Article Text
Abstract
Background SINE-VNTR-Alu (SVA) retrotransposons move from one genomic location to another in a ‘copy-and-paste’ manner. They continue to move actively and cause monogenic diseases through various mechanisms. Currently, disease-causing SVA retrotransposons are classified into human-specific young SVA_E or SVA_F subfamilies. In this study, we identified an evolutionarily old SVA_D retrotransposon as a novel cause of occipital horn syndrome (OHS). OHS is an X-linked, copper metabolism disorder caused by dysfunction of the copper transporter, ATP7A.
Methods We investigated a 16-year-old boy with OHS whose pathogenic variant could not be detected via routine molecular genetic analyses.
Results A 2.8 kb insertion was detected deep within the intron of the patient’s ATP7A gene. This insertion caused aberrant mRNA splicing activated by a new donor splice site located within it. Long-read circular consensus sequencing enabled us to accurately read the entire insertion sequence, which contained highly repetitive and GC-rich segments. Consequently, the insertion was identified as an SVA_D retrotransposon. Antisense oligonucleotides (AOs) targeting the new splice site restored the expression of normal transcripts and functional ATP7A proteins. AO treatment alleviated excessive accumulation of copper in patient fibroblasts in a dose-dependent manner. Pedigree analysis revealed that the retrotransposon had moved into the OHS-causing position two generations ago.
Conclusion This is the first report of a human monogenic disease caused by the SVA_D retrotransposon. The fact that the evolutionarily old SVA_D is still actively transposed, leading to increased copy numbers may make a notable impact on rare genetic disease research.
- Neurology
- Genetic Diseases, X-Linked
- Pediatrics
- Sequence Analysis
Data availability statement
Data are available upon reasonable request.
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Data availability statement
Data are available upon reasonable request.
Footnotes
Contributors NY and TY designed the study and wrote the manuscript draft. NY, PFC, KKK, AL-F, TM, YK, KK, KM and TH collected and analysed the data. NY, TM, KKK, AY, MA, MH, TK, RK, JT and TY interpreted the results. All authors have reviewed and revised the manuscript. All authors have approved the final version of the manuscript for publication. TY is responsible for the overall content as guarantor.
Funding This study was supported by a JSPS Grant-in-Aid for Research Activity Start up awarded to NY. (grant number: 23K19588).
Competing interests None declared.
Provenance and peer review Not commissioned; externally peer reviewed.
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