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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PIK3C2A
phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha
Chromosome 11 Β· 11p15.1
NCBI Gene: 5286Ensembl: ENSG00000011405.15HGNC: HGNC:8971UniProt: B4DG55
159PubMed Papers
21Diseases
0Drugs
30Pathogenic Variants
FUNCTIONAL ROLE
Kinase
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytosolmembraneclathrin-coated vesiclevesicleoculocerebrodental syndromeShort statureAlzheimer diseasemultiple sclerosis
✦AI Summary

PIK3C2A is a Class II phosphatidylinositol 3-kinase that catalyzes phosphorylation of phosphatidylinositol to generate PI(3)P and PI(3,4)P2 second messengers 1. These lipids regulate diverse cellular processes including proliferation, metabolism, and cell motility 2. Functionally, PIK3C2A is essential for primary cilia formation and maintenance, clathrin-mediated endocytosis, and cytokinetic abscission through ESCRT-dependent mechanisms 32. The protein participates in receptor-mediated endocytosis at the ciliary base and regulates metabolic pathways including mTORC1 signaling 45. Dysregulation of PIK3C2A is associated with multiple pathological conditions. Loss-of-function mutations cause oculoskeletodental syndrome characterized by short stature, cataracts, skeletal abnormalities, and impaired cilia formation 12. Reduced PIK3C2A expression correlates with acute coronary syndrome development, serving as an independent risk factor for coronary artery disease 6. In renal clear cell carcinoma, PIK3C2A downregulation associates with poor prognosis and altered immune infiltration 7. Conversely, loss of PI3K-C2Ξ³ (a related isoform) in pancreatic cancer increases mTORC1 hyperactivation and metabolic vulnerability 4. Post-stroke neurogenesis impairment involves disruption of the CXCL12-PIK3C2A-CREB3L2 axis 5. PIK3C2A suppression via miR-509-3p inhibits cancer cell proliferation and migration 8.

Sources cited
1
PIK3C2A catalyzes phosphorylation of PI into PI(3)P and PI(4)P into PI(3,4)P2; mutations cause syndromic short stature, cataracts, and impaired cilia formation
PMID: 31034465
2
PIK3C2A regulates cilia formation and maintenance; defective enzyme causes impaired ciliogenesis and reduced proliferative capacity in patient fibroblasts
PMID: 40542664
3
PIK3C2A and its lipid product PI(3,4)P2 are required for lens-specific cytokinesis through ESCRT-II; loss leads to impaired cytokinesis and cataract formation
PMID: 34882480
4
PIK3C2A is significantly downregulated in acute coronary syndrome patients; independent risk factor for coronary artery disease development
PMID: 36830671
5
PI3K-C2Ξ³ loss prevents mTOR inactivation and increases tumor aggressiveness in pancreatic cancer through metabolic rewiring
PMID: 35623884
6
PIK3C2A downregulation in renal clear cell carcinoma correlates with poor prognosis and altered immune infiltration patterns
PMID: 37063922
7
CXCL12-PIK3C2A-CREB3L2 axis disruption impairs post-stroke hippocampal neurogenesis in cerebral amyloid angiopathy
PMID: 39392753
8
miR-509-3p targets PIK3C2A and inhibits cancer cell proliferation, migration, and colony formation
PMID: 24802056
Disease Associationsβ“˜21
oculocerebrodental syndromeOpen Targets
0.75Strong
Short statureOpen Targets
0.33Weak
Alzheimer diseaseOpen Targets
0.33Weak
multiple sclerosisOpen Targets
0.32Weak
lysosomal storage diseaseOpen Targets
0.32Weak
neurodegenerative diseaseOpen Targets
0.32Weak
Parkinson diseaseOpen Targets
0.32Weak
obesityOpen Targets
0.29Weak
schizophreniaOpen Targets
0.28Weak
bipolar disorderOpen Targets
0.28Weak
overnutritionOpen Targets
0.22Weak
hepatocellular carcinomaOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.08Suggestive
acute myocardial infarctionOpen Targets
0.08Suggestive
COVID-19–associated multisystem inflammatory syndrome in adultsOpen Targets
0.07Suggestive
