PLEKHO2

pleckstrin homology domain containing O2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 15:64841882-64868002

Previous symbols: [ "PLEKHQ1" ]

Links

ENSG00000241839 ∙ NCBI:80301 ∙ ∙ HGNC:30026 ∙ Uniprot:Q8TD55 ∙ 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 PLEKHO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHO2 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	42	2	0

Variants in PLEKHO2

This is a list of pathogenic ClinVar variants found in the PLEKHO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64848608-G-A		not specified	Uncertain significance (Jun 21, 2023)
15-64848614-A-C		not specified	Uncertain significance (Feb 12, 2024)
15-64848732-A-G		not specified	Uncertain significance (Nov 21, 2022)
15-64848738-A-G		not specified	Uncertain significance (Nov 07, 2022)
15-64854917-C-G			Likely benign (Jan 01, 2023)
15-64854934-G-A		not specified	Uncertain significance (Nov 08, 2022)
15-64854950-G-C		not specified	Uncertain significance (Aug 10, 2021)
15-64854961-A-G		not specified	Uncertain significance (Dec 27, 2023)
15-64854990-C-T		not specified	Uncertain significance (Nov 17, 2022)
15-64855006-G-A		not specified	Uncertain significance (Sep 27, 2021)
15-64855012-T-G		not specified	Uncertain significance (May 07, 2024)
15-64859916-C-G		not specified	Uncertain significance (Feb 03, 2022)
15-64861486-G-A		not specified	Uncertain significance (Jun 30, 2023)
15-64861529-G-T		not specified	Uncertain significance (Jan 31, 2022)
15-64864907-T-A		not specified	Uncertain significance (Feb 05, 2024)
15-64864929-C-T		not specified	Uncertain significance (Dec 06, 2023)
15-64864975-C-A		not specified	Uncertain significance (Mar 31, 2023)
15-64864995-G-T		not specified	Uncertain significance (Aug 26, 2022)
15-64865059-C-T		not specified	Uncertain significance (May 30, 2023)
15-64865079-G-A		not specified	Uncertain significance (Mar 29, 2022)
15-64865137-C-G		not specified	Uncertain significance (Dec 01, 2022)
15-64865208-G-T		not specified	Uncertain significance (Aug 02, 2021)
15-64865284-C-T		not specified	Likely benign (May 10, 2022)
15-64865287-C-T		not specified	Uncertain significance (Aug 22, 2023)
15-64865330-G-C		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHO2	protein_coding	protein_coding	ENST00000323544	6	26119

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0336	0.965	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.246	269	281	0.959	0.0000155	3138
Missense in Polyphen		93	95.851	0.97025		1072
Synonymous	0.0501	112	113	0.994	0.00000594	1041
Loss of Function	2.77	6	19.0	0.315	0.00000114	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000669	0.0000615
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• loftool: 0.383
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.76

Haploinsufficiency Scores

• pHI: 0.368
• hipred: N
• hipred_score: 0.154
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.363

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekho2

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: extracellular region;ficolin-1-rich granule lumen