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ORIGINAL RESEARCH article
Front. Immunol.
Sec. Primary Immunodeficiencies
Volume 15 - 2024 |
doi: 10.3389/fimmu.2024.1499415
This article is part of the Research Topic Molecular Diagnostics of Patients with Suspected Monogenic Immune Diseases View all articles
Molecular assessment of splicing variants in a cohort of inborn errors of immunity patients: methodological approach and interpretation remarks
Provisionally accepted
Laura Miguel Berenguel
1*
Carla Gianelli
1,2,3*
Elisabet Matas Pérez
1*
Teresa Del Rosal Rabes
4
Ana Méndez Echevarría
4*
Ángel Robles Marhuenda
5*
Marta Feito Rodríguez
6*
Maria Teresa Caballero Molina
7*
Lorena Magallares García
8*
Brenda Sánchez Garrido
1*
Samantha Hita Díaz
1*
LUIS M ALLENDE
10,9
Pilar Nozal Aranda
1,3
Carmen Cámara Hijón
1,2,7*
Eduardo Lopez-Granados
1,2,3
Rebeca Rodríguez-Pena
1,2,3
María Bravo García-Morato
1,2,3- 1 Department of Immunology, La Paz University Hospital, Madrid, Spain
- 2 Center of Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
- 3 La Paz Institute of Biomedical Research, Madrid, Spain
- 4 Department of Pediatric Infectious Disease, La Paz University Hospital, Madrid, Spain
- 5 Department of Internal Medicine, La Paz University Hospital, Madrid, Spain
- 6 Department of Dermatology, La Paz University Hospital, Madrid, Spain
- 7 Department of Allergy, La Paz University Hospital, Madrid, Spain
- 8 Department of Pediatric Gastroenterology, La Paz University Hospital, Madrid, Spain
- 9 Department of Immunology, 12 de Octubre University Hospital, Madrid, Spain
- 10 Research Institute Hospital 12 de Octubre, Madrid, Catalonia, Spain
Background. Splicing is the molecular mechanism to produce mature messenger RNA (mRNA) before its translation into protein. It is estimated that 50% of disease-causing mutations disrupt splicing, mostly of them affecting canonical positions. However, variants occurring in coding regions or deepintronic variants can also affect splicing. In these cases, interpretation of the results may be challenging and molecular validation is required.Methods. The study includes 23 patients with splicing variants out of a cohort of 187 patients diagnosed with inborn errors of immunity (IEI). Clinical features and immunophenotypes are shown. Reverse transcription-polymerase chain reaction (RT-PCR) is the molecular assay employed for pathogenicity validation.Results. We detected 23 patients of 20 pedigrees with splicing variants in IEI genes, which constitutes the 12.3% of our cohort. In total, 21 splicing variants were analyzed, 10 of which had previously been reported in the literature and 11 novel ones. Among the 23 patients, 16 showed variants at canonical splice sites. Molecular validation was required only in the cases of genes of uncertain significance (GUS), high homology pseudogenes or incompatible clinical phenotype. Seven patients showed variants outside canonical positions. All of them needed molecular validation, with the exception of two patients, whose variants had previously been well characterize in the medical literature.This study shows the proportion of splicing variants in a cohort of IEI patients, providing their clinical phenotypic characteristics and the methodology used to validate the splicing defects. Based on the results, an algorithm is proposed to clarify when a splicing variant should be validated by complementary methodology and when, by contrast, it can be directly considered disease causing.
Keywords: Splicing mutations, Reverse-transcription PCR (RT-PCR), inborn errors of immunity, Genetic validation algorithm, Canonical sites of splicing, Deep-intronic variants
Received: 20 Sep 2024; Accepted: 27 Dec 2024.
Copyright: © 2024 Berenguel, Gianelli, Matas Pérez, Del Rosal Rabes, Méndez Echevarría, Robles Marhuenda, Feito Rodríguez, Caballero Molina, Magallares García, Sánchez Garrido, Díaz, ALLENDE, Nozal Aranda, Cámara Hijón, Lopez-Granados, Rodríguez-Pena and Bravo García-Morato. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Laura Miguel Berenguel, Department of Immunology, La Paz University Hospital, Madrid, Spain
Carla Gianelli, Department of Immunology, La Paz University Hospital, Madrid, Spain
Elisabet Matas Pérez, Department of Immunology, La Paz University Hospital, Madrid, Spain
Ana Méndez Echevarría, Department of Pediatric Infectious Disease, La Paz University Hospital, Madrid, Spain
Ángel Robles Marhuenda, Department of Internal Medicine, La Paz University Hospital, Madrid, Spain
Marta Feito Rodríguez, Department of Dermatology, La Paz University Hospital, Madrid, Spain
Maria Teresa Caballero Molina, Department of Allergy, La Paz University Hospital, Madrid, Spain
Lorena Magallares García, Department of Pediatric Gastroenterology, La Paz University Hospital, Madrid, Spain
Brenda Sánchez Garrido, Department of Immunology, La Paz University Hospital, Madrid, Spain
Samantha Hita Díaz, Department of Immunology, La Paz University Hospital, Madrid, Spain
Carmen Cámara Hijón, Department of Immunology, La Paz University Hospital, Madrid, Spain
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