PIK3C2B

phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta, the group of Phosphatidylinositol 3-kinase subunits

Basic information

Region (hg38): 1:204422627-204494805

Links

ENSG00000133056 ∙ NCBI:5287 ∙ OMIM:602838 ∙ HGNC:8972 ∙ Uniprot:O00750 ∙ 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 PIK3C2B gene.

• Inborn genetic diseases (50 variants)
• not provided (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3C2B 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				5	2	7
missense			46	9	2	57
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	46	14	4

Variants in PIK3C2B

This is a list of pathogenic ClinVar variants found in the PIK3C2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-204424871-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-204424894-G-A		PIK3C2B-related disorder	Likely benign (Aug 08, 2019)
1-204424895-G-C		PIK3C2B-related disorder	Likely benign (Mar 25, 2019)
1-204424945-G-A		PIK3C2B-related disorder	Benign (Feb 19, 2019)
1-204424953-C-T		PIK3C2B-related disorder	Benign (Dec 31, 2019)
1-204425000-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-204425681-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-204425748-T-C		PIK3C2B-related disorder	Likely benign (Jun 14, 2019)
1-204427702-G-A		PIK3C2B-related disorder	Benign (Aug 02, 2019)
1-204427703-G-T		not specified	Uncertain significance (Sep 12, 2023)
1-204427729-T-C		PIK3C2B-related disorder	Likely benign (Mar 21, 2019)
1-204429923-C-T		not specified	Uncertain significance (May 25, 2022)
1-204429933-A-G		PIK3C2B-related disorder	Benign (Aug 02, 2019)
1-204429936-G-A		PIK3C2B-related disorder	Benign (Aug 02, 2019)
1-204429947-T-C		not specified	Uncertain significance (Nov 16, 2022)
1-204429986-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-204429987-C-G		not specified	Uncertain significance (Oct 06, 2021)
1-204431709-T-C		not specified	Uncertain significance (Feb 15, 2023)
1-204431716-T-C		PIK3C2B-related disorder	Benign (Mar 08, 2019)
1-204431741-T-A		not specified	Uncertain significance (Jan 03, 2024)
1-204431758-G-A		PIK3C2B-related disorder	Benign (Mar 18, 2019)
1-204431758-G-T		PIK3C2B-related disorder	Likely benign (Aug 29, 2022)
1-204431759-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-204431763-T-C		not specified	Likely benign (Jan 25, 2023)
1-204432237-C-A		not specified	Uncertain significance (Aug 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIK3C2B	protein_coding	protein_coding	ENST00000367187	32	72097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00349	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	749	972	0.770	0.0000601	10645
Missense in Polyphen		287	425.99	0.67373		4619
Synonymous	1.67	350	392	0.893	0.0000228	3290
Loss of Function	6.91	15	82.8	0.181	0.00000464	906

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000141	0.000131
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates PtdIns and PtdIns4P with a preference for PtdIns. Does not phosphorylate PtdIns(4,5)P2. May be involved in EGF and PDGF signaling cascades. {ECO:0000269|PubMed:10805725}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Sorafenib Pharmacodynamics;VEGF Signaling Pathway;Signaling Pathways in Glioblastoma;Signal Transduction of S1P Receptor;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;EGF-EGFR Signaling Pathway;Regulation of Actin Cytoskeleton;DNA Damage Response (only ATM dependent);Metabolism of lipids;TCR;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;EGFR1;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;Signaling events mediated by Stem cell factor receptor (c-Kit) (Consensus)

Recessive Scores

• pRec: 0.245

Intolerance Scores

• loftool: 0.455
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.93

Haploinsufficiency Scores

• pHI: 0.289
• hipred: Y
• hipred_score: 0.637
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pik3c2b

Gene ontology

• Biological process: biological_process;cellular response to starvation;phosphatidylinositol 3-kinase signaling;cell migration;phosphatidylinositol-3-phosphate biosynthetic process;protein kinase B signaling;phosphatidylinositol phosphorylation;phosphatidylinositol-mediated signaling;autophagosome organization
• Cellular component: nucleoplasm;cytoplasm;endoplasmic reticulum;cytosol;plasma membrane;phosphatidylinositol 3-kinase complex;membrane;endocytic vesicle
• Molecular function: lipid kinase activity;protein binding;ATP binding;1-phosphatidylinositol-3-kinase activity;1-phosphatidylinositol-4-phosphate 3-kinase activity;phosphatidylinositol binding