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Foo CTY, To YH, Irwanto A, Ng AYJ, Yan B, Chew STH, Liu J, Ti LK. Variant landscape of the RYR1 gene based on whole genome sequencing of the Singaporean population. Sci Rep 2022; 12:5429. [PMID: 35361824 PMCID: PMC8971428 DOI: 10.1038/s41598-022-09310-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
The RYR1 gene codes for a ryanodine receptor which is a calcium release channel in the skeletal muscle sarcoplasmic reticulum. It is associated with Malignant Hyperthermia (MH) and congenital myopathies including Central Core Disease (CCD), Multiminicore Disease (MMD) and Congenital Fibre-Type Disproportion (CFTD). There is currently little information on the epidemiology of RYR1 variants in Asians. Our study aims to describe the RYR1 variant landscape in a Singapore cohort unselected for RYR1-associated conditions. Data was retrieved from the SG10K pilot project, where whole genome sequencing was performed on volunteers unselected and undetermined for RYR1-associated conditions. Variants were classified based on pathogenicity using databases ClinVar and InterVar. Allele frequencies of pathogenic variants were compared between Chinese, Indians and Malays. Using databases ExAC, GnomAD and GenomeAsia 100k study, we further compared local allele frequencies to those in Europe, America and Asia. Data was analysed using R Commander. Significant P value was set at p < 0.05. Majority of the RYR1 variants were missense mutations. We identified four pathogenic and four likely pathogenic RYR1 variants. All were related to the aforementioned RYR1-associated conditions. There were 6 carriers of RYR1 pathogenic variants amongst 4810 individuals, corresponding to an allele frequency of 0.06%. The prevalence of pathogenic variants was the highest amongst Indians (4 in 1127 individuals) (p = 0.030). Majority of pathogenic and likely pathogenic mutations were missense and located in mutational hotspots. These variants also occurred at higher frequencies in Asians than globally. This study describes the variant landscape of the RYR1 gene in Singapore. This knowledge will facilitate genetic screening for RYR1-related conditions.
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Affiliation(s)
- Claribel Tian Yu Foo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yi Hui To
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Astrid Irwanto
- Nalagenetics Pte. Ltd, Singapore, Singapore.,Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Alvin Yu-Jin Ng
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Benedict Yan
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | | | - Jianjun Liu
- Agency for Science, Technology and Research, Genome Institute of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lian Kah Ti
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Anaesthesia, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
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