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Updated: Sep 5, 2025

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
Identification of the pathogenic effects of missense variants causing PRKAG2 cardiomyopathy
Evrim Komurcu-Bayrak1, Muhammed Abdulvahid Kalkan2, Neslihan Coban3
1Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, Istanbul, Turkiye; Istanbul University, Istanbul Faculty of Medicine, Departments of Medical Genetics, Istanbul, Turkiye.
Insights
Pathogenic variants in the PRKAG2 gene reduce adenosine monophosphate-activated protein kinase (AMPK) activity, leading to PRKAG2 cardiomyopathy. These mutations, including E506K, E506Q, and R531G, cause cardiac disease by disrupting AMPK function and promoting glycogen deposits.
Area of Science:
- Cardiovascular Genetics
- Molecular Cardiology
- Biochemistry
Background:
- Pathogenic missense variants in the PRKAG2 gene, encoding the gamma 2 regulatory subunit of adenosine monophosphate-activated protein kinase (AMPK), are linked to PRKAG2 cardiomyopathy, a severe progressive cardiac disease.
- A previously identified E506K variant in PRKAG2 was associated with this condition, prompting further investigation into related variants.
Purpose of the Study:
- To functionally characterize three PRKAG2 missense variants: E506K, E506Q, and R531G.
- To determine the impact of these variants on AMPK activity and cellular processes.
Main Methods:
- In vitro mutagenesis experiments were performed using HEK293 cells transfected with wild-type and mutant PRKAG2 transcripts.
- Quantitative RT-PCR, immunofluorescence staining, and enzyme-linked immunosorbent assay were employed to analyze PRKAG2 expression and AMPK activity.
- Long-term clinical monitoring of a proband with PRKAG2 cardiomyopathy was conducted.
Main Results:
- Overexpression of PRKAG2 variants was observed post-transfection, with expression levels returning to wild-type levels within three weeks, except for the E506K variant.
- All three variants (E506K, E506Q, R531G) significantly reduced AMPK activity.
- Reduced AMPK activity led to the formation of cytoplasmic glycogen deposits in affected cells.
Conclusions:
- Missense variants in PRKAG2, specifically at the CBS4 domain involved in ATP/AMP-binding, impair AMPK activity.
- Understanding how these PRKAG2 variants affect AMPK is crucial for developing improved therapeutic strategies for patients with metabolic cardiomyopathy.
Background:
Pathogenic missense variants in PRKAG2, the gene for the gamma 2 regulatory subunit of adenosine monophosphate-activated protein kinase (AMPK), cause severe progressive cardiac disease and sudden cardiac death, named PRKAG2 cardiomyopathy. In our previous study, we reported a E506K variant in the PRKAG2 gene that was associated with this disease. This study aimed to functionally characterize the three missense variants (E506K, E506Q, and R531G) of PRKAG2 and determine the possible effects on AMPK activity.
Methods:
The proband was clinically monitored for eight years. To investigate the functional effects of three missense variants of PRKAG2, in vitro mutagenesis experiments using HEK293 cells with wild and mutant transcripts and proteins were comparatively analyzed using quantitative RT-PCR, immunofluorescence staining, and enzyme-linked immunosorbent assay.
Results:
In the long-term follow-up, the proband was deceased due to progressive heart failure. In the in vitro experimental studies, PRKAG2 was overexpressed after 48 h of transfection in three mutated cells, after which the expression levels of PRKAG2 were regressed to the level of wild-type cells in 3-weeks stably transformed cells, except for the cells with E506K variant. E506K, E506Q, and R531G variants had caused a reduction in the AMPK activity and resulted in the formation of cytoplasmic glycogen deposits.
Conclusion:
Three missense variants that alter AMPK activity affect a residue in the CBS4 domain associated with ATP/AMP-binding. Detailed information on the influence of PRKAG2 pathogenic variants on AMPK activity would be helpful to improve the treatment and management of patients with metabolic cardiomyopathy.
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