Misclassification of a frequent loss of function variant fromPMS2CLpseudogene as aPMS2variant in Brazilian patients

Abstract

AbstractPMS2, a Lynch Syndrome gene, presents challenges in genetic testing due to the existence of multiple pseudogenes. This study aims to describe a series of cases harboring a rare LoF variant in thePMS2CLpseudogene that has been incorrectly assigned toPMS2with different nomenclatures. We reviewed data from 647 Brazilian patients who underwent multigene genetic testing at a single center to identify those harboring thePMS2V1:c.2186_2187delTC or V2:c.2182_2184delACTinsG variants, allegedly located atPMS2exon 13. Gene-specific PCR and transcript sequencing was performed. Among the 647 individuals, 1.8% (12) carried the investigated variants, with variant allele frequencies ranging from 15 to 34%. By visually inspecting the alignments, we confirmed that both V1 and V2 represented the same variant and through gene-specific PCR andPMS2transcript analysis, we demonstrated that V1/V2 is actually located in thePMS2CLpseudogene. Genomic databases (ExAC and gnomAD) report an incidence of 2.5% - 5.3% of this variant in the African population. Currently, V1 is classified as “uncertain significance” and V2 as “conflicting” in ClinVar, with several laboratories classifying them as “pathogenic”. We identified a frequent AfricanPMS2CLLoF variant in the Brazilian population that is misclassified as aPMS2variant. It is likely that V1/V2 have been erroneously assigned toPMS2in several manuscripts and by clinical laboratories, underscoring a disparity-induced matter. Considering the limitations of short-read NGS differentiating between certain regions ofPMS2andPMS2CL, using complementary methodologies is imperative to provide an accurate diagnosis.