Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome

Abstract

Lynch syndrome is the most common familial cancer condition that mainly predisposes to tumors of the colon and endometrium. Cancer susceptibility is caused by the autosomal dominant inheritance of a loss-of-function mutation or epimutation in one of the DNA mismatch repair (MMR) genes. Cancer risk assessment is often possible with nonsynonymous coding region mutations, but in many cases patients present with DNA sequence changes within noncoding regions, including the promoters, of MMR genes. The pathogenic role of promoter variants, and hence clinical significance, is unclear and this hinders the clinical management of carriers. In this review, we provide an overview of the classification of MMR gene variants, outline the laboratory assays and online resources that can be used to assess the causality of promoter variants in Lynch syndrome, and highlight some of the practical challenges of demonstrating the pathogenicity of these variants. In conclusion, we propose a guide that could be integrated into the current InSiGHT classification scheme to help determine if a MMR gene promoter variant is pathogenic.

Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional MLH1 epimutation

“…In our attempt to classify the MLH1 promoter variant c.-63_-58delins18 we detected in two siblings with an epimutation, we would reach class 4—likely pathogenic with the ACMG criteria, but only class 3—uncertain significance as CEM is not included in the current InSiGHT classification rules and Liu et al 45 due to the lack of functional tests (table 2). This outstanding work addressing the problem of promoter variant classification and interpretation is regarding a CEM as secondary and heritable if a promoter variant is detected 45.…”

“…All variants are regarded as class 3 by default. Our classification of the variants applying the InSiGHT43 and ACMG44 guidelines and proposal by Liu et al  45 due to our results are given including the arguments and literature. ACMG arguments in detail were: PS3: abrogated mRNA expression, PM2: absence in controls, BS1: allele frequency higher than expected for disorder, BS2: observed in a health adult, BS3: in vivo functional studies (here: cDNA analyses) show no damaging effect on splicing, BP2: observed in trans or in cis with a pathogenic variant in any inheritance pattern, BP5: variant found in a case with an alternate molecular basis for disease (= control group).…”

“…So far, no specific rules for the classification of promoter variants have been described by the current InSiGHT or ACMG scheme, neither in presence nor in absence of CEM,43 44  but the necessity is already underscored in a pioneer publication 45. Only with criteria such as a high population frequency and/or homozygous state in healthy controls it is possible to reach a benign or likely benign classification, as it was the case for our MLH1 promoter variant c.-593G>C. The exception is one promoter variant in MSH2 c.-78_-77delGT, which was graded as class 4—likely pathogenic in LOVD 46.…”

“…Only with criteria such as a high population frequency and/or homozygous state in healthy controls it is possible to reach a benign or likely benign classification, as it was the case for our MLH1 promoter variant c.-593G>C. The exception is one promoter variant in MSH2 c.-78_-77delGT, which was graded as class 4—likely pathogenic in LOVD 46. For the classification of our 10 rare promoter variants identified, we apply the five-tiered InSiGHT scheme,43 ACMG guidelines44 and the guide proposed by Liu et al 45 (results compiled in table 2), and suggest amendments specific for promoter variants. The loss of TFBS and the nucleotide conservation in vertebrates (depicted in online supplementary figure 1B) are listed in table 2, but have no consented predictive value.…”

“…This outstanding work addressing the problem of promoter variant classification and interpretation is regarding a CEM as secondary and heritable if a promoter variant is detected 45. We nevertheless suggest to investigate the heredity of CEM for each case, also in absence of promoter variants.…”