1. All Reported Non-Canonical Splice Site Variants in GLA Cause Aberrant Splicing
- Author
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Eri Okada, Tomoko Horinouchi, Tomohiko Yamamura, Yuya Aoto, Ryota Suzuki, Yuta Ichikawa, Yu Tanaka, Chika Masuda, Hideaki Kitakado, Atsushi Kondo, Nana Sakakibara, Shinya Ishiko, China Nagano, Shingo Ishimori, Joichi Usui, Kunihiro Yamagata, Masafumi Matsuo, and Kandai Nozu
- Subjects
History ,Polymers and Plastics ,Nephrology ,Physiology ,Physiology (medical) ,Business and International Management ,Industrial and Manufacturing Engineering - Abstract
Background Fabry disease is an X-linked lysosomal storage disorder caused by insufficient α-galactosidase A (GLA) activity resulting from variants in the GLA gene, which leads to glycosphingolipid accumulation and life-threatening, multi-organ complications. Approximately 50 variants have been reported that cause splicing abnormalities in GLA. Most were found within canonical splice sites, which are highly conserved GT and AG splice acceptor and donor dinucleotides, whereas one-third were located outside canonical splice sites, making it difficult to interpret their pathogenicity. In this study, we aimed to investigate the genetic pathogenicity of variants located in non-canonical splice sites within the GLA gene. Methods 13 variants, including four deep intronic variants, were selected from the Human Gene Variant Database Professional. We performed an in vitro splicing assay to identify splicing abnormalities in the variants. Results All candidate non-canonical splice site variants in GLA caused aberrant splicing. Additionally, all but one variant was protein-truncating. The four deep intronic variants generated abnormal transcripts, including a cryptic exon, as well as normal transcripts, with the proportion of each differing in a cell-specific manner. Conclusions Validation of splicing effects using an in vitro splicing assay is useful for confirming pathogenicity and determining associations with clinical phenotypes.
- Published
- 2022