ClinVar Genomic variation as it relates to human health

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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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.

The MLH3 p.Glu624Gln variant was identified in 7 of 1036 proband chromosomes (frequency: 0.00676) from individuals or families with suspected Lynch syndrome or colorectal cancer (Wu_2001_PMID: 11586295, Liu_2003_PMID: 12702580, Rohlin_2017_PMID: 27696107, & Hienonen_2003_PMID: 12800209). The variant was also identified in the following databases: dbSNP (ID: rs28756986) as “With Uncertain significance allele”, ClinVar (classified as benign by Invitae with the associated phenotype of Hereditary nonpolyposis colorectal cancer type 7/MLH3-Related Lynch Syndrome; and uncertain significance by OMIM), and LOVD 3.0 (multiple entries with classifications of VUS, likely benign, and pathogenic). The variant was not identified in the Cosmic database. The variant was identified in control databases in 2120 of 282638 chromosomes (11 homozygous) at a frequency of 0.007501 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 1516 of 129054 chromosomes (freq: 0.01175), European (Finnish) in 201 of 25108 chromosomes (freq: 0.008005), Other in 49 of 7218 chromosomes (freq: 0.006789), Latino in 210 of 35396 chromosomes (freq: 0.005933), Ashkenazi Jewish in 39 of 10362 chromosomes (freq: 0.003764), African in 51 of 24968 chromosomes (freq: 0.002043), South Asian in 53 of 30584 chromosomes (freq: 0.001733) and East Asian in 1 of 19948 chromosomes (freq: 0.00005). To clarify the role of the p.E624Q, in vitro functional studies were conducted transfecting wildtype and mutant MLH3 into HEK293T cells which showed no difference in protein expression, stability, localization or interaction with wildtype MLH1 (Ou_2009_PMID: 19156873). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, and GeneSplicer) do not predict a difference in splicing. The p.Glu624 residue is conserved in mammals but not in more distantly related organisms, however four out of five computational analyses (SIFT, AlignGVGD, BLOSUM, and MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. 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.