ClinVar Genomic variation as it relates to human health

Co-occurrence without CMMRD phenotype & MAF 0.01-1%. Multifactorial likelihood analysis posterior probability 0.001-0.049

Variant summary: MLH1 c.2101C>A (p.Gln701Lys) results in a conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain of the encoded protein sequence that is necessary for interaction with PSM2 (Fan_2007). Three of five in-silico tools predict a benign effect of the variant on protein function. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0005 in 251174 control chromosomes (gnomAD and publication data), predominantly at a frequency of 0.0066 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 9 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Lynch Syndrome phenotype (0.00071), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. This variant has been reported in multiple sequencing studies among individuals of East Asian ancestry with a variety of cancers to include, Lynch Syndrome, biliary tract cancer and colon cancer (Zhi_2011, Talseth-Palmer_2016, Chan_2018, Kim_2017, Wardell_2018). Thus, these reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In addition, at-least one co-occurrence with the other potentially pathogenic variant (MLH1 c.208-1G>A) has been reported, providing supporting evidence for a benign role (Sheng_2008). A functional study demonstrated the variant to retain about 70% of its ability to interact with PMS2 (Fan_2007). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS (n=2), likely benign (n=2), and benign (n=2)). One expert panel (InSiGHT) has submitted clinical-significance assessment for this variant to ClinVar before 2014 and classified the variant as likely benign. As all of the evidence outlined above, spanning over a decade supports a non-pathogenic outcome, the variant was classified as benign.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

This alteration is classified as 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.

This variant is associated with the following publications: (PMID: 16929514, 30521064, 23760103, 17011982, 18931482, 18726168, 18383312, 24933000, 22136435, 22995991, 18094436, 26811195, 23431106, 26900293, 26078562, 24710284, 23047549, 26332594, 29192238, 29050249, 25338684, 25479140, 29360550, 30093976, 31784484)

The MLH1 p.Gln701Lys variant was identified in 17 of 1894 proband chromosomes (frequency: 0.009) from individuals or families with Lynch syndrome or gastric cancer and was present in 3 of 1818 control chromosomes (frequency: 0.002) from healthy individuals (Chen 2013, Fan 2007, Sheng 2008, Talseth-Palmer 2016, Yap 2009, Zhang 2006, Zhi 2011). The variant was also identified in the following databases: dbSNP (ID: rs63750114) as "With Pathogenic, other allele", ClinVar (3x likely benign including InSiGHT expert panel, 2x benign, 2x uncertain significance), Clinvitae (4x), Cosmic (1x, confirmed somatic, in adenocarcinoma of large intestine), Insight Colon Cancer Gene Variant Database (10x, Likely not pathogenic/little clinical significance), Zhejiang Colon Cancer Database (4x), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (11x). The variant was not identified in MutDB or the UMD-LSDB database. The variant was identified in control databases in 129 of 276412 chromosomes at a frequency of 0.0005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 1 of 23994 chromosomes (freq: 0.00004), Other in 2 of 6450 chromosomes (freq: 0.0003), and East Asian in 126 of 18826 chromosomes (freq: 0.007). The variant was not observed in the Latino, European, Ashkenazi Jewish, Finnish, or South Asian populations. A functional study utilizing a yeast two-hybrid assay showed that MLH1 p.Gln701Lys interacts with PMS2 at reduced efficiency (16.6% relative activity in comparison with wild-type MLH1) (Fan 2007). In the same study, a co-immunoprecipitation assay demonstrated p.Gln701Lys retains 70% interaction with PMS2 (Fan 2007). Thus, the functional studies do not show consistent results. A study by Zhi 2011 found that the c.2101C>A genotype was associated with an increased risk of gastric cancer (OR = 8.42, 95% CI = 1.04-68.06) in Chinese males. The p.Gln701 residue is conserved in mammals but not in more distantly related organisms, and four out of five 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 p.Gln701Lys variant occurs in the 3rd last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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.

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).