PLEKHA5

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

Basic information

Region (hg38): 12:19129669-19376400

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.

• not_specified (115 variants)
• PLEKHA5-related_disorder (24 variants)
• Cleft_lip_with_or_without_cleft_palate (5 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. These statistics are base on transcript: NM_001256470.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				11	2	13
missense		1	116	7	4	128
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	116	18	6

Highest pathogenic variant AF is 0.000005502154

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