Submissions for variant NM_007194.4(CHEK2):c.1033C>T (p.His345Tyr)

dbSNP: rs864622537

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000205862	SCV000261022	uncertain significance	Familial cancer of breast	2022-10-05	criteria provided, single submitter	clinical testing	This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 345 of the CHEK2 protein (p.His345Tyr). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 220465). 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"). 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.
Ambry Genetics	RCV000565935	SCV000669240	uncertain significance	Hereditary cancer-predisposing syndrome	2023-09-08	criteria provided, single submitter	clinical testing	The p.H345Y variant (also known as c.1033C>T), located in coding exon 9 of the CHEK2 gene, results from a C to T substitution at nucleotide position 1033. The histidine at codon 345 is replaced by tyrosine, an amino acid with similar properties. This alteration has been reported in both breast and/or ovarian cancer cohort patients, as well as unaffected control individuals across studies (Decker B et al. J Med Genet, 2017 Nov;54:732-741; Dorling et al. N Engl J Med 2021 02;384:428-439; Hauke J et al. Cancer Med, 2018 Apr;7:1349-1358; Song H et al. J Med Genet, 2021 May;58:305-313). This alteration was reported as functionally impaired in a study assessing CHEK2-complementation through quantification of KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells (Stolarova L et al. Clin Cancer Res, 2023 Aug;29:3037-3050). This amino acid position is highly 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.
Counsyl	RCV000205862	SCV000786094	uncertain significance	Familial cancer of breast	2018-02-20	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000565935	SCV001351702	uncertain significance	Hereditary cancer-predisposing syndrome	2019-02-08	criteria provided, single submitter	clinical testing
GeneDx	RCV001566699	SCV001790259	uncertain significance	not provided	2019-07-26	criteria provided, single submitter	clinical testing	Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV003150092	SCV003838783	uncertain significance	Breast and/or ovarian cancer	2021-06-15	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000205862	SCV004020099	uncertain significance	Familial cancer of breast	2023-03-08	criteria provided, single submitter	clinical testing	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.
Baylor Genetics	RCV000205862	SCV004217512	uncertain significance	Familial cancer of breast	2023-10-11	criteria provided, single submitter	clinical testing
Department of Genetics, HCU Lozano Blesa	RCV003493502	SCV004242321	likely pathogenic	Li-Fraumeni syndrome 2	2023-05-01	no assertion criteria provided	clinical testing	Variant summary: CHEK2 c.1033C>T results in the replacement of His345 by a Tyr residue (p.His345Tyr). The variant was identified in 1 out of 396 patients analysed (freq: 0.0025, doi: 10.3389/fgene.2023.1274108). The patient was a woman that developed breast cancer at the age of 38 years (luminal-B tumor phenotype). One first-degree relative of her was also diagnosed with BC, although a co-segregation study could not be performed. His345 is located in the kinase domain, and is part of the well-conserved motif HRD (His345–Arg-346–Asp347) in the catalytic loop of the protein. In this motif, His345 establishes an H-bond with the key catalytic residue Asp347. Thus, its replacement by a Tyr residue (bulkier) may detrimentally affect the catalytic activity of the protein. In addition, His345 forms a fair H-bond (~2.7 Å) with the backbone of Asp368, located in the activation T-loop crucial for homodimerization. The variant is reported in gnomAD v4 in 23 cases out of 1460156 alleles analysed (freq=1.6x10-3 %). In ClinVar 8 reports appear classifying the variant as of Uncertain significance. Other replacements found at this position (H345Q, H345P, H345R, H345L, and H345D) are also classified by ClinVar as of Uncertain Significance. The metapredictor PirePred (relies on verdicts from other 15 predictor or metapredictor tools) and the AI-based predictor AlphaMissense classify His345Tyr as Pathogenic, whereas the ACMG classification tool Franklin suggests this variant as VUS (Uncertain Significance). Our in-silico study on the protein stability based on relaxation molecular dynamics simulations (doi: 10.3389/fgene.2023.1274108) indicates that His345Tyr induces conformational unstability on CHEK2 protein. Moreover, Stolarova L. et al’s functional study on KAP1 phosphorylation and CHEK2 autophosphorylation protein capability reports this variant as functionally impaired (PMID: 37449874). With all this information, we believe this variant have more chances of being Pathogenic.