PLEKHB2

pleckstrin homology domain containing B2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:131104847-131353709

Links

ENSG00000115762 ∙ NCBI:55041 ∙ OMIM:618452 ∙ HGNC:19236 ∙ Uniprot:Q96CS7 ∙ 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 PLEKHB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHB2 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in PLEKHB2

This is a list of pathogenic ClinVar variants found in the PLEKHB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-131120956-G-C		not specified	Uncertain significance (Sep 12, 2023)
2-131120973-G-A		not specified	Uncertain significance (Oct 25, 2022)
2-131125768-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-131125798-C-T		not specified	Uncertain significance (Dec 30, 2023)
2-131125816-A-G		not specified	Uncertain significance (Nov 18, 2022)
2-131125828-A-C		not specified	Uncertain significance (Feb 01, 2025)
2-131125875-A-C		not specified	Uncertain significance (Mar 08, 2025)
2-131125884-C-T		not specified	Uncertain significance (Dec 10, 2024)
2-131126693-C-A		not specified	Uncertain significance (Nov 30, 2022)
2-131126705-A-G		not specified	Uncertain significance (Dec 15, 2023)
2-131132906-A-G		not specified	Uncertain significance (Apr 17, 2024)
2-131132918-C-T		not specified	Uncertain significance (May 29, 2024)
2-131132939-C-T		not specified	Uncertain significance (Oct 12, 2024)
2-131140204-C-T		not specified	Uncertain significance (Aug 29, 2024)
2-131140218-G-C		not specified	Uncertain significance (Dec 20, 2023)
2-131140225-A-G		not specified	Uncertain significance (Apr 06, 2024)
2-131140227-G-A		not specified	Uncertain significance (Jan 10, 2025)
2-131140270-A-G		not specified	Uncertain significance (May 20, 2024)
2-131146642-T-C		not specified	Uncertain significance (Dec 15, 2022)
2-131218415-G-A			Likely benign (Dec 01, 2022)
2-131218648-T-C			Likely benign (Aug 01, 2022)
2-131218873-C-G			Likely benign (Dec 01, 2022)
2-131263612-C-T			Likely benign (Jun 01, 2023)
2-131263867-G-A			Likely benign (Jul 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHB2	protein_coding	protein_coding	ENST00000409158	7	248863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.69e-11	0.0697	125576	0	171	125747	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	109	146	0.745	0.00000895	1484
Missense in Polyphen		32	45.919	0.69688		559
Synonymous	0.291	58	60.9	0.953	0.00000430	449
Loss of Function	0.133	16	16.6	0.965	9.89e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000732	0.000547
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00117	0.00113
Middle Eastern	0.00	0.00
South Asian	0.000197	0.000196
Other	0.00163	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in retrograde transport of recycling endosomes. {ECO:0000269|PubMed:21911378, ECO:0000269|PubMed:22281740}.

Intolerance Scores

• loftool: 0.442
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.300
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.325

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhb2

Gene ontology

• Biological process: regulation of cell differentiation
• Cellular component: integral component of membrane;recycling endosome membrane
• Molecular function: protein binding;phosphatidylinositol-3,4,5-trisphosphate binding