PRKD1

Chr 14AD

protein kinase D1

Also known as: CHDED, PKC-MU, PKCM, PKD, PRKCM

NCBI Gene: 5587ENSG00000184304UniProt: Q15139

The protein encoded by this gene is a serine/threonine protein kinase involved in many cellular processes, including Golgi body membrane integrity and transport, cell migration and differentiation, MAPK8/JNK1 and Ras pathway signaling, MAPK1/3 (ERK1/2) pathway signaling, cell survival, and regulation of cell shape and adhesion. [provided by RefSeq, Jan 2017]

Primary Disease Associations & Inheritance

Congenital heart defects and ectodermal dysplasiaMIM #617364
AD
0
Active trials
0
Pathogenic / LP
0
ClinVar variants
21
Pubs (1 yr)
1.4
Missense Z
0.62
LOEUF
Clinical Summary— PRKD1
🧬
Gene-Disease Validity (ClinGen)
congenital heart disease · ARLimited

Limited evidence — not for standalone diagnostic reporting

2 total gene-disease associations curated

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.62LOEUF
pLI 0.000
Z-score 3.52
OE 0.42 (0.29–0.62)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.43Z-score
OE missense 0.82 (0.76–0.89)
411 obs / 501.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.42 (0.29–0.62)
0≤0.351.4
Missense OE0.82 (0.76–0.89)
0≤0.61.4
Synonymous OE1.05
0≤1.21.6
LoF obs/exp: 18 / 42.9Missense obs/exp: 411 / 501.2Syn Z: -0.52
GOF
DN
0.5477th %ile
GOF
0.6346th %ile
LOF
0.50top 25%

The highest-scoring mechanism for this gene is gain-of-function.

GOF1 literature citation

Literature Evidence

GOFFunctional analysis using in vitro kinase assays with recombinant proteins showed that the mutation c.1808G>A, p.(Arg603His) represents a gain-of-function mutation encoding an enzyme with a constitutive, lipid-independent catalytic activity.PMID:32817298

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

PRKD1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

PRKD1-related syndromic congenital heart defects

definitive
ADUndeterminedAltered Gene Product Structure
Dev. Disorders
G2P ↗
missense variantinframe deletioninframe insertion

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Generation of human induced pluripotent stem cell lines carrying a heterozygous and homozygous PRKD1 c.1774G > A genetic variant causing syndromic congenital defects.
Witthoff F et al.·Stem Cell Res
2026
Cribriform Adenocarcinoma of the Nasal Cavity Harboring a Novel NAP1L1::PRKD1 Fusion, Expanding the Molecular Landscape of Minor Salivary Gland Tumors.
Duarte EM et al.·Case Rep Pathol
2025Open Access
Tetralogy of Fallot and craniosynostosis - differential manifestation in a familial case of CHDED syndrome caused by novel pathogenic PRKD1 variant.
Oza PS et al.·J Hum Genet
2026
Hedgehog Components Are Present in Polymorphous Adenocarcinoma of the Salivary Gland Regardless of PRKD1 Mutation and Tissue Invasion.
De Santana DA et al.·J Oral Pathol Med
2025Open Access
Protein Kinase D1 (PRKD1) as a Diagnostic, Prognostic, and Immunomodulatory Biomarker in Human Cancers.
Abdelrazig R et al.·Cureus
2025Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients