Description
This missense variant replaces threonine with methionine at codon 476 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 demonstrated inconsistent results. The mutant protein has shown significantly reduced kinase activity in vitro using bacteria produced protein (PMID: 22114986, 31050813), but displayed normal kinase activity in a human cell assay (PMID: 31050813, 37449874). DNA damage repair assays in yeast have shown the mutant protein to exhibit partial to complete loss of function (PMID: 22419737, 30851065). This variant has been reported in individuals affected with breast cancer (PMID: 15095295, 21244692, 22114986, 22862163, 24595525, 25186627, 26681312, 28008555, 28495237 30426508, 32658311, 32805687, 32906215, 33030641, 36315097, 37628581), prostate cancer (PMID: 29368341, 29520813), colorectal cancer (PMID: 28008555, 28135145, 28944238, 32658311), pancreatic cancer (PMID: 26483394, 26845104 29945567), and endometrial cancer (PMID: 27443514), as well as in individuals unaffected with cancer (PMID: 32658311). A history weighting algorithm score was inconsistent with that expected for CHEK2 pathogenic mutations (Mundt, et al. poster #154, ACMG 2017). This variant has been identified in 83/265178 chromosomes in the general population by the Genome Aggregation Database (gnomAD). This variant has been reported in two large case-control meta analyses; this variant has been identified in 83/60383 cases and 45/53416 controls (OR=1.632, 95%CI [1.135 to 2.346]) (PMID: 33471991) and 101/73048 BC cases and 60/88658 controls (OR=2.043, 95%Ci [1.4841 to 2.8125]) (PMID: 37449874). In summary, functional studies have been inconclusive regarding the impact of this variant on protein function, and this variant has been observed in individuals affected with breast cancer as well as in the general population. 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.
# | Sample | Method | Observation |
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Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
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1 | germline | unknown | not provided | not provided | not provided | | not provided | not provided | not provided | not provided |