PKN1
Chr 19protein kinase N1
Also known as: DBK, PAK-1, PAK1, PKN, PKN-ALPHA, PRK1, PRKCL1
PKN1 encodes a serine/threonine protein kinase that regulates the actin cytoskeleton and intermediate filaments by phosphorylating proteins including vimentin, neurofilament proteins, and tau, and also functions in transcriptional regulation. Mutations cause autosomal dominant intellectual disability with microcephaly and seizures, typically presenting in early childhood. The gene shows significant constraint against loss-of-function variants (LOEUF = 0.39), consistent with its role in neurodevelopmental disease.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
239 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 13 | 0 | 13 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 170 | 3 | 0 | 173 |
Likely Benign | 0 | 4 | 2 | 3 | 9 |
Benign | 0 | 1 | 1 | 2 | 4 |
| Total | 0 | 175 | 20 | 5 | 200 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PKN1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools