PRKCD

protein-coding

protein kinase C delta, the group of C2 domain containing protein kinases|AGC family kinases

Gene summary

The protein encoded by this gene is a member of the protein kinase C family of serine- and threonine-specific protein kinases. The encoded protein is activated by diacylglycerol and is both a tumor suppressor and a positive regulator of cell cycle progression. Also, this protein can positively or negatively regulate apoptosis. Defects in this gene are a cause of autoimmune lymphoproliferative syndrome. [provided by RefSeq, Aug 2017]

MANE transcript

NM_006254.4

Inheritance

AR

ClinVar variants

P:21U:236B:168

Top phenotype

Autoimmune lymphoproliferative syndrome type III

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr3:53,156,009-53,192,717

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

systemic lupus erythematosusDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0007915

Submitter: ClinGen

Protein kinase C delta (*PRKCD*) was first reported in relation to autosomal recessive systemic lupus erythematosus (SLE) in 2013 (Belot et al, PMID: 23666743). Clinical reports have described affected individuals as having SLE, SLE-like, ALPS, ALPS-like, or CVID-like disease. While there is variability in severity of phenotype, per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no significant difference in molecular mechanism(s) or inheritance pattern. Therefore, the following disease entities have been lumped into one disease entity: Autoimmune lymphoproliferative syndrome, type III (OMIM:615559), and systemic lupus erythematosus (MONDO ID: 0007915). Eleven variants (2 nonsense, 2 frameshift, 3 splicing, and 5 missense) have been reported in 10 probands in 8 publications (PMIDs: 23666743, 28003329, 34264265, 36650346, 26233237, 23319571, 23430113, 33047643) which are included in this curation. Of these ten probands, all had family members tested which confirmed segregation of the *PRKCD* variant with disease. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is also supported by experimental evidence including animal models, expression studies, and *in vitro* functional assays (PMIDs: 23666743, 11976687, 23430113), all of which demonstrated that variants in *PRKCD* result in partial or complete loss of expression, reduced phosphorylation activity, and recapitulate human immune phenotypes in mice and patient cells. *PRKCD* mutant lymphoblastoid cell lines are resistant to apoptosis, but are rescued by coexpression of wild type protein. There is additional experimental evidence in Neehus et al. 2021 (PMID: 34264265), which was not included because the overall classification has reached the definitive level. In summary, there is **definitive** evidence supporting the relationship between *PRKCD* and autosomal recessive systemic lupus erythematosus. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Monogenic Systemic and Incomplete Lupus Erythematosus GCEP on the meeting date October 11, 2024 (SOP Version 11).

autoimmune lymphoproliferative syndrome, type III caused by mutation in PRKCDSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:8000024

Submitter: PanelApp Australia

autoimmune lymphoproliferative syndrome, type III caused by mutation in PRKCDSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:8000024

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Autoimmune lymphoproliferative syndrome type IIIAR

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; medical management (eg, with immunosuppressive agents) of autoimmune manifestations has been described as beneficial

Refs: 23319571; 23430113; 23666743Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRKCD variants in ClinVar

7 Conditions Cataloged
Autoimmune lymphoproliferative syndrome, type III caused by mutation in PRKCDTotal: 542
not specifiedTotal: 67
not providedTotal: 66
Inborn genetic diseasesTotal: 55
PRKCD-related disorderTotal: 15
EBV-positive nodal T- and NK-cell lymphomaTotal: 1
See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006254.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
7
clinvar
151
clinvar
3
clinvar
161
missense
1
clinvar
2
clinvar
215
clinvar
13
clinvar
1
clinvar
232
nonsense
5
clinvar
2
clinvar
1
clinvar
8
start loss
0
frameshift
4
clinvar
4
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
13
clinvar
20
Total1292361644425

Highest pathogenic variant AF is 0.00001162953

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006254.4RefSeqNP_006245.217MANE Select
ENST00000330452.8EnsemblENSP00000331602.317MANE Select
NM_001316327.2RefSeqNP_001303256.117Standard
NM_001354676.2RefSeqNP_001341605.118Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
  • Fc gamma R-mediated phagocytosis - Homo sapiens (human)
  • Neurotrophin signaling pathway - Homo sapiens (human)
  • Type II diabetes mellitus - Homo sapiens (human)
  • Insulin resistance - Homo sapiens (human)

Biological Process

  • stimulatory C-type lectin receptor signaling pathway
  • protein phosphorylation
  • apoptotic process
  • cell cycle
  • signal transduction

Molecular Function

  • protein kinase activity
  • protein serine/threonine kinase activity
  • protein kinase C activity
  • calcium-independent protein kinase C activity
  • non-membrane spanning protein tyrosine kinase activity

Cellular Component

  • extracellular region
  • nucleus
  • nucleoplasm
  • cytoplasm
  • endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000394729
Coding exons
17
Length
36709
Individuals with no LoFs
125743
Homozygous LoFs
0
Heterozygous LoFs
3
Defined
125746
p
0.0000119
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.112414210.5730.00002624525
Missense (PolyPhen)80201.720.396582127
Synonymous1.221501700.8810.00001191217
Loss of Function5.31236.80.05440.00000185421

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Calcium-independent, phospholipid- and diacylglycerol (DAG)-dependent serine/threonine-protein kinase that plays contrasting roles in cell death and cell survival by functioning as a pro-apoptotic protein during DNA damage-induced apoptosis, but acting as an anti-apoptotic protein during cytokine receptor- initiated cell death, is involved in tumor suppression as well as survival of several cancers, is required for oxygen radical production by NADPH oxidase and acts as positive or negative regulator in platelet functional responses. Negatively regulates B cell proliferation and also has an important function in self- antigen induced B cell tolerance induction. Upon DNA damage, activates the promoter of the death-promoting transcription factor BCLAF1/Btf to trigger BCLAF1-mediated p53/TP53 gene transcription and apoptosis. In response to oxidative stress, interact with and activate CHUK/IKKA in the nucleus, causing the phosphorylation of p53/TP53. In the case of ER stress or DNA damage-induced apoptosis, can form a complex with the tyrosine-protein kinase ABL1 which trigger apoptosis independently of p53/TP53. In cytosol can trigger apoptosis by activating MAPK11 or MAPK14, inhibiting AKT1 and decreasing the level of X-linked inhibitor of apoptosis protein (XIAP), whereas in nucleus induces apoptosis via the activation of MAPK8 or MAPK9. Upon ionizing radiation treatment, is required for the activation of the apoptosis regulators BAX and BAK, which trigger the mitochondrial cell death pathway. Can phosphorylate MCL1 and target it for degradation which is sufficient to trigger for BAX activation and apoptosis. Is required for the control of cell cycle progression both at G1/S and G2/M phases. Mediates phorbol 12-myristate 13-acetate (PMA)- induced inhibition of cell cycle progression at G1/S phase by up- regulating the CDK inhibitor CDKN1A/p21 and inhibiting the cyclin CCNA2 promoter activity. In response to UV irradiation can phosphorylate CDK1, which is important for the G2/M DNA damage checkpoint activation. Can protect glioma cells from the apoptosis induced by TNFSF10/TRAIL, probably by inducing increased phosphorylation and subsequent activation of AKT1. Is highly expressed in a number of cancer cells and promotes cell survival and resistance against chemotherapeutic drugs by inducing cyclin D1 (CCND1) and hyperphosphorylation of RB1, and via several pro- survival pathways, including NF-kappa-B, AKT1 and MAPK1/3 (ERK1/2). Can also act as tumor suppressor upon mitogenic stimulation with PMA or TPA. In N-formyl-methionyl-leucyl- phenylalanine (fMLP)-treated cells, is required for NCF1 (p47- phox) phosphorylation and activation of NADPH oxidase activity, and regulates TNF-elicited superoxide anion production in neutrophils, by direct phosphorylation and activation of NCF1 or indirectly through MAPK1/3 (ERK1/2) signaling pathways. May also play a role in the regulation of NADPH oxidase activity in eosinophil after stimulation with IL5, leukotriene B4 or PMA. In collagen-induced platelet aggregation, acts a negative regulator of filopodia formation and actin polymerization by interacting with and negatively regulating VASP phosphorylation. Downstream of PAR1, PAR4 and CD36/GP4 receptors, regulates differentially platelet dense granule secretion; acts as a positive regulator in PAR-mediated granule secretion, whereas it negatively regulates CD36/GP4-mediated granule release. Phosphorylates MUC1 in the C- terminal and regulates the interaction between MUC1 and beta- catenin. The catalytic subunit phosphorylates 14-3-3 proteins (YWHAB, YWHAZ and YWHAH) in a sphingosine-dependent fashion (By similarity). Phosphorylates ELAVL1 in response to angiotensin-2 treatment (PubMed:18285462). {ECO:0000250, ECO:0000269|PubMed:11748588, ECO:0000269|PubMed:11877440, ECO:0000269|PubMed:15774464, ECO:0000269|PubMed:16940418, ECO:0000269|PubMed:18285462, ECO:0000269|PubMed:19587372, ECO:0000269|PubMed:19801500}.;
Disease
DISEASE: Autoimmune lymphoproliferative syndrome 3 (ALPS3) [MIM:615559]: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low. CVID9 patients have B-cell deficiency and severe autoimmunity. {ECO:0000269|PubMed:23319571}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.641

Intolerance Scores

LoFtool
0.201
RVIS EVS
-1.04
RVIS percentile EVS
7.77

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.966

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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