Submissions for variant NM_000249.4(MLH1):c.1652A>G (p.Asn551Ser)

gnomAD frequency: 0.00001  dbSNP: rs63750271

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000781995	SCV000920452	benign	Lynch syndrome	2018-10-18	reviewed by expert panel	curation	Multifactorial likelihood analysis posterior probability < 0.001 (0.00084)
Invitae	RCV000228672	SCV000284023	likely benign	Hereditary nonpolyposis colorectal neoplasms	2023-12-26	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000563396	SCV000662030	uncertain significance	Hereditary cancer-predisposing syndrome	2024-03-06	criteria provided, single submitter	clinical testing	The p.N551S variant (also known as c.1652A>G), located in coding exon 14 of the MLH1 gene, results from an A to G substitution at nucleotide position 1652. The asparagine at codon 551 is replaced by serine, an amino acid with highly similar properties. This alteration was identified in a family meeting Amsterdam II criteria for Lynch syndrome with tumor results for the proband showing high microsatellite instability (MSI-H) and reduced staining for MLH1/PMS2 proteins on IHC (Hardt K et al. Fam. Cancer, 2011 Jun;10:273-84). In addition, this variant has been reported in an individuals with early onset colorectal and breast cancers (DeRycke MS et al. Mol Genet Genomic Med, 2017 Sep;5:553-569; Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). Functional studies in yeast were performed for this alteration and both the yeast two hybrid and dominant negative mutator effect (DNE) were similar to wild type; however, there was reduced MLH1 variant protein expression relative to wild type in both yeast and human cells (Hardt K et al. Fam. Cancer, 2011 Jun;10:273-84). This alteration has been classified as benign using the following lines of evidence: in silico prediction models, segregation with disease, clinical phenotype including tumor characteristics, mutation co-occurrence, and functional studies (Thompson BA et al. Hum. Mutat. 2013 Jan;34:200-9; Thompson BA et al. Nat. Genet. 2014 Feb;46:107-15; available at [www.insight-group.org/variants/classifications/]). This amino acid position is highly 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.
Color Diagnostics, LLC DBA Color Health	RCV000563396	SCV001341312	uncertain significance	Hereditary cancer-predisposing syndrome	2023-09-01	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with serine at codon 551 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown this variant retained wild type activity via dominant mutator effect and yeast-2-hybrid assay (PMID 21404117). This variant has been reported in individuals affected with Lynch syndrome, colorectal cancer and breast cancer (PMID: 21404117, 28944238, 32885271). This variant has been identified in 2/251286 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.
GeneDx	RCV001556097	SCV001777615	uncertain significance	not provided	2022-01-28	criteria provided, single submitter	clinical testing	Observed in a patient with colon cancer and tumor studies consistent with pathogenic variants in this gene (Hardt 2011); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: reduced protein expression, dominant negative mutator effect and interaction with PMS2 similar to wild type (Hardt 2011); This variant is associated with the following publications: (PMID: 21404117, 12799449, 20533529, 22753075)
All of Us Research Program, National Institutes of Health	RCV000781995	SCV004843189	uncertain significance	Lynch syndrome	2023-09-17	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with serine at codon 551 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. Experimental functional studies in yeast have shown this variant to have normal function (PMID 21404117). This variant has been reported in an individual affected with colorectal cancer in the literature (PMID 21404117). This variant has been identified in 2/251286 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.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001356613	SCV001551829	uncertain significance	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 p.Asn551Ser variant was identified in the literature however the frequency of this variant in an affected population was not provided (Hardt 2011). The variant was also identified in dbSNP (ID: rs63750271) as “With Uncertain significance allele”, and ClinVar (as uncertain significance by Invitae and Ambry Genetics). The variant was not identified in COGR, Cosmic, MutDB, UMD-LSDB, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The variant was identified in control databases in 2 of 246060 chromosomes at a frequency of 0.000008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (Non-Finnish) in 2 of 111590 chromosomes (freq: 0.000018), while the variant was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. One study, which investigated MLH1 missense variants by two functional in vivo assays in yeast found the p.Asn551Ser variant, which is located within the MLH1 protein interaction domain, showed a ß-gal activity similar to wild type MLH1; this variant was classified as a VUS (Hardt 2011). The p.Asn551 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.