Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity

Area of Science:

• Genetics and Genomics
• Molecular Biology
• Oncology

Background:

• Lynch syndrome is an inherited disorder associated with an increased risk of various cancers, often caused by mutations in DNA mismatch repair (MMR) genes.
• Variants of Uncertain Significance (VUS) in MMR genes pose challenges in clinical interpretation and genetic counseling.
• The MLH1 gene is a key component of the MMR system, and its dysfunction is a common cause of Lynch syndrome.

Purpose of the Study:

• To investigate the clinical significance of a previously unreported MLH1 variant (c.1664T>C, p.Leu555Pro) identified in an Irish kindred.
• To determine if this VUS is pathogenic and causative of Lynch syndrome in the affected family members.

Main Methods:

• Genetic testing to identify the MLH1 variant.
• Immunohistochemical (IHC) analysis and microsatellite instability (MSI) studies to assess protein expression and mutator phenotype.
• In silico prediction tools and an in vitro MMR activity assay to evaluate the variant's functional impact.

Main Results:

• The MLH1 c.1664T>C (p.Leu555Pro) variant co-segregated with Lynch syndrome-associated malignancies in three affected individuals across two generations.
• Consistent loss of MLH1 and PMS2 protein expression was observed via IHC in affected individuals.
• In silico and in vitro analyses indicated a deleterious effect of the variant on MLH1 protein function and abrogation of MMR activity.

Conclusions:

• The MLH1 c.1664T>C (p.Leu555Pro) variant is likely pathogenic and the causative agent of Lynch syndrome in this family.
• This study highlights the importance of integrated clinical, histological, immunohistochemical, and molecular data for VUS interpretation.
• The findings contribute to a better understanding of MLH1 variants and their role in Lynch syndrome.