Clinical correlation and molecular evaluation confirm that the MLH1 p.Arg182Gly (c.544A>G) mutation is pathogenic and causes Lynch syndrome

Abstract

Approximately 25 % of mismatch repair (MMR) variants are exonic nucleotide substitutions. Some result in the substitution of one amino acid for another in the protein sequence, so-called missense variants, while others are silent. The interpretation of the effect of missense and silent variants as deleterious or neutral is challenging. Pre-symptomatic testing for clinical use is not recommended for relatives of individuals with variants classified as 'of uncertain significance'. These relatives, including non-carriers, are considered at high-risk as long as the contribution of the variant to disease causation cannot be determined. This results in continuing anxiety, and the application of potentially unnecessary screening and prophylactic interventions. We encountered a large Irish Lynch syndrome kindred that carries the c.544A>G (p.Arg182Gly) alteration in the MLH1 gene and we undertook to study the variant. The clinical significance of the variant remains unresolved in the literature. Data are presented on cancer incidence within five kindreds with the same germline missense variant in the MLH1 MMR gene. Extensive testing of relevant family members in one kindred, a review of the literature, review of online MMR mutation databases and use of in silico phenotype prediction tools were undertaken to study the significance of this variant. Clinical, histological, immunohistochemical and molecular evidence from these families and other independent clinical and scientific evidence indicates that the MLH1 p.Arg182Gly (c.544A>G) change causes Lynch syndrome and supports reclassification of the variant as pathogenic.

A review of mismatch repair gene transcripts: issues for interpretation of mRNA splicing assays

“…For example, variant MLH1 c.113A>G p.Asn38Ser was reported to result in minor upregulation of the MLH1 ▾1q transcript -a splicing event inconsistent with bioinformatic predictions (46) but was not detected in allele-separation assays assessing the same variant (47). Further, as expected from bioinformatic predictions, MLH1 c.544A>G was shown to increase the production of MLH1 Δ6 transcripts (r.454_545del, p.Glu153Phefs*8) in two studies using RT-PCR methodology (48,49). This effect was not detected in two other studies using the less sensitive protein truncation test (50,51).…”

Lynch Syndrome: From Multidisciplinary Management to Precision Prevention

“…The molecular phenotype differs significantly from sporadic MLH1 epigenetic mutations, where biallelic methylation is widely diffused only in CRC cells [ 18 ]. Lately, several single-nucleotide polymorphisms in MLH1 (i.e., the c.-27C>A, c.85G>T, and c.544A>G variants), as well as in the MSH2 (c.2063T>G in exon 13), have been identified as being responsible for LS [ 19 , 20 , 21 ].…”

Contribution of Lynch syndrome to early onset malignancy in Ireland.

“…Other associated malignancies include endometrial, gastric, ovarian, small bowel, central nervous system and urological cancers [1]. LSassociated cancers develop as a result of pathogenic mutations in one of five genes necessary for mismatch repair (MMR): MLH1, MSH2, MSH6, PMS2 and EPCA M [6,7]. Impaired ability to correct erroneous strands of DNA results in microsatellite instability (MSI), a phenotypic hallmark of LS-associated CRC [6].…”

“…LSassociated cancers develop as a result of pathogenic mutations in one of five genes necessary for mismatch repair (MMR): MLH1, MSH2, MSH6, PMS2 and EPCA M [6,7]. Impaired ability to correct erroneous strands of DNA results in microsatellite instability (MSI), a phenotypic hallmark of LS-associated CRC [6]. In Ireland, patients with a new diagnosis of LS-associated cancer are assessed for LS risk using the revised Amsterdam and Bethesda criteria.…”