Identification of a pathogenic mutation in ATP2A1 via in silico analysis of exome data for cryptic aberrant splice sites. Issue 3 (28th January 2019)

• Record Type: Journal Article
• Authors: Bruels, Christine C.; Li, Chengcheng; Mendoza, Tonatiuh; Khan, Jamillah; Reddy, Hemakumar M.; Estrella, Elicia A.; Ghosh, Partha S.; Darras, Basil T.; Lidov, Hart G. W.; Pacak, Christina A.; Kunkel, Louis M.; Modave, François; Draper, Isabelle; Kang, Peter B.
• Is Part Of: Molecular genetics & genomic medicine. Volume 7:Issue 3(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-01-28
• Subjects: Aberrant RNA splicing -- ATP2A1 -- Brody myopathy -- cryptic variants; Medical genetics -- Periodicals; Genomics -- Periodicals; 616.042
• DOI: 10.1002/mgg3.552
• Languages: English
• ISSNs: 2324-9269

Abstract

Abstract: 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. Abstract : We developed a novel bioinformatics pipeline to identify potentially aberrant novel essential splice site (PANESS) mutations in next‐generation sequencing data, and used it successfully to identify a pathogenic splice site mutation in ATP2A1 for a family with a myotonic phenotype. The pathogenic nature of the mutation was confirmed via RT‐PCR, western blot, and immunohistochemistry, along with functional studies in Drosophila.