ClinVar Genomic variation as it relates to human health

Variant summary: CHEK2 c.917G>C (p.Gly306Ala) results in a non-conservative amino acid change located in the Protein kinase domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.6e-05 in 284924 control chromosomes (gnomAD and publication). This frequency is not significantly higher than expected for a pathogenic variant in CHEK2 causing Hereditary Breast and Ovarian Cancer (4.6e-05 vs 0.00031). c.917G>C has been reported in the literature in multiple individuals affected with Breast Cancer (Lu_2018, Lolas Hamameh_2017, Susswein_2016, Roeb_2012). These data indicate that the variant is likely to be associated with disease. A co-occurrence with another pathogenic variant has been reported in one case (ATM c.2897_2899delTTCinsGCCAA, p.Val966GlyfsX6); the authors of the study classified the variant of interest as likely pathogenic (Susswein_2016). Experimental evidence evaluating an impact on protein function demonstrated the variant to cause loss of CHEK2-mediated response to DNA damage (Roeb_2012). Six ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely pathogenic (4x) and twice as uncertain significance. Based on the evidence outlined above, until the functional impact of this variant is unequivocally established and additional clinical correlations are ascertained the variant was classified as likely pathogenic

The CHEK2 c.917G>C (p.Gly306Ala) variant has been reported in the published literature in individuals with breast cancer (PMIDs: 26681312 (2015), 27751358 (2016), 28486781 (2017), 28580595 (2018), 30128536 (2018), 30303537 (2019), 32068069 (2020), 32658311 (2021)), ovarian cancer (PMID: 30322717 (2018)), melanoma (PMID: 33050356 (2020)), and colorectal cancer (PMID: 31118792 (2019)). Functional studies using yeast-based assays have produced conflicting results (PMIDs: 30851065 (2019), 22419737 (2012)), but a functional study utilizing human cells suggested this variant is damaging (PMID: 31050813 (2019)). The frequency of this variant in the general population, 0.00015 (3/19946 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as likely pathogenic.

The p.G306A variant (also known as c.917G>C), located in coding exon 8 of the CHEK2 gene, results from a G to C substitution at nucleotide position 917. The glycine at codon 306 is replaced by alanine, an amino acid with similar properties. This alteration has been detected in cohorts of breast, ovarian and colorectal cancer patients (Carter NJ et al. Gynecol Oncol. 2018 12;151:481-488; Girard E et al. Int. J. Cancer 2019 04;144(8):1962-1974; Gong R et al. Cancer Manag Res. 2019 Apr;11:3721-3739; Kwong A et al. J Mol Diagn. 2020 04;22:544-554; Akcay IM et al. Int J Cancer. 2021 01;148:285-295). However, this variant has also been reported in healthy controls, including one large case-control study in which this alteration was reported in 3/60,466 breast cancer cases and in 5/53,461 controls (Dorling et al. N Engl J Med 2021 02;384:428-439). Functional studies for this variant have reported conflicting results. This alteration was reported to result in complete loss of DNA damage response in vivo (Roeb W et al. Hum. Mol. Genet. 2012 Jun; 21(12):2738-44), but behaved as functional in a second in vivo, yeast-based assay (Delimitsou A et al. Hum Mutat. 2019 05;40:631-648). A complementation assay quantifying KAP1-S473 phosphorylation in nontransformed human RPE1 cells showed that p.G306A resulted in 16% function compared to wild-type (Kleiblova P et al. Int. J. Cancer 2019 10;145(7):1782-1797). However, a more recent publication of studies in RPE1-CHEK2-knockout cells reported this alteration as having an "intermediate" impact on protein function (Stolarova L et al. Clin Cancer Res. 2023 Jul:OF1-OF14). 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 conflicting at this time, the clinical significance of this alteration remains unclear.

