Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients
Limb–girdle muscular dystrophy type R1 (LGMDR1) is caused by mutations in CAPN3 and is the most common type of recessive LGMD. Even with the use of whole-exome sequencing (WES), only one mutant allele of CAPN3 is found in a significant number of LGMDR patients. This points to a role of non-coding, i...
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnins.2021.692482/full |
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| author | Anna Macias Jakub Piotr Fichna Malgorzata Topolewska Maria J. Rȩdowicz Anna M. Kaminska Anna Kostera-Pruszczyk |
| author_facet | Anna Macias Jakub Piotr Fichna Malgorzata Topolewska Maria J. Rȩdowicz Anna M. Kaminska Anna Kostera-Pruszczyk |
| author_sort | Anna Macias |
| collection | DOAJ |
| description | Limb–girdle muscular dystrophy type R1 (LGMDR1) is caused by mutations in CAPN3 and is the most common type of recessive LGMD. Even with the use of whole-exome sequencing (WES), only one mutant allele of CAPN3 is found in a significant number of LGMDR patients. This points to a role of non-coding, intronic or regulatory, sequence variants in the disease pathogenesis. Targeted sequencing of the whole CAPN3 gene including not only intronic, 3′ and 5′ UTRs but also potential regulatory regions was performed in 27 patients suspected with LGMDR1. This group included 13 patients with only one mutated CAPN3 allele detected previously with exome sequencing. A second rare variant in the non-coding part of CAPN3 was found in 11 of 13 patients with previously identified single mutation. Intronic mutations were found in 10 cases, with c.1746-20C>G variant present in seven patients. In addition, a large deletion of exons 2–8 was found in one patient. In the patients with no causative mutation previously found, we detected rare CAPN3 variants in 5 out of 10 patients and in two of them in a compound heterozygous state. Rare variants within putative regulatory sequences distant from the CAPN3 gene were found in 15 patients, although in 11 of these cases, other variants are deemed causative. The results indicate that intronic mutations are common in Polish LGMDR patients, and testing for non-coding mutations in CAPN3 should be performed in apparently single heterozygous patients. |
| first_indexed | 2024-12-22T13:49:24Z |
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| id | doaj.art-337ad31ac4cd4a9d8166ab21a5852521 |
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| issn | 1662-453X |
| language | English |
| last_indexed | 2024-12-22T13:49:24Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-337ad31ac4cd4a9d8166ab21a58525212022-12-21T18:23:43ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2021-10-011510.3389/fnins.2021.692482692482Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy PatientsAnna Macias0Jakub Piotr Fichna1Malgorzata Topolewska2Maria J. Rȩdowicz3Anna M. Kaminska4Anna Kostera-Pruszczyk5Department of Neurology, Medical University of Warsaw, Warsaw, PolandLaboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, PolandLaboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandLaboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandDepartment of Neurology, Medical University of Warsaw, Warsaw, PolandDepartment of Neurology, Medical University of Warsaw, Warsaw, PolandLimb–girdle muscular dystrophy type R1 (LGMDR1) is caused by mutations in CAPN3 and is the most common type of recessive LGMD. Even with the use of whole-exome sequencing (WES), only one mutant allele of CAPN3 is found in a significant number of LGMDR patients. This points to a role of non-coding, intronic or regulatory, sequence variants in the disease pathogenesis. Targeted sequencing of the whole CAPN3 gene including not only intronic, 3′ and 5′ UTRs but also potential regulatory regions was performed in 27 patients suspected with LGMDR1. This group included 13 patients with only one mutated CAPN3 allele detected previously with exome sequencing. A second rare variant in the non-coding part of CAPN3 was found in 11 of 13 patients with previously identified single mutation. Intronic mutations were found in 10 cases, with c.1746-20C>G variant present in seven patients. In addition, a large deletion of exons 2–8 was found in one patient. In the patients with no causative mutation previously found, we detected rare CAPN3 variants in 5 out of 10 patients and in two of them in a compound heterozygous state. Rare variants within putative regulatory sequences distant from the CAPN3 gene were found in 15 patients, although in 11 of these cases, other variants are deemed causative. The results indicate that intronic mutations are common in Polish LGMDR patients, and testing for non-coding mutations in CAPN3 should be performed in apparently single heterozygous patients.https://www.frontiersin.org/articles/10.3389/fnins.2021.692482/fullLGMDCAPN3non-codingenhancersilencercalpain-3 |
| spellingShingle | Anna Macias Jakub Piotr Fichna Malgorzata Topolewska Maria J. Rȩdowicz Anna M. Kaminska Anna Kostera-Pruszczyk Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients Frontiers in Neuroscience LGMD CAPN3 non-coding enhancer silencer calpain-3 |
| title | Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients |
| title_full | Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients |
| title_fullStr | Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients |
| title_full_unstemmed | Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients |
| title_short | Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb–Girdle Muscular Dystrophy Patients |
| title_sort | targeted next generation sequencing reveals mutations in non coding regions and potential regulatory sequences of calpain 3 gene in polish limb girdle muscular dystrophy patients |
| topic | LGMD CAPN3 non-coding enhancer silencer calpain-3 |
| url | https://www.frontiersin.org/articles/10.3389/fnins.2021.692482/full |
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