ClinVar

Description

The CHEK2 p.Ser428Phe variant was identified in 65 of 4516 proband chromosomes (frequency: 0.014) from Ashkenazi Jewish individuals or families with breast, ovarian, cancer and French Canadian patients with prostate cancer (Laitman 2007, Shaag 2005, Walsh 2006, Tischkowitz 2008). The variant was also identified in the following databases: dbSNP (ID: rs137853011) as “With Pathogenic allele”, ClinVar (7x, as pathogenic by GeneDx, Ambry Genetics, Invitae, University of Washington, Color Genomics, Illumina and 1x, as uncertain significance by Illumina), Clinvitae (6x, as pathogenic, 1x as uncertain significance), Cosmic (1x urinary tract carcinoma), Zhejiang Colon Cancer Database (3x). The variant was not identified in MutDB. The variant was identified in control databases in 127 of 276646 (1 homozygous) chromosomes at a frequency of 0.0005 in the following populations: other in 5 of 6452 chromosomes (freq. 0.0008), European in 9 of 126256 chromosomes (freq. 0.00007), Ashkenazi Jewish in 112 of 10144 (1 homozygous) chromosomes (freq. 0.001), and South Asian in 1 of 30732 chromosomes (freq. 0.00003) (Genome Aggregation Consortium Feb 27, 2017). Population studies have identified the p.Ser428Phe variant as a founder allele in the AJ population; one study concluded that the CHEK2, p.Ser428Phe variant increases breast cancer risk by two fold among Ashkenazi Jewish women (Shaag 2005) though it has been noted that the control group in this study included a large proportion (43.3%) of adults who underwent pre-marriage counseling in Jerusalem and were likely much younger than the cases (Mundt 2017). Functional studies revealed this variant to have loss of CHEK2-mediated DNA damage response (Roeb 2012) and to impair protein function in yeast complementation assays (Shaag 2005, Tischkowitz 2008); however, these studies are not considered sufficient evidence of pathogenicity because of the known variability of yeast assays for CHEK2 (Mundt 2017). Co-segregation with breast cancer has been reported in at least three Ashkenazi Jewish families with the CHEK2 p.Ser428Phe variant (Laitman 2007, Roeb 2012). Loss of heterozygosity was observed in breast tumors from two individuals heterozygous for CHEK2 p.Ser428Phe, suggesting this variant may be involved in tumor growth (Shaag 2005). The p.Ser428Phe 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The variant is located within the kinase domain increasing the likelihood that it may have clinical significance. The challenge of interpreting these data has been highlighted by two papers (Mundt 2017, Balmana 2016). Conflicting interpretation of functional data as well as interpretation of the variant’s relatively high allele frequency in control databases are thought to reflect the challenges of describing a so-called low-penetrance susceptibility allele in a format designed for high-penetrance alleles and rather than being universally low-penetrance, variants in this category may be associated with an increased risk for a subset of individuals, especially for those with a personal or family history of early-onset breast cancer (Byrnes 2008). Given the high frequency of this variant in the Ashkenazi Jewish population and the apparent low penetrance with this variant, a classification of likely pathogenic is conservative. 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 likely pathogenic.