A Lynch syndrome patient with multiple cancers who was found to have a novel pathogenic variant generating aberrant splicing of MLH1

Abstract Lynch syndrome is an autosomal dominant cancer predisposition syndrome caused by inactivating germline variants in DNA mismatch repair genes. Here, we describe a woman who developed colorectal, gastric, and endometrial cancers and was found to have a rare missense variant, MLH1:c.545G > T/p.Arg182Met. The variant, which was located at the last nucleotide of MLH1exon 6, was initially reported by a clinical testing laboratory as being a variant of uncertain significance. In silico analyses predicted that it would cause splicing aberration, and reverse-transcription polymerase chain reaction analysis of total RNA from the patient’s peripheral blood cells identified an aberrant MLH1 transcript that skipped the entire exon 6 and caused generation of a premature stop codon (p.Glu153Phefs*8). In accordance with the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines, we reclassified the variant as likely pathogenic. Further additional analysis enabled carrier diagnosis in the patient’s relatives. Genetics summary Disorder: Lynch syndrome Ethnicity of the patient: Japanese Gene: MLH1 (19 exons) GenBank accession number: NM_000249.4 Chromosomal assignment: 3p21.3 Type of DNA variant: a germline splice aberration variant Mutation: c.545G > T in exon 6 of MLH1 Methods of mutation detection: PCR-sequencing, RT-PCR