ClinVar

Description

Variant summary: CHEK2 c.1036C>T (p.Arg346Cys) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) 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 5.2e-05 in 251222 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CHEK2 causing Prostate Cancer (5.2e-05 vs 0.00025), allowing no conclusion about variant significance. c.1036C>T has been reported in the literature in individuals affected with various types of Cancer, including Breast cancer, Biliary tract cancer, Langer Hans Cell Histiocytosis and B-cell acute lymphoblastic leukemia (example, Guindalini_2022, Bhai_2021, Wagener_2022, Pereira_2022), and was also reported in the control cohorts from at-least two large case-control studies of cancer risk (example, Dorling_2021, Okawa_2023). These report(s) do not provide unequivocal conclusions about association of the variant with Prostate Cancer and other CHEK2-related conditions. At least two publications report experimental evidence evaluating an impact on protein function. In a yeast growing assay, this variant significantly inhibit the normal growth of yeast (Delimitsou_2019), however in a subsequent study using an osteosarcoma cell line, this variant did not affect CHK2 function, as it resulted in comparable/slightly increased CHEK2 levels and was able to induce Phosphorylation of CHK2-Thr68 (Wagener_2022). The following publications have been ascertained in the context of this evaluation (PMID: 34326862, 30851065, 33471991, 35264596, 36243179, 35980532, 36468172). ClinVar contains an entry for this variant (Variation ID: 142222). Based on the evidence outlined above, the variant was classified as uncertain significance.