Key result
The PANESS bioinformatics pipeline identified a homozygous ATP2A1 variant causing aberrant splicing in a family with a myotonic disorder, expanding the phenotypic spectrum beyond Brody myopathy.
Why the study?
Pathogenic mutations causing aberrant splicing are often difficult to detect because standard NGS analysis focuses on canonical splice sites.
A novel bioinformatics pipeline successfully identified a cryptic ATP2A1 splice site mutation in a family with myotonia, expanding the phenotypic spectrum beyond classic Brody myopathy.
Answers are grounded in this paper and cite their sources.
May support ATP2A1 testing in atypical myotonia; leaves open pipeline generalizability beyond this family.
Background Pathogenic mutations causing aberrant splicing are often difficult to detect. Standard variant analysis of next‐generation sequence (NGS) data focuses on canonical splice sites. Noncanonical splice sites are more difficult to ascertain. Methods We developed a bioinformatics pipeline that screens existing NGS data for potentially aberrant novel essential splice sites (PANESS) and performed a pilot study on a family with a myotonic disorder. Further analyses were performed via qRT‐PCR, immunoblotting, and immunohistochemistry. RNAi knockdown studies were performed in Drosophila to model the gene deficiency. Results The PANESS pipeline identified a homozygous ATP2A1 variant (NC_000016.9:g.28905928G>A; NM_004320.4:c.1287G>A:p.(Glu429=)) that was predicted to cause the omission of exon 11. Aberrant splicing of ATP2A1 was confirmed via qRT‐PCR, and abnormal expression of the protein product sarcoplasmic/endoplasmic reticulum Ca ++ ATPase 1 (SERCA1) was demonstrated in quadriceps femoris tissue from the proband. Ubiquitous knockdown of SERCA led to lethality in Drosophila, as did knockdown targeting differentiating or fusing myoblasts. Conclusions This study confirms the potential of novel in silico algorithms to detect cryptic mutations in existing NGS data; expands the phenotypic spectrum of ATP2A1 mutations beyond classic Brody myopathy; and suggests that genetic testing of ATP2A1 should be considered in patients with clinical myotonia.
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Bruels et al. (2019) studied Myotonic disorder. PANESS bioinformatics pipeline was evaluated on Identification of pathogenic mutations causing aberrant splicing. The PANESS bioinformatics pipeline identified a homozygous ATP2A1 variant causing aberrant splicing in a family with a myotonic disorder, expanding the phenotypic spectrum beyond Brody myopathy.
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