PLEKHA3

pleckstrin homology domain containing A3, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:178480457-178516463

Links

ENSG00000116095 ∙ NCBI:65977 ∙ OMIM:607774 ∙ HGNC:14338 ∙ Uniprot:Q9HB20 ∙ 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 PLEKHA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA3 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in PLEKHA3

This is a list of pathogenic ClinVar variants found in the PLEKHA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-178480876-G-T		not specified	Uncertain significance (Dec 30, 2024)
2-178490782-G-A		not specified	Uncertain significance (Sep 08, 2024)
2-178493883-C-G		not specified	Uncertain significance (Sep 10, 2024)
2-178493967-A-G		not specified	Uncertain significance (Dec 05, 2024)
2-178494019-G-A		TTN-related disorder	Likely benign (Jan 08, 2024)
2-178495623-C-A		not specified	Uncertain significance (Dec 13, 2022)
2-178499217-C-T		not specified	Uncertain significance (Oct 06, 2024)
2-178499242-G-C		not specified	Uncertain significance (Mar 19, 2024)
2-178501117-G-A		not specified	Uncertain significance (Feb 20, 2025)
2-178501150-G-A		not specified	Likely benign (Apr 09, 2024)
2-178503784-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-178503838-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-178503847-A-T		not specified	Uncertain significance (Dec 14, 2021)
2-178503853-A-T		not specified	Uncertain significance (Jun 24, 2022)
2-178503873-T-A		not specified	Uncertain significance (Jul 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA3	protein_coding	protein_coding	ENST00000234453	8	35995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0160	0.979	125717	0	12	125729	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	108	158	0.685	0.00000784	1978
Missense in Polyphen		25	53.895	0.46387		686
Synonymous	1.18	42	52.9	0.794	0.00000269	550
Loss of Function	2.47	6	17.0	0.353	9.74e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in Golgi to cell surface membrane traffic. Induces membrane tubulation. Binds preferentially to phosphatidylinositol 4-phosphate (PtdIns4P). {ECO:0000269|PubMed:15107860}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.759
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.454
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;biological_process;ER to Golgi ceramide transport;ceramide transport;intermembrane lipid transfer;ceramide 1-phosphate transport
• Cellular component: Golgi membrane;Golgi apparatus;cytosol;membrane
• Molecular function: lipid binding;phosphatidylinositol-4-phosphate binding;ceramide 1-phosphate binding;ceramide 1-phosphate transporter activity