This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 306 of the CHEK2 protein (p.Gly306Ala). This variant is present in population databases (rs587780192, gnomAD 0.02%). This missense change has been observed in individual(s) with a personal and/or family history of breast and/or ovarian cancer (PMID: 21244692, 22419737, 26681312, 27751358, 28486781, 28580595, 30128536, 30303537, 30322717, 31050813). This variant is also known as c.1046G>C, p.Gly349Ala. ClinVar contains an entry for this variant (Variation ID: 128089). 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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 22419737, 30851065, 31050813). In summary, this variant is a rare missense change that has been observed in affected individuals. However, it is also present in the population, and there is a lack of family segregation and case-control studies in evaluating cancer risk, which are important to determine the disease-causing role of this variant in this lower-penetrance gene. Moreover, experimental studies have reported conflicting results regarding the effect of this variant on CHEK2 protein function. Therefore, it has been classified as a Variant of Uncertain Significance.

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This missense variant replaces glycine with alanine at codon 306 of the CHEK2 protein. Computational prediction tool 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). The mutant protein has been reported to be non-functional in a yeast complementation assay and in a study that measured kinase activities in a human cell line and in a cell-free kinase assay (PMID: 22419737, 31050813) and has been reported to have intermediate impact on KAP1 and CHK2 phosphorylation in a human cell complementation assay (PMID: 37449874). However, this variant has been shown to have neutral impact on DNA damage response in a similar yeast complementation assay system (PMID: 30851065). This variant has been reported in multiple individuals affected with breast cancer (PMID: 21244692, 26681312, 26822949, 28486781, 28580595, 30128536, 30303537, 31050813, 32068069, 34606182, 36521553, 37239058) as well as in unaffected individuals (PMID: 31050813).This variant has been reported in two large breast cancer case-control meta-analyses, observed in 3/60466 cases and 5/53461 unaffected controls (PMID: 33471991; Leiden Open Variation Database DB-ID CHEK2_000190) and 8/73048 cases and 7/88658 unaffected controls (PMID: 37449874). This variant has been identified in 12/282524 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Due to the conflicting functional study results and lack of clear disease association, the role of this variant in disease cannot be determined conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

Observed in individuals with early-onset and/or familial breast cancer and/or colorectal cancer (PMID: 21244692, 22419737, 25186627, 28486781, 28580595, 30303537, 32658311, 32068069, 38061684); Published functional studies demonstrate at least an intermediate impact on kinase activity in human cell-based assays and mixed results in yeast studies (PMID: 22419737, 30851065, 31050813, 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: 37239058, 30128536, 32805687, 30322717, 31118792, 21244692, 26787654, 26681312, 27751358, 28580595, 28301460, 25186627, 28486781, 30851065, 31050813, 30303537, 32068069, 32860008, 33050356, 32658311, 29922827, 33471991, 35264596, 37449874, 16794575, 36521553, 22419737, 19782031, 38062336, 38061684, 34326862)

The CHEK2 p.Gly306Ala variant was identified in 11 of 114364 proband chromosomes (frequency: 0.00009) from individuals or families with breast cancer and was not identified in 2218 control chromosomes from healthy individuals (Le Calvez-Kelm 2011, Leedom 2016, Susswein 2016). The variant was also identified in dbSNP (ID: rs587780192) as "With Likely pathogenic allele ", and in ClinVar (classified as likely pathogenic by GeneDx, Ambry Genetics and two other submitters; as uncertain significance by Invitae and one clinical laboratory). The variant was identified in control databases in 12 of 276948 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 1 of 6460 chromosomes (freq: 0.0002), European in 8 of 126606 chromosomes (freq: 0.00006), East Asian in 3 of 18862 chromosomes (freq: 0.0002), while the variant was not observed in the African, Latino, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Gly306 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the G 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In addition, the yeast-based in vivo assay CHEK2-mediated response to DNA damage showed the variant disturbs CHEK2 DNA damage respond (Roeb 2012). 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.

Variant interpreted as Uncertain significance and reported on 11-17-2017 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.