PLEKHA4

pleckstrin homology domain containing A4, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 19:48837092-48868617

Links

ENSG00000105559 ∙ NCBI:57664 ∙ OMIM:607769 ∙ HGNC:14339 ∙ Uniprot:Q9H4M7 ∙ 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 PLEKHA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA4 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			84	4		88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	84	4	0

Variants in PLEKHA4

This is a list of pathogenic ClinVar variants found in the PLEKHA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48837330-C-G		not specified	Uncertain significance (Oct 10, 2023)
19-48837344-G-T		not specified	Uncertain significance (Sep 20, 2024)
19-48837353-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-48837356-G-A		not specified	Uncertain significance (Jun 03, 2022)
19-48837369-C-A		not specified	Likely benign (Apr 06, 2022)
19-48837381-G-T		not specified	Uncertain significance (Jul 10, 2024)
19-48837387-A-C		not specified	Uncertain significance (Jul 10, 2024)
19-48837399-C-G		not specified	Uncertain significance (Sep 24, 2024)
19-48837449-G-A		not specified	Uncertain significance (Dec 14, 2024)
19-48837488-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-48837504-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-48837525-G-C		not specified	Uncertain significance (Aug 12, 2021)
19-48838045-C-G		not specified	Uncertain significance (Feb 28, 2023)
19-48838112-G-A		not specified	Uncertain significance (Jun 07, 2023)
19-48838117-G-A		not specified	Likely benign (Feb 17, 2024)
19-48839220-G-A		not specified	Uncertain significance (Jul 25, 2024)
19-48839233-A-G		not specified	Uncertain significance (Jun 26, 2024)
19-48841210-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-48841211-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-48841213-G-A		not specified	Uncertain significance (Aug 28, 2024)
19-48841217-A-G		not specified	Uncertain significance (Sep 09, 2024)
19-48841258-C-T		not specified	Uncertain significance (Jan 24, 2023)
19-48841259-G-A		not specified	Uncertain significance (May 18, 2023)
19-48841265-G-A		not specified	Uncertain significance (May 24, 2023)
19-48841298-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA4	protein_coding	protein_coding	ENST00000263265	19	31536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-12	0.988	125620	0	127	125747	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.610	456	494	0.923	0.0000320	4848
Missense in Polyphen		136	158.36	0.85883		1534
Synonymous	0.153	199	202	0.986	0.0000126	1747
Loss of Function	2.50	26	43.9	0.592	0.00000268	424

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00104
Ashkenazi Jewish	0.000218	0.000198
East Asian	0.000437	0.000435
Finnish	0.000247	0.000231
European (Non-Finnish)	0.000496	0.000484
Middle Eastern	0.000437	0.000435
South Asian	0.000989	0.000980
Other	0.000689	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds specifically to phosphatidylinositol 3-phosphate (PtdIns3P), but not to other phosphoinositides. {ECO:0000269|PubMed:11001876}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.916
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.83

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: N
• hipred_score: 0.375
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha4

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;biological_process
• Cellular component: cellular_component;cytoplasm;plasma membrane
• Molecular function: phosphatidylinositol-3-phosphate binding