22-28696959-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM5PP3_StrongPP5
The NM_007194.4(CHEK2):c.1037G>A(p.Arg346His) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R346C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_007194.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251242Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135800
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460894Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726798
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
Familial cancer of breast Pathogenic:1Uncertain:3
- -
- -
This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 37449874, 34903604, 31050813]. This variant is expected to disrupt protein structure [PMID: 16794575]. -
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 346 of the CHEK2 protein (p.Arg346His). This variant is present in population databases (rs730881688, gnomAD 0.002%). This missense change has been observed in individual(s) with breast cancer (PMID: 21244692, 26822949, 31050813, 34326862, 35534704). ClinVar contains an entry for this variant (Variation ID: 182431). 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. Experimental studies have shown that this missense change affects CHEK2 function (PMID: 30851065, 31050813, 37449874). 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. -
Hereditary cancer-predisposing syndrome Uncertain:3
- -
This missense variant replaces arginine with histidine at codon 346 of the CHEK2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Experimental studies have shown a deleterious effect on protein function in CHEK2 kinase activity studies (PMID 31050813, 34903604, 37449874) and in a yeast-based DNA damage repair assay (PMID 30851065). This variant has been reported in individuals affected with breast cancer (PMID: 21244692, 26822949, 29522266, 31050813, 33471991, 37449874) and prostate cancer in the literature (PMID: 31214711). However, a meta-analysis of 12 case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls, did not report a significant association between this variant and breast cancer due to too few affected cases (PMID: 37449874; OR=3.6411, 95% CI 0.735-18.041, P = 0.1135 at medcalc.org). This variant has been identified in 3/282644 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although the available evidence indicates that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
The p.R346H variant (also known as c.1037G>A), located in coding exon 9 of the CHEK2 gene, results from a G to A substitution at nucleotide position 1037. The arginine at codon 346 is replaced by histidine, an amino acid with highly similar properties. In one study, this variant was detected in conjunction with another CHEK2 alteration (p.E239K) in 1/1303 female breast cancer cases and 0/1109 cancer-free controls (Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13(1):R6). In another large study, this variant was reported in 6/60,466 breast cancer cases and in 2/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). Several other studies have reported this alteration in individuals suspected to be affected with hereditary breast cancer (Young EL et al. J Med Genet, 2016 06;53:366-76; Hauke J et al. Cancer Med, 2018 04;7:1349-1358). Earlier functional analyses for this alteration reported neutral or conflicting results (Kleiblova P. Int J Cancer. 2019 10;145(7):1782-1797; Kleiblová P. et al Klin Onkol. 2019;32(Supplementum2):36-50), but this variant was reported as non-functional in a yeast-based assay (Delimitsou A et al. Hum Mutat. 2019 May;40(5):631-648 ), and more recent studies performed in murine embyonic and human cell lines support a deleterious impact (Boonen RACM et al. Cancer Res, 2022 02;82:615-631; Stolarova L et al. Clin Cancer Res. 2023 Aug;29(16):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. Based on the available evidence, the clinical significance of this variant remains unclear. -
not provided Pathogenic:1Uncertain:1
The frequency of this variant in the general population, 0.000023 (3/129024 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer (PMID: 21244692 (2011), 31050813 (2019)) and in breast cancer cases and controls in a large-scale breast cancer association study (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/CHEK2)). In addition, this variant was demonstrated to have a damaging effect on CHEK2 protein function in functional analyses (PMID: 30851065 (2019) and 34903604 (2021)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -
Identified in individuals with personal and/or family history of breast cancer (PMID: 21244692, 29522266, 31050813, 34903604, 37449874); Published functional studies demonstrate a damaging effect: impaired auto-phosphorylation, reduced/absent kinase activity, and defective DNA-damage response in yeast and cell-based assays (PMID: 30851065, 39146382, 31050813, 34903604); 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.1166G>A, p.(R389H); This variant is associated with the following publications: (PMID: 27071721, 27294619, 31056747, 26424751, 26787654, 21244692, 28188106, 27191893, 29522266, 30851065, 31050813, 33471991, 31206626, 26822949, 37449874, 36243179, 22419737, 19782031, 39642869, 34326862, 34903604, 35534704, 38415346, 39146382