neoplasmOpen Targets
0.07Suggestive
autosomal dominant macrothrombocytopeniaOpen Targets
0.06Suggestive
Beta-thalassemia - X-linked thrombocytopeniaOpen Targets
0.06Suggestive
beta-thalassemia-X-linked thrombocytopenia syndromeOpen Targets
0.06Suggestive
Increased total leukocyte countOpen Targets
0.06Suggestive
Oculoskeletodental syndromeUniProt
Pathogenic Variants30
NM_002645.4(PIK3C2A):c.4243del (p.Thr1415fs)Pathogenic
not provided|Oculocerebrodental syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 1415
NM_002645.4(PIK3C2A):c.4531_4534del (p.Leu1511fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1511
NM_002645.4(PIK3C2A):c.2846+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_002645.4(PIK3C2A):c.2193_2196del (p.Tyr732fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 732
NM_002645.4(PIK3C2A):c.3214C>T (p.Gln1072Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1072
NM_002645.4(PIK3C2A):c.3415-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_002645.4(PIK3C2A):c.3035+1G>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_002645.4(PIK3C2A):c.2196C>A (p.Tyr732Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 732
NM_002645.4(PIK3C2A):c.3775C>T (p.Arg1259Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1259
NM_002645.4(PIK3C2A):c.2108+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_002645.4(PIK3C2A):c.2040G>A (p.Trp680Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 680
NM_002645.4(PIK3C2A):c.2662_2663insAT (p.Ser888fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 888
NM_002645.4(PIK3C2A):c.3699_3702del (p.Tyr1234fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1234
NM_002645.4(PIK3C2A):c.3456_3457del (p.Met1152fs)Likely pathogenic
Oculocerebrodental syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 1152
NM_002645.4(PIK3C2A):c.2750del (p.Pro917fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 917
NM_002645.4(PIK3C2A):c.493C>T (p.Gln165Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 165
NM_002645.4(PIK3C2A):c.4451+1G>TLikely pathogenic
Oculocerebrodental syndrome
β˜…β˜†β˜†β˜†2024
NM_002645.4(PIK3C2A):c.486C>G (p.Tyr162Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 162
NM_002645.4(PIK3C2A):c.3541C>T (p.Arg1181Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 1181
NM_002645.4(PIK3C2A):c.3226C>T (p.Gln1076Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 1076
View on ClinVar β†—
Related Genes
PIK3CDProtein interaction100%CLTCProtein interaction100%PIK3R5Protein interaction98%SYNJ1Protein interaction95%PTENProtein interaction95%PIK3R2Protein interaction95%
Tissue Expression6 tissues
Heart
100%
Lung
99%
Bone Marrow
88%
Ovary
77%
Brain
65%
Liver
59%
Gene Interaction Network
Click a node to explore
PIK3C2APIK3CDCLTCPIK3R5SYNJ1PTENPIK3R2
PROTEIN STRUCTURE
Preparing viewer…
PDB6BTY Β· 1.68 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.63LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.47 [0.35–0.63]
RankingsWhere PIK3C2A stands among ~20K protein-coding genes
  • #2,834of 20,598
    Most Researched159 Β· top quartile
  • #1,796of 5,498
    Most Pathogenic Variants30
  • #4,499of 17,882
    Most Constrained (LOEUF)0.63
Genes detectedPIK3C2A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
PIK3C2A-Related Clinical Phenotype and Cellular Charaterization Linked to Functional SHH Primary Cilia Defect.
PMID: 40542664
Clin Genet Β· 2025
1.00
2
Various Expressions of
PMID: 36830671
Biomolecules Β· 2023
0.90
3
PI(3,4)P2-mediated cytokinetic abscission prevents early senescence and cataract formation.
PMID: 34882480
Science Β· 2021
0.80
4
Lysosomal lipid switch sensitises to nutrient deprivation and mTOR targeting in pancreatic cancer.
PMID: 35623884
Gut Β· 2023
0.70
5
Low expression of PIK3C2A gene: A potential biomarker to predict the risk of acute myocardial infarction.
PMID: 30946353
Medicine (Baltimore) Β· 2019
0.64