ClinVar Genomic variation as it relates to human health

Multifactorial likelihood analysis posterior probability >0.99

This sequence change creates a premature translational stop signal (p.Lys751Serfs*3) in the MLH1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 6 amino acid(s) of the MLH1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 8797773, 18566915, 18931482, 24802709, 27295708). It is commonly reported in individuals of Italian ancestry (PMID: 24802709). ClinVar contains an entry for this variant (Variation ID: 90101). RNA analysis performed to evaluate the impact of this premature translational stop signal on mRNA splicing indicates it does not significantly alter splicing (Invitae). For these reasons, this variant has been classified as Pathogenic.

Frameshift variant predicted to result in abnormal protein length as the last 6 amino acids are replaced with 2 different amino acids, and other similar variants have been reported in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 9559627, 18566915, 8797773, 24802709, 29238914, 27295708, 18931482, 15365995, 28874130, 26884312, 27978560, 29151953, 21642682, 25345868, 27606285, 31447099, 30787465, 12799449, 20533529, 22753075, 32782288)

This c.2252_2253delAA (p.Lys751Serfs*3) variant in the MLH1 gene has been reported in multiple individuals with Lynch syndrome (PMID 8797773, 24802709, 27295708, 28874130). Microsatellite instability (MSI) and protein expression studies in tumors from patients with this variant showed MSI-high mutator phenotype and loss of PMS2 expression (PMID 24802709). This variant is absent from large databases of genetic variation in the general population. Therefore, the c.2252_2253delAA (p.Lys751Serfs*3) variant in the MLH1 gene is classified as pathogenic.

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

The c.2252_2253delAA pathogenic mutation, located in coding exon 19 of the MLH1 gene, results from a deletion of two nucleotides at nucleotide positions 2252 to 2253, causing a translational frameshift with a predicted alternate stop codon (p.K751Sfs*3). This mutation has been identified in numerous individuals with features of Lynch syndrome (Sheng JQ et al, Cytogenet. Genome Res. 2008 ; 122(1):22-7; Nilbert M et al, Fam. Cancer 2009 ; 8(1):75-83; Han HJ et al, J. Natl. Cancer Inst. 1996 Sep; 88(18):1317-9; Cajal AR et al. Medicina (B Aires), 2016;76:180-2). Borelli, et al. describes this as an Italian founder mutation and demonstrates that it segregates with disease in 11 families (10 meeting Amsterdam criteria) with a total of 24 MSI-H tumors (Borelli I et al, Fam. Cancer 2014 Sep; 13(3):401-13).This alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation.

The MLH1 p.Lys751SerfsX3 variant was identified in 14 of 2728 proband chromosomes (frequency: 0.005) from individuals or families with colorectal cancer, and was not identified in 924 control chromosomes from healthy individuals (Borelli 2014, Han 1996, Nilbert 2009, Shin 2004). The variant was also identified in dbSNP (ID: rs267607907) as “With Pathogenic allele”, “Mismatch Repair Genes Variant Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), ClinVar database (classified as uncertain significance by InSight, pathogenic by Ambry genetics, likely pathogenic by Mayo clinic). 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. The c.2252_2253del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 751 and leads to a premature stop codon 3 codons downstream. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the MLH1 gene are an established mechanism of disease in Lynch syndrome and this is the type of variant expected to cause the disorder. A study by Borelli (2014) identified 11 patients with colorectal cancer with this variant and showed the MSI-high mutator phenotype with loss of PMS2 expression in all but one tumor. There was also a statistically significant (p = 0.0057) higher frequency of pancreatic tumours compared to families with other MLH1 pathogenic variants. Moreover the clinical features, tissue analysis and co-segregation with disease strongly support the hypothesis that the MLH1 c.2252_2253delAA variant has a pathogenic effect. In addition, in an in silico model study the variant fell in the >99% probability range for known class 5 (pathogenic) variant (Joeri van der Velde 2015). The c-terminus of the MLH1 protein is known to be well conserved and important for PMS2 binding and DNA mismatch repair (Mohd 2006). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.