ClinVar Miner

Submissions for variant NM_000249.4(MLH1):c.1468A>G (p.Met490Val)

gnomAD frequency: 0.00001  dbSNP: rs776671941
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000220644 SCV000276511 uncertain significance Hereditary cancer-predisposing syndrome 2023-06-06 criteria provided, single submitter clinical testing The p.M490V variant (also known as c.1468A>G), located in coding exon 13 of the MLH1 gene, results from an A to G substitution at nucleotide position 1468. The methionine at codon 490 is replaced by valine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV000630039 SCV000750995 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2022-10-23 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MLH1 protein function. ClinVar contains an entry for this variant (Variation ID: 232383). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. This variant is present in population databases (rs776671941, gnomAD 0.002%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 490 of the MLH1 protein (p.Met490Val).
All of Us Research Program, National Institutes of Health RCV003997967 SCV004841018 uncertain significance Lynch syndrome 2023-05-04 criteria provided, single submitter clinical testing This missense variant replaces methionine with valine at codon 490 of the MLH1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MLH1-related disorders in the literature. This variant has been identified in 2/251482 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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