ClinVar Genomic variation as it relates to human health

This variant is associated with the following publications: (PMID: 10671064, 11793442, 27300758, 28932927, 11555625, 22753075, 26247049, 16083711, 22949387, 12547705, 14871975, 18415027, 18033691, 17510385, 17210669, 19863800, 20020535, 12513688, 17594722, 21120944, 29575718, 32081490)

Variant summary: MLH1 c.277A>G (p.Ser93Gly) results in a non-conservative amino acid change located in the DNA mismatch repair protein family, N-terminal and Histidine kinase/HSP90-like ATPase domains of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251392 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.277A>G has been reported in the literature in affected individuals (Schneider_2018, Jansen_2016, Barnetson _2008, Hendriks _2003, Nystrom-Lahti_2002, Quaresima _1998). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. Jansen_2016 reports a patient that carried the variant of interest along with another pathogenic germline MUTYH variant, c1187G>A (p.G396D) and a somatic MLH1 variant, c.281delT (p.(S95LfsX13), providing supporting evidence for a benign role. Several functional studies have been performed to assess the variant's impact on interaction and binding with PMS2 and Exo1, MMR activity, nuclear localization and expression, and splice pattern (Andersen_2012, Drost_2010, Takahashi_2007, Wanat_2007, Raevaara_2005, Nystrom-Lahti_2002, Ellison_2001). Thru these studies, the variant of interest was found to perform comparably to wild-type function. Six ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as benign (n=1), likely benign (n=3) and uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as likely benign.

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The MLH1 p.Ser93Gly variant was identified in 16 of 2132 proband chromosomes (frequency: 0.007) from individuals or families with Lynch syndrome (Barnetson 2008, Jansen 2016, van Puijenbroek 2008, Raevaara 2005). The variant was also identified in dbSNP (ID: rs41295282 as "With Uncertain significance allele"), ClinVar (1x as benign by Invitae; 3x as likely benign by GeneDx, Ambry Genetics, and Mayo Clinic; and 2x as uncertain significance by InSiGHT and Counsyl), MutDB, UMD-LSDB (1x as unclassified variant), Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors database (37x). The variant was not identified in the Gene Insight-COGR, Cosmic, or Zhejiang University databases. The variant was identified in control databases in 6 of 277126 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 24028 chromosomes (freq: 0.00004), European in 4 of 126634 chromosomes (freq: 0.00003), and South Asian in 1 of 30780 chromosomes (freq: 0.00003), while the variant was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, or Finnish populations. In addition, several functional studies using in vitro Mismatch Repair Assays identify the variant has normal MMR activity (Andersen 2012, Drost 2010, Kansikas 2011, Ou 2007, Takahashi 2007, Thompson 2013, Wanat 2007, Raevaara 2005). However, the variant exhibited reduction of protein efficiency compared to the wild-type, suggesting this may be a low penetrance variant (Vogelsang 2009). The p.Ser93 residue is conserved in mammals but not in more distantly related organisms; however, 4 of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In addition, analysis using the pCAS reporter assay showed splice patterns of the variant allele were the same as the wild type (van der Klift 2015). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.