PLEKHA8

pleckstrin homology domain containing A8, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 7:30027404-30130483

Links

ENSG00000106086 ∙ NCBI:84725 ∙ OMIM:608639 ∙ HGNC:30037 ∙ Uniprot:Q96JA3 ∙ 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 PLEKHA8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA8 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in PLEKHA8

This is a list of pathogenic ClinVar variants found in the PLEKHA8 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-30028800-G-A		not specified	Uncertain significance (Nov 17, 2022)
7-30045087-T-C		not specified	Uncertain significance (Jan 04, 2024)
7-30045091-A-G		not specified	Uncertain significance (Jan 30, 2024)
7-30045117-G-C		not specified	Uncertain significance (Sep 22, 2023)
7-30045120-A-G		not specified	Uncertain significance (Apr 28, 2022)
7-30045122-A-G		not specified	Uncertain significance (Mar 21, 2023)
7-30046273-A-G		not specified	Uncertain significance (Oct 17, 2024)
7-30047847-C-G		not specified	Uncertain significance (May 24, 2023)
7-30047910-T-C		not specified	Uncertain significance (Feb 21, 2024)
7-30047921-A-G		not specified	Uncertain significance (Aug 30, 2021)
7-30049235-T-A		not specified	Uncertain significance (Nov 18, 2022)
7-30049273-T-C		not specified	Uncertain significance (Sep 19, 2023)
7-30049299-A-G		not specified	Uncertain significance (Dec 04, 2024)
7-30049302-G-A		not specified	Uncertain significance (Mar 21, 2023)
7-30049342-C-T		not specified	Uncertain significance (Oct 20, 2023)
7-30052729-G-A		not specified	Uncertain significance (Jun 09, 2022)
7-30052782-A-C		not specified	Uncertain significance (Mar 30, 2024)
7-30052800-T-C		not specified	Uncertain significance (Mar 07, 2024)
7-30052818-A-G		not specified	Uncertain significance (Nov 21, 2022)
7-30052822-A-G		not specified	Uncertain significance (Oct 06, 2022)
7-30054720-A-G		not specified	Uncertain significance (Jul 05, 2023)
7-30054763-A-G		not specified	Likely benign (Jul 12, 2022)
7-30054780-G-A		not specified	Uncertain significance (May 25, 2022)
7-30054814-G-T		not specified	Uncertain significance (Nov 10, 2022)
7-30054822-G-A		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA8	protein_coding	protein_coding	ENST00000449726	14	103077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.18e-9	0.877	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.937	217	259	0.836	0.0000125	3407
Missense in Polyphen		78	109.31	0.71358		1371
Synonymous	-0.242	98	95.0	1.03	0.00000476	951
Loss of Function	1.74	18	27.9	0.644	0.00000131	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000173	0.000167
Middle Eastern	0.000165	0.000163
South Asian	0.000167	0.000131
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cargo transport protein that is required for apical transport from the Golgi complex. Transports AQP2 from the trans- Golgi network (TGN) to sites of AQP2 phosphorylation. Mediates the non-vesicular transport of glucosylceramide (GlcCer) from the trans-Golgi network (TGN) to the plasma membrane and plays a pivotal role in the synthesis of complex glycosphingolipids. Binding of both phosphatidylinositol 4-phosphate (PIP) and ARF1 are essential for the GlcCer transfer ability. Also required for primary cilium formation, possibly by being involved in the transport of raft lipids to the apical membrane, and for membrane tubulation. {ECO:0000269|PubMed:15107860, ECO:0000269|PubMed:16103222, ECO:0000269|PubMed:17687330}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.314
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0880
• hipred: N
• hipred_score: 0.427
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.671

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekha8
• Phenotype: reproductive system phenotype

Gene ontology

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