NM_000251.3:c.362A>G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_000251.3(MSH2):āc.362A>Gā(p.Tyr121Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000624 in 1,602,528 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000251.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250740Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135502
GnomAD4 exome AF: 0.00000552 AC: 8AN: 1450324Hom.: 0 Cov.: 29 AF XY: 0.00000554 AC XY: 4AN XY: 721962
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
not provided Uncertain:3
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in a patient with juvenile polyposis syndrome who also harbored a canonical splice variant in SMAD4 (PMID: 36359527); Published functional study demonstrates mismatch repair activity similar to wild-type (PMID: 33357406); This variant is associated with the following publications: (PMID: 25318351, 27720647, 36359527, 33357406, 18822302, 21120944, 24326041, 30584090) -
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The MSH2 c.362A>G;p.Tyr121Cys variant has been published in the medical literature in at least one individual suspected of having hereditary cancer (Mu 2016). The variant is listed in the ClinVar database (Variation ID: 127643) and the dbSNP variant database (rs587779971) with an allele frequency of 0.003253 percent (9/276636 alleles) in the Genome Aggregation Database. The amino acid at this position is located in the mismatch binding domain (Lutzen 2008), but the amino acid is weakly conserved and computational algorithms do not reach a consensus as to the effect of this variant (AlignGVGD: C15, SIFT: Tolerated, MutationTaster: disease causing). However, this variant occurs near an exon/intron boundary and splicing prediction programs (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict this variant may alter splicing. Considering available information, there is insufficient evidence to classify the variant at this time. Pathogenic MSH2 variants are causative for Lynch syndrome (MIM#120435). References Lutzen A et al. Functional analysis of HNPCC-related missense mutations in MSH2. Mutat Res. 2008 Oct 14;645(1-2):44-55. Mu W et al. Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next-Generation Sequencing Panel Testing. J Mol Diagn. 2016 Nov;18(6):923-932. -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
This missense variant replaces tyrosine with cysteine at codon 121 of the MSH2 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). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 9/282148 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. -
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. -
not specified Uncertain:1
Variant summary: MSH2 c.362A>G (p.Tyr121Cys) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS-like, N-terminal domain (IPR007695) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 250740 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.362A>G has been reported in the literature in individuals affected with breast and ovarian cancer without strong evidence for causality (examples: Harismendy_2013 and Li_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 24326041, 30584090). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=4) and benign (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Lynch syndrome 1 Uncertain:1
This variant has been reported in the literature as identified on hereditary cancer gene panel testing (Mu 2016). This variant has an overall allele frequency of 0.00003 in the Broad Institute gnomAD Browser (https://gnomad.broadinstitute.org/). In silico analyses indicate that this variant does not alter protein structure/function. Thus, it is unknown at this time whether this variant increases cancer risk. BP4 -
Lynch syndrome Uncertain:1
This missense variant replaces tyrosine with cysteine at codon 121 of the MSH2 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). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 9/282148 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. -
Hereditary nonpolyposis colorectal neoplasms Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at