ClinVar Genomic variation as it relates to human health

The p.E302D variant (also known as c.906A>C), located in coding exon 7 of the CHEK2 gene, results from an A to C substitution at nucleotide position 906. The glutamic acid at codon 302 is replaced by aspartic acid, an amino acid with highly similar properties. This alteration was detected in 1/5589 German BRCA1/2-negative probands diagnosed with breast cancer (Hauke J et al. Cancer Med, 2018 Apr;7:1349-1358). This alteration behaved as semi-functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum Mutat, 2019 05;40:631-648). This alteration has also been reported in 2/1197 individuals from Greece, Romania, and Turkey undergoing evaluation for inherited cancer predisposition (Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Variant summary: CHEK2 c.906A>C (p.Glu302Asp) results in a conservative amino acid change located in the Protein kinase domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 3e-05 in 202734 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.906A>C has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Tsaousis_2019, Rizzolo_2019, Bucalo_2023) without evidence for causality. These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 37262986, 30613976, 31159747). ClinVar contains an entry for this variant (Variation ID: 128087). Based on the evidence outlined above, the variant was classified as uncertain significance.

The CHEK2 c.906A>C variant is predicted to result in the amino acid substitution p.Glu302Asp. This variant was reported in an individual with male breast cancer and individuals undergoing genetic testing for hereditary cancer predisposition (Table S5, Tsaousis et al. 2019. PubMed ID: 31159747; Table S3, referred to as c.1035A>C (p.Glu345Asp), Rizzolo et al. 2019. PubMed ID: 30613976; Table S1, Vargas-Parra et al. 2020. PubMed ID: 32906215). Experimental studies using a yeast-based system suggest this variant is semi-functional (Table 1, Delimitsou et al. 2019. PubMed ID: 30851065). This variant is reported in 0.0067% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-29099495-T-G) and is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/128087/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 302 of the CHEK2 protein (p.Glu302Asp). This variant is present in population databases (rs587780190, gnomAD 0.007%). This missense change has been observed in individual(s) with CHEK2-related cancers (PMID: 30613976, 31159747). This variant is also known as c.1035A>C p.Glu345Asp. ClinVar contains an entry for this variant (Variation ID: 128087). 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. 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.

Published functional studies are inconclusive: intermediate response to DNA damage (Delimitsou 2019); Identified in individuals with personal or family history of breast/ovarian cancer (Rizzolo 2019, Tsaousis 2019, Vargas-Parra 2020); 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; Also known as c.1035A>C; p.Glu345Asp; This variant is associated with the following publications: (PMID: 31159747, 22419737, 19782031, 32906215, 30613976, 33320972, 30851065)

This missense variant replaces glutamic acid with aspartic acid at codon 302 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). A functional study has demonstrated an intermediate impact of this variant on CHEK2 protein function in a yeast-based DNA damage response assay (PMID: 30851065). This variant has been reported in individuals affected with breast cancer (PMID: 29522266, 30613976). In a large breast cancer case-control meta analysis conducted by the BRIDGES consortium, this variant was reported in 3/60466 cases and 3/53461 unaffected controls (PMID: 33471991; Leiden Open Variation Database DB-ID CHEK2_000406). This variant has been identified in 8/234112 chromosomes 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.

The CHEK2 p.Glu302Asp variant was not identified in the literature. The variant was identified in dbSNP (rs587780190) as “with uncertain significance allele” and ClinVar (classified as uncertain significance by Invitae, Color, GeneDx, Ambry Genetics, and 3 other submitters). The variant was identified in control databases in 8 of 234,112 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Latino in 2 of 29,918 chromosomes (freq: 0.00007) and European in 6 of 101,258 chromosomes (freq: 0.00006), while the variant was not observed in the African, Ashkenazi Jewish, East Asian, Finnish, Other or South Asian populations. The p.Glu302 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 p.Glu302Asp variant occurs in the last codon of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. 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.