 23, 2022)
12-19274579-A-G		PLEKHA5-related disorder	Benign (Mar 29, 2019)
12-19274580-G-A		PLEKHA5-related disorder	Likely benign (May 31, 2022)
12-19274641-A-G		not specified	Uncertain significance (Dec 13, 2021)
12-19274726-G-T		PLEKHA5-related disorder	Likely benign (Aug 25, 2022)
12-19274803-G-A		PLEKHA5-related disorder	Benign (Jun 06, 2019)
12-19274830-T-C		PLEKHA5-related disorder	Benign (Feb 19, 2019)
12-19274832-A-G		PLEKHA5-related disorder	Benign (Feb 19, 2019)
12-19274860-G-A		not specified	Likely benign (Feb 13, 2023)
12-19274878-T-C		not specified	Uncertain significance (Oct 04, 2023)
12-19274919-A-G		Cleft lip with or without cleft palate	Uncertain significance (-)
12-19283321-A-T		not specified	Uncertain significance (May 26, 2022)
12-19283442-C-T		PLEKHA5-related disorder	Likely benign (Mar 26, 2019)
12-19283467-A-G		not specified	Uncertain significance (Oct 10, 2023)
12-19283497-G-A		not specified	Uncertain significance (Dec 19, 2023)
12-19283519-A-G		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA5	protein_coding	protein_coding	ENST00000429027	31	246687

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.65e-11	125737	0	6	125743	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	580	670	0.865	0.0000344	8389
Missense in Polyphen		217	295.73	0.73379		3659
Synonymous	1.33	211	237	0.890	0.0000126	2370
Loss of Function	7.93	3	79.0	0.0380	0.00000429	953

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000734	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of lipids;Metabolism;EGFR1;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.273
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• pHI: 0.156
• hipred: Y
• hipred_score: 0.595
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.745

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha5
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: biological_process;reproductive system development
• Cellular component: nucleoplasm;cytosol;postsynaptic density;membrane;glutamatergic synapse
• Molecular function: protein binding;phosphatidylinositol-5-phosphate binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-4-phosphate binding;phosphatidylinositol-3,5-bisphosphate binding