ClinVar Genomic variation as it relates to human health

This variant is denoted CHEK2 c.967A>C at the cDNA level, p.Thr323Pro (T323P) at the protein level, and results in the change of a Threonine to a Proline (ACC>CCC). This variant was observed in an individual with early-onset breast cancer as well as in both tumor and adjacent normal tissues from an individual with prostate cancer (Dong 2003, Le Calvez-Kelm 2011). In a yeast-based assay CHEK2 Thr323Pro demonstrated DNA damage response comparable to wild-type, but led to partially reduced kinase activity in mammalian cells (Wu 2006, Roeb 2012). CHEK2 Thr323Pro was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Threonine and Proline differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CHEK2 Thr323Pro occurs at a position that is conserved in mammals and is located in the kinase domain (Desrichard 2011, Roeb 2012). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether CHEK2 Thr323Pro is pathogenic or benign. We consider it to be a variant of uncertain significance.

This missense variant replaces threonine with proline at codon 323 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 that this variant causes a partial loss of CHEK2 kinase activity (PMID: 16835864) but does not affect DNA damage response of the CHEK2 protein (PMID: 22419737). This variant has been observed in individuals affected with early-onset breast caner (PMID: 21244692), familial breast cancer (PMID: 22419737) and prostate cancer (PMID: 16835864). This variant has not been identified 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 missense change has been observed in individual(s) with prostate and breast cancer (PMID: 16835864, 21244692, 22419737). ClinVar contains an entry for this variant (Variation ID: 420003). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 16835864, 22419737). 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. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 323 of the CHEK2 protein (p.Thr323Pro).

The p.T323P variant (also known as c.967A>C), located in coding exon 8 of the CHEK2 gene, results from an A to C substitution at nucleotide position 967. The threonine at codon 323 is replaced by proline, an amino acid with highly similar properties. This alteration has been reported in both breast and prostate cancer cases (Wu X et al. Hum. Mutat. 2006 Aug;27(8):742-; Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13(1):R6; 7; Young EL et al. J Med Genet, 2016 06;53:366-76). Functional analysis of this alteration revealed CHEK2-mediated DNA damage response is similar to wild-type; however, this alteration has also been reported to result in partially reduced CHEK2 kinase activity (Wu X et al. Hum. Mutat. 2006 Aug;27(8):742-7; Roeb W, Higgens J, and King MC. Hum. Mol. Genet. 2012 Jun;21(12):2738-44). This residue is located in the alpha-helix of the kinase c-lobe domain; proline substitutions are typically destabilizing to the protein structure in alpha-helix regions (Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13(1):R6). This amino acid position is well 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.

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.