Total submissions: 2
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Fulgent Genetics, |
RCV005036840 | SCV005663120 | uncertain significance | Li-Fraumeni syndrome 2; Bone osteosarcoma; Familial prostate cancer | 2024-06-18 | criteria provided, single submitter | clinical testing | |
| Department of Genetics, |
RCV003494019 | SCV004242320 | likely pathogenic | Li-Fraumeni syndrome 2 | 2023-05-01 | no assertion criteria provided | clinical testing | Variant summary: CHEK2 c.844C>G results in the replacement of His282 by an Asp residue (p.His282Asp). 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 45 years (luminal-A tumor phenotype). One first-degree relative of her was also diagnosed with BC, although a co-segregation study could not be performed. His282 is located in the kinase domain, and appears well-conserved in vertebrate species. This histidine is found at the protein surface, putatively forming a cation/π interaction with Tyr337. Substitution of His282 by aspartate implies the loss of the positive charge of the histidine and the introduction of a smaller, negatively charged residue, which may affect the abovementioned interaction with Tyr337. Moreover, His282 does not appear to be directly related to any of the CHEK2 conserved motifs and key functional elements either. Our in-silico study on the protein stability based on relaxation molecular dynamics simulations (doi: 10.3389/fgene.2023.1274108) indicates that His282Asp does not induce conformational unstability on CHEK2 protein. The variant has not been reported in gnomAD v4 or ClinVar as of now. Other replacements described at this position (H282Q, H282R, H282N, and H282Y) are 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 His282Asp as Pathogenic, whereas the ACMG classification tool Franklin suggests this variant as VUS (Uncertain Significance). No functional study on this variation has been reported so far. However, this variant is annotated in VarSome as affecting the splicing, which could explain its pathogenicity. All this information, even if not conclusive, appears to indicate this variant have more chances of being Pathogenic. |