1. MLH1 intronic variants mapping to + 5 position of splice donor sites lead to deleterious effects on RNA splicing.
- Author
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Piñero TA, Soukarieh O, Rolain M, Alvarez K, López-Köstner F, Torrezan GT, Carraro DM, De Oliveira Nascimento IL, Bomfim TF, Machado-Lopes TMB, Freitas JC, Toralles MB, Sandes KA, Rossi BM, Junior SA, Meira J, Dominguez-Valentin M, Møller P, Vaccaro CA, Martins A, and Pavicic WH
- Subjects
- Adult, Argentina, Brazil, Chile, Colorectal Neoplasms genetics, Colorectal Neoplasms, Hereditary Nonpolyposis metabolism, DNA Mismatch Repair, Exons, Female, Genetic Counseling, Humans, Male, Middle Aged, Mismatch Repair Endonuclease PMS2 deficiency, Mismatch Repair Endonuclease PMS2 genetics, Mismatch Repair Endonuclease PMS2 metabolism, MutL Protein Homolog 1 deficiency, MutL Protein Homolog 1 metabolism, Pedigree, Protein Isoforms, Colorectal Neoplasms, Hereditary Nonpolyposis genetics, Introns, MutL Protein Homolog 1 genetics, RNA Splice Sites, RNA Splicing
- Abstract
Germline pathogenic variants in the DNA mismatch repair genes (MMR): MLH1, MSH2, MSH6, and PMS2, are causative of Lynch syndrome (LS). However, many of the variants mapping outside the invariant splice site positions (IVS ± 1, IVS ± 2) are classified as variants of unknown significance (VUS). Three such variants (MLH1 c.588+5G>C, c.588+5G>T and c.677+5G>A) were identified in 8 unrelated LS families from Argentina, Brazil and Chile. Herein, we collected clinical information on these families and performed segregation analysis and RNA splicing studies to assess the implication of these VUS in LS etiology. Pedigrees showed a clear pattern of variant co-segregation with colorectal cancer and/or other LS-associated malignancies. Tumors presented deficient expression of MLH1-PMS2 proteins in 7/7 of the LS families, and MSI-high status in 3/3 cases. Moreover, RNA analyses revealed that c.588+5G>C and c.588+5G>T induce skipping of exon 7 whereas c.677+5G>A causes skipping of exon 8. In sum, we report that the combined clinical findings in the families and the molecular studies provided the evidences needed to demonstrate that the three MLH1 variants are causative of LS and to classify c.588+5G>C and c.677+5G>A as class 5 (pathogenic), and c.588+5G>T as class 4 (likely-pathogenic). Our findings underline the importance of performing clinical and family analyses, as well as RNA splicing assays in order to determine the clinical significance of intronic variants, and contribute to the genetic counseling and clinical management of patients and their relatives.
- Published
- 2020
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