Information on PIK3CD

Basic details

Alt. symbols: p110D

Approved name: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta
Alt. names: phosphoinositide-3-kinase, catalytic, delta polypeptide, phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta | phosphatidylinositol 3-kinase, catalytic, delta polypeptide, phosphoinositide-3-kinase C

Location: 1p36.22: 9629889 - 9729114 (+)
Gene type: protein_coding, 23 transcripts.

Scores: LoFtool: 0.183000 | pLI: 0.99998429 | LOEUF: 0.196

HGNC: 8977

NCBI: 5293, RefSeq: NG_023434.1

Ensembl: ENSG00000171608.18

LRG_191 | Status: public

OMIM: 602839

Expression | ProteinAtlas

Normal function

PIK3CD encodes the delta catalytic subunit of the class I phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K), which is also known as phosphoinositide 3-kinase delta (PI3K-delta) or p110-delta protein. Class I PI3Ks are heterodimers composed of a catalytic subunit (p110-alpha, p110-beta, p110-gamma, or p110-delta) and a regulatory subunit (p85-alpha, p85-beta, p55-gamma, p150, p101, or p87). The most highly expressed regulatory subunit is p85-alpha (PIK3R1 gene), and the catalytic subunit p110-delta (PIK3CD) is specially enriched in leukocytes and other immune cells. Generally, PI3Ks phosphorylate PftdIns(4,5)P2 (Phosphatidylinositol 4,5-bisphosphate) to generate phosphatidylinositol 3,4,5-trisphosphate (PIP3). PIP3 is essential for the recruitment of PH domain-containing proteins to the plasma membrane, thus activating signalling cascades involved in cell growth, survival, proliferation, differentiation, motility and morphology. Like the other PI3 kinases, the PI3K-delta isoform phosphorylates other proteins such as signalling molecules that transmit chemical signals within lymphocytes and other immune cells. In T cells, p110-delta is required for proliferation, signalling and cytokine production of naive, effector and memory T-cells. The cell receptor (TCR) and co-stimulatory membrane receptors (CD28 and ICOS) are thought to recruit and activate p110-delta to transmit the TCR-mediated signalling. Activation by TCR leads to antigen-dependent memory T-cell migration and retention to antigenic tissues. It also participates in T-cell development, and contributes to T-helper cell expansion and differentiation. In B cells, p110-delta is required for B-cell receptor (BCR) signalling, which is essential for B-cell development, proliferation, migration, and function. In this manner, p110-delta mediates B-cell proliferation in response to anti-IgM, anti-CD40 and IL4 stimulation; and it promotes cytokine production in response to TLR4 and TLR9. p110-delta is also needed for antibody class switch mediated by TLR9, for antigen presentation function of B-cells and for B-cell chemotaxis in response to CXCL13 and sphingosine 1-phosphate (S1P). In natural killer (NK) cells, p110-delta, together with p110-gamma, participates in NK cell receptor activation, NK development, maturation, cytokine production and migration towards the sites of inflammation. In neutrophils, p110-delta, in conjunction with p110-gamma, controls the release of reactive oxygen species, and participates in neutrophil chemotaxis and extravasation. In mast cells, p110-delta controls the release of the granules responsible for allergic reactions and is involved in mast-cell development. In dendritic cells (DC), p110-delta controls lipopolysaccharide induced Toll-like-receptor-4 mediated innate immune responses.

Dysfunction and disease

Heterozygous gain-of-function (GOF) mutations in PIK3CD have been shown to cause autosomal dominant activated PI3K-delta type I syndrome (APDS1), also known as Immunodeficiency 14 [MIM:615513], in over 60 affected individuals from over 30 families to date (Jou et al., 2006; Angulo et al., 2013; Crank et al., 2014; Lucas et al., 2014; Hartman et al., 2015; Nademi et al., 2017; Takeda et al., 2017). Most affected individuals with activated APDS1 present with recurrent sinopulmonary infections, inc luding pneumonias, and other viral infections like EBV, CMV, HSV and VZV in early childhood. The majority of them develop bronchiectasis. Laboratory studies show defects in both B- and T-cell populations and increased serum IgM, with an inability to control infection by EBV and CMV. Patient CD8+ T cells are skewed toward differentiation and senescence. Many patients develop lymphadenopathy, splenomegaly, hepatomegaly, autoimmune disease, mucosal lymphoid aggregates, and/or enteropathy (Coulter et al., 2017). The first and most predominantly reported mutation in PIK3CD is the p.E1021K, with at least 50 patients identified. Additional pathogenic missense mutations are the p.E525K p.C416R, and p.N334K. A PI3K-delta enzyme containing the altered p110? subunit is abnormally activated. Overactive signalling causes T cells to mature and die too quickly, and blocks maturation of B cells at an early stage; which cannot respond to pathogens and likely self-destruct. Overactivation of PI3K-delta signalling can also stimulate abnormal proliferation of lymphocytes, and lymphadenopathy. Activated PI3K-delta syndrome also increases the risk of developing B-cell lymphomas. [Load More]

[Reviewed by Andrés Caballero-Oteyza on 2023-07-25 16:37:00]

Associated conditions

Acronym Condition's_name MOI Mode_of_actionwww icon OMIM_ID No.cases
APDS1 Activated p110-delta syndrome 1 ADdict. icon Gain of Function 615513www icon 66 (41 fams)
AGM12 Agammaglobulinemia 12 ARdict. icon Loss of Function 619281www icon 0 (0 fams)

Please mind that full curation (inclusion of all published patients) of this gene has not been completed yet. It is currently ongoing.

Transcripts of PIK3CD

Name ENSEMBL_ID LRG_ID CCDS_ID MANE Transcript.type Exons Canonical CDS_length REFSEQ_ID
202 ENST00000377346.9 1 CCDS104 Select protein_coding 24 Yes 5412 NM_005026
210 ENST00000698710.1 protein_coding 24 No XM_024447663
212 ENST00000698712.1 CCDS104 protein_coding 23 No XM_006710689
213 ENST00000698713.1 CCDS104 protein_coding 24 No NM_001350235
215 ENST00000698715.1 protein_coding 24 No NM_001350234
214 ENST00000698714.1 protein_coding No XM_047422574

Published variants

Found 6 variants

Var.name Exon/Intron cDNA_pos. CDS_change Prot.change Var.type Var.class. Patients
E81K EX4 450 c.241G>A p.Glu81Lys missense_variant Pathogenic 2
N334K EX8 1211 c.1002C>A p.Asn334Lys missense_variant Pathogenic 1
E525K EX13 1782 c.1573G>A p.Glu525Lys missense_variant Pathogenic 7
L603L EX14 2018 c.1809G>C p.Leu603= splice_region_variant Likely Benign 0
R870* EX21 2817 c.2608C>T p.Arg870Ter stop_gained Likely Pathogenic 0
E1021K EX24 3270 c.3061G>A p.Glu1021Lys missense_variant Pathogenic 57

Please mind that full curation (inclusion of all published variants) of this gene has not been completed yet. It is currently ongoing.

Diagnostic pitfalls & paradigms

Considerations to take into account when analyzing this gene

Year Paradigm ⓘ PMID Notes
- Regions of Homology - NM_005026.3: EX24 (90-98%)
2020Uniparental disomy319537112-mo girl with respiratory tract infections, lymphoproliferation, bronchiectasis and atelectasis in the lungs, which compromised her growth and development. She had a homozygous p.E1021K mutation due to loss of heterozygosity in Chrom. 1. Patient did not inherit that region from father. Interestingly, the patient's mother showed gonosomal mosaicism because the mutant allele frequency was 1.64%.
2017Mosaicism27577878
-Cryptic splicing-Unreported or not recorded in our DB.
-Incomplete penetrance-Unreported or not recorded in our DB.
-Di-/oligo-genic inheritance-Unreported or not recorded in our DB.
-Somatic reversion-Unreported or not recorded in our DB.

References linked to variants in PIK3CD

ID Year Title Journal PMID Variants
60 2006 Identification of variations in the human phosphoinositide 3... Int. J. Immunogen 16984281 1
61 2013 Phosphoinositide 3-Kinase delta Gene Mutation Predisposes to... Science 24136356 1
62 2013 Dominant-activating germline mutations in the gene encoding ... Nat. Immun. 24165795 3
382 2017 Conformational disruption of PI3K? regulation by immunodefic... PNAS 28167755 1
793 2008 Reduced memory B cells in patients with hyper IgE syndrome... Clin. Immunol. 18835223 1
1107 2021 Resolving the polygenic aetiology of a late onset combined i... Clin. Immunol. 34922003 1
1112 2022 Integrating Clinics, Laboratory, and Imaging for the Diagnos... Front. Immunol. 35281075 1

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