Immunohistochemistry and RNA-sequencing have been useful in evaluating the pathological significance of a non-consensus site intronic variant in suspected cases of Lynch syndrome.

Immunohistochemistry of mismatch repair proteins is a universal strategy for Lynch syndrome screening. In this case, Lynch syndrome was suspected, because MLH1 and PMS2 expression was negative by IHC. However, mismatch repair genetic analysis revealed a variant of unknown significance of c.454-13A > G in MLH1. Therefore, we performed reverse transcription-PCR using mRNA extracted from the patient's lymphocytes and detected a heterozygous gene allele indicating splicing abnormalities that complex splicing, with exon 5 followed by only the first codon (ACG) of exon 6 and leading to exon 7 of the MLH1. Two years later, this mutation was corrected to "likely pathogenic". For Lynch syndrome in which mismatch repair protein expression is undetectable by immunohistochemistry, reverse transcription-PCR may be useful to identify an intronic variant of unknown significance as the likely pathogenic variant. © The Japan Society of Clinical Oncology 2021.