PLEKHO1

pleckstrin homology domain containing O1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 1:150149183-150164720

Links

ENSG00000023902 ∙ NCBI:51177 ∙ OMIM:608335 ∙ HGNC:24310 ∙ Uniprot:Q53GL0 ∙ 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 PLEKHO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHO1 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				2	1	3
missense			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2			2
Total	0	0	34	2	1

Variants in PLEKHO1

This is a list of pathogenic ClinVar variants found in the PLEKHO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150150276-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-150150908-G-T			Benign (Jan 19, 2018)
1-150150943-C-T		not specified	Uncertain significance (Jul 02, 2024)
1-150150946-C-G		not specified	Uncertain significance (Apr 20, 2024)
1-150150984-G-A		not specified	Uncertain significance (Oct 25, 2023)
1-150156081-A-T		not specified	Uncertain significance (May 24, 2023)
1-150156121-G-C		not specified	Uncertain significance (Jan 22, 2025)
1-150156177-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-150156184-A-G		not specified	Uncertain significance (Nov 16, 2022)
1-150156198-G-A		not specified	Uncertain significance (Jun 22, 2023)
1-150156918-A-C		not specified	Uncertain significance (Oct 08, 2024)
1-150156919-C-G		not specified	Uncertain significance (Jul 12, 2022)
1-150157001-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-150157002-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-150157445-C-T		not specified	Uncertain significance (Sep 04, 2024)
1-150158915-C-G		not specified	Uncertain significance (Mar 10, 2025)
1-150158931-A-G		not specified	Uncertain significance (Jun 26, 2024)
1-150158948-G-T		not specified	Uncertain significance (Jan 24, 2025)
1-150158960-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-150158964-G-A		not specified	Uncertain significance (Feb 22, 2025)
1-150158978-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-150158979-G-A		not specified	Uncertain significance (Sep 10, 2024)
1-150159000-G-A		not specified	Uncertain significance (May 04, 2022)
1-150159033-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-150159072-A-G		not specified	Uncertain significance (Jan 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHO1	protein_coding	protein_coding	ENST00000369124	6	15544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.483	0.516	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0693	244	247	0.988	0.0000148	2628
Missense in Polyphen		83	99.348	0.83545		1068
Synonymous	-0.288	105	101	1.04	0.00000567	837
Loss of Function	3.19	4	19.0	0.210	0.00000113	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of the actin cytoskeleton through its interactions with actin capping protein (CP). May function to target CK2 to the plasma membrane thereby serving as an adapter to facilitate the phosphorylation of CP by protein kinase 2 (CK2). Appears to target ATM to the plasma membrane. Appears to also inhibit tumor cell growth by inhibiting AKT- mediated cell-survival. Also implicated in PI3K-regulated muscle differentiation, the regulation of AP-1 activity (plasma membrane bound AP-1 regulator that translocates to the nucleus) and the promotion of apoptosis induced by tumor necrosis factor TNF. When bound to PKB, it inhibits it probably by decreasing PKB level of phosphorylation. {ECO:0000269|PubMed:14729969, ECO:0000269|PubMed:15706351, ECO:0000269|PubMed:15831458, ECO:0000269|PubMed:16325375, ECO:0000269|PubMed:16987810, ECO:0000269|PubMed:17197158, ECO:0000269|PubMed:17942896}.

Recessive Scores

• pRec: 0.0873

Intolerance Scores

• loftool: 0.380
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.0969
• hipred: Y
• hipred_score: 0.825
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.552

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekho1
• Phenotype: skeleton phenotype

Zebrafish Information Network

• Gene name: plekho1b
• Affected structure: fast muscle myoblast
• Phenotype tag: abnormal
• Phenotype quality: irregular spatial pattern

Gene ontology

• Biological process: myoblast fusion;regulation of cell shape;myoblast migration;lamellipodium morphogenesis
• Cellular component: nucleus;cytoplasm;ruffle membrane;muscle cell projection membrane
• Molecular function: protein binding