{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:36:27Z","timestamp":1774312587524,"version":"3.50.1"},"reference-count":16,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,12,26]],"date-time":"2024-12-26T00:00:00Z","timestamp":1735171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: The advent of next-generation sequencing (NGS) has revolutionized the analysis of genetic data, enabling rapid identification of pathogenic variants in patients with inborn errors of immunity (IEI). Sometimes, the use of NGS-based technologies is associated with challenges in the evaluation of the clinical significance of novel genetic variants. Methods: In silico prediction tools, such as SpliceAI neural network, are often used as a first-tier approach for the primary examination of genetic variants of uncertain clinical significance. Such tools allow us to parse through genetic data and emphasize potential splice-altering variants. Further variant assessment requires precise RNA assessment by agarose gel electrophoresis and\/or cDNA Sanger sequencing. Results: We found two novel heterozygous variants in the coding region of the LYST gene (c.10104G&gt;T, c.10894A&gt;G) in an individual with a typical clinical presentation of Chediak\u2013Higashi syndrome (CHS). The SpliceAI neural network predicted both variants as probably splice-altering. cDNA assessment by agarose gel electrophoresis revealed the presence of abnormally shortened splicing products in each variant\u2019s case, and cDNA Sanger sequencing demonstrated that c.10104G&gt;T and c.10894A&gt;G substitutions resulted in a shortening of the 44 and 49 exons by 41 and 47 bp, respectively. Both mutations probably lead to a frameshift and the formation of a premature termination codon. This, in turn, may disrupt the structure and\/or function of the LYST protein. Conclusions: We identified two novel variants in the LYST gene, predicted to be deleterious by the SpliceAI neural network. Agarose gel cDNA electrophoresis and cDNA Sanger sequencing allowed us to verify inappropriate splicing patterns and establish these variants as disease-causing.<\/jats:p>","DOI":"10.3390\/genes16010018","type":"journal-article","created":{"date-parts":[[2024,12,26]],"date-time":"2024-12-26T19:33:07Z","timestamp":1735241587000},"page":"18","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Novel LYST Variants Lead to Aberrant Splicing in a Patient with Chediak\u2013Higashi Syndrome"],"prefix":"10.3390","volume":"16","author":[{"given":"Maxim","family":"Aleksenko","sequence":"first","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Vlasova","sequence":"additional","affiliation":[{"name":"Regional Children\u2019s Clinical Hospital, 620102 Yekaterinburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amina","family":"Kieva","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9179-8430","authenticated-orcid":false,"given":"Ruslan","family":"Abasov","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulia","family":"Rodina","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Maschan","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Shcherbina","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Raykina","sequence":"additional","affiliation":[{"name":"Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1093\/hmg\/6.7.1091","article-title":"Identification of Mutations in Two Major MRNA Isoforms of the Chediak-Higashi Syndrome Gene in Human and Mouse","volume":"6","author":"Barbosa","year":"1997","journal-title":"Hum. 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