title: Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity.
abstract: Genetic testing of an Irish kindred identified an exonic nucleotide substitution c.1664T>C (p.Leu555Pro) in the MLH1 mismatch repair (MMR) gene. This previously unreported variant is classified as a "variant of uncertain significance" (VUS). Immunohistochemical (IHC) analysis and microsatellite instability (MSI) studies, genetic testing, a literature and online MMR mutation database review, in silico phenotype prediction tools, and an in vitro MMR activity assay were used to study the clinical significance of this variant. The MLH1 c.1664T>C (p.Leu555Pro) VUS co-segregated with three cases of classic Lynch syndrome-associated malignancies over two generations, with consistent loss of MLH1 and PMS2 protein expression on IHC, and evidence of the MSI-High mutator phenotype. The leucine at position 555 is well conserved across a number of species, and this novel variant has not been reported as a normal polymorphism in the general population. In silico and in vitro analyses suggest that this variant may have a deleterious effect on the MLH1 protein and abrogate MMR activity. Evidence from clinical, histological, immunohistochemical, and molecular genetic data suggests that MLH1 c.1664T>C (p.Leu555Pro) is likely to be the pathogenic cause of Lynch syndrome in this family.
authors.affiliation: Cancer Genetics Department, Mater Private Hospital, 73 Eccles St, Dublin 7, Ireland, MFarrell@materprivate.ie.
authors.forename: M P
authors.initials: MP
authors.lastname: Farrell
authors.forename: D J
authors.initials: DJ
authors.lastname: Hughes
authors.forename: M
authors.initials: M
authors.lastname: Drost
authors.forename: A J
authors.initials: AJ
authors.lastname: Wallace
authors.forename: R J
authors.initials: RJ
authors.lastname: Cummins
authors.forename: T A
authors.initials: TA
authors.lastname: Fletcher
authors.forename: M A
authors.initials: MA
authors.lastname: Meany
authors.forename: E W
authors.initials: EW
authors.lastname: Kay
authors.forename: N
authors.initials: N
authors.lastname: de Wind
authors.forename: D G
authors.initials: DG
authors.lastname: Power
authors.forename: E J
authors.initials: EJ
authors.lastname: Andrews
authors.forename: A J
authors.initials: AJ
authors.lastname: Green
authors.forename: D J
authors.initials: DJ
authors.lastname: Gallagher
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics* / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000235:genetics* / Q000378:metabolism; D000328:Adult; D003123:Colorectal Neoplasms, Hereditary Nonpolyposis / Q000235:genetics* / Q000473:pathology; D053843:DNA Mismatch Repair / Q000235:genetics*; D045643:DNA Repair Enzymes / Q000235:genetics* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005260:Female; D005500:Follow-Up Studies; D006801:Humans; D007124:Immunoenzyme Techniques; D008297:Male; D053842:Microsatellite Instability; D008875:Middle Aged; D000070976:Mismatch Repair Endonuclease PMS2; D015999:Multivariate Analysis; D000070957:MutL Protein Homolog 1; D009154:Mutation / Q000235:genetics*; D009367:Neoplasm Staging; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D010375:Pedigree; D010641:Phenotype; D011379:Prognosis; D055815:Young Adult
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D004268:DNA-Binding Proteins; C501486:MLH1 protein, human; D009687:Nuclear Proteins; D000251:Adenosine Triphosphatases; C094934:PMS2 protein, human; D000070976:Mismatch Repair Endonuclease PMS2; D000070957:MutL Protein Homolog 1; D045643:DNA Repair Enzymes