ClinVar Genomic variation as it relates to human health

Coding sequence variation introducing a premature termination codon

Variant summary: MSH2 c.1226_1227delAG (p.Gln409ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 246188 control chromosomes (gnomAD). The variant, c.1226_1227delAG, has been reported in the literature in multiple individuals affected with Lynch Syndrome (Goodfellow_2015, Mangold_2005). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cites the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.

Diagnosed case of FAP

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

The c.1226_1227delAG pathogenic mutation, located in coding exon 7 of the MSH2 gene, results from a deletion of two nucleotides at nucleotide positions 1226 to 1227, causing a translational frameshift with a predicted alternate stop codon (p.Q409Rfs*7). This alteration has been identified in numerous ethnically diverse individuals/ families with HNPCC/Lynch syndrome (Liu T et al. Genes Chromosomes Cancer. 2000 Jan;27:17-25; Mueller-Koch Y et al. Gut. 2005 Dec;54:1733-40; Lagerstedt Robinson K et al. J. Natl. Cancer Inst. 2007 Feb;99:291-9; Papp J et al. World J Gastroenterol. 2007 May;13:2727-32; Tang R et al. Clin Genet. 2009 Apr;75:334-45; Pérez-Cabornero L et al. Cancer Prev. Res. (Phila). 2011 Oct;4:1546-55; Egoavil C et al. PLoS ONE. 2013 Nov;8:e79737; Siraj AK et al. Cancer. 2015 Jun;121:1762-71; Goodfellow PJ et al. J. Clin. Oncol. 2015 Dec;33:4301-8). Additionally, this alteration has been identified in individuals with pancreatic, prostate, and urinary tract malignancies, as well as sebaceous carcinoma (Dudley B et al. Cancer 2018 Apr;124:1691-1700; Burris CKH et al. Case Rep Ophthalmol. May 2019;10:180-185; Wischhusen JW et al. Cancer Epidemiol Biomarkers Prev. 2020 01;29:193-199; Wu Y et al. Eur Urol Oncol. 2020 04;3:224-230). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; 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: 21778331, 16216036, 8872463, 17569143, 24244552, 19419416, 25712738, 26552419, 29360161, 28874130, 26681312, 30787465, 31692600, 31664942, 31830689, 31948886, 31615790)

This variant deletes 2 nucleotides in exon 7 of the MSH2 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in multiple individuals affected with Lynch syndrome (PMID: 8872463, 17569143, 25712738, 26552419). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

This sequence change creates a premature translational stop signal (p.Gln409Argfs*7) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). 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 and endometrial cancer (PMID: 8872463, 15849733, 17569143, 19419416, 21778331, 24244552, 26552419, 26845104). ClinVar contains an entry for this variant (Variation ID: 90577). For these reasons, this variant has been classified as Pathogenic.

This variant deletes 2 nucleotides in exon 7 of the MSH2 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in multiple individuals affected with Lynch syndrome (PMID: 8872463, 17569143, 25712738, 26552419). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

The MSH2 c.1226_1227delAG variant is predicted to result in a frameshift and premature protein termination (p.Gln409Argfs*7). This variant has been reported in multiple individuals with Lynch syndrome (see for example, Table 4, Goodfellow et al. 2015. PubMed ID: 26552419; Table 3, Rossi et al. 2017. PubMed ID: 28874130; Table 2, Dudley et al. 2018. PubMed ID: 29360161). This variant has also been reported in multiple individuals with various cancers including endometrial, prostate, and urinary tract cancers (Table 1, Susswein et al. 2015. PubMed ID: 26681312; Table S1, Wu et al. 2020. PubMed ID: 31948886; Table S1, Wischhusen et al. 2019. PubMed ID: 31615790). This variant has not been reported in a large population database, indicating this variant is rare. This variant has been classified as pathogenic by an expert panel in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/90577/). Frameshift variants in MSH2 are expected to be pathogenic. This variant is interpreted as pathogenic.