ClinVar Genomic variation as it relates to human health

Variant summary: CHEK2 c.1141A>G (p.Met381Val) results in a conservative amino acid change located in the Protein kinase domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-05 in 276850 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in CHEK2 causing Hereditary Breast and Ovarian Cancer (4e-05 vs 0.00031), allowing no conclusion about variant significance. c.1141A>G has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Tung_2014). This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 381 of the CHEK2 protein (p.Met381Val). This variant is present in population databases (rs375130261, gnomAD 0.008%). This missense change has been observed in individual(s) with breast cancer and colorectal cancer (PMID: 25186627, 28944238, 30613976, 32959997). This variant is also known as c.1270A>G or p.Met424Val. ClinVar contains an entry for this variant (Variation ID: 140959). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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.

Published functional studies suggest no damaging effect: demonstrates auto-phosphorylation and/or kinase activity similar to wild type in yeast and human cell-based assay(s) (PMID: 30851065, 37449874); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31398194, 27535334, 28944238, 29981437, 30269267, 25186627, 30613976, 32959997, 35264596, 32885271, 36717774, 30851065, 19782031, 22419737, 35493704, 35957908, 35534704, 37449874)

BS3_supporting

This missense variant replaces methionine with valine at codon 381 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown no significant impact of this variant on DNA damage repair activity in yeast (PMID: 30851065) and intermediate impact on KAP1 phosphorylation and no impact on CHEK2 autophosphorylation in mammalian cells (PMID: 37449874). This variant has been reported in individuals affected with breast, pancreatic, and colorectal cancer (PMID: 25186627, 28944238, 32885271, 32959997, 36717774) and in one unaffected individual (PMID: 37449874). This variant has been identified in 10/282330 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 variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

The p.M381V variant (also known as c.1141A>G), located in coding exon 10 of the CHEK2 gene, results from an A to G substitution at nucleotide position 1141. The methionine at codon 381 is replaced by valine, an amino acid with highly similar properties. This alteration has been detected in a cohort of 1231 colorectal cancer cases (DeRycke MS et al. Mol Genet Genomic Med. 2017 Sep;5:553-569) and in a woman with breast cancer undergoing multi-gene panel testing (Tung N et al. Cancer, 2015 Jan;121:25-33). This variant was also observed in 4/3251 individuals who met eligibility criteria for hereditary breast and ovarian cancer syndrome (Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). This alteration behaved as functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum. Mutat., 2019 05;40:631-648). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The CHEK2 c.1141A>G variant is predicted to result in the amino acid substitution p.Met381Val. This variant has been identified in an individual with colorectal cancer (Table S2, DeRycke et al. 2017. PubMed ID: 28944238), and in several individuals with breast cancer, including male breast cancer (Uyisenga et al 2020. PubMed ID: 32959997; Rizzolo P et al 2019. PubMed ID: 30613976; de Oliveira JM et al 2022. PubMed ID: 35534704; Tung N et al 2014. PubMed ID: 25186627). This variant has also been called c.1270A>G or p.Met424Val in the literature. This variant is reported in 0.0062% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-29091816-T-C) and is classified in ClinVar as a variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/140959/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

The CHEK2 p.Met381Val variant was not identified in the literature nor was it identified in the MutDB, Zhejiang Colon Cancer Database, databases. The variant was identified in the following databases: dbSNP (ID: rs375130261) as With Uncertain significance allele, ClinVar (classified as uncertain significance by Ambry Genetics, GeneDx, Invitae, Counsyl, Color Genomics), Clinvitae, and Cosmic. The variant was identified in control databases in 11 of 276850 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: Latino in 1 of 34410 chromosomes (freq: 0.00003), European in 10 of 126376 chromosomes (freq: 0.0001); it was not observed in the African, Other, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Met381 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume 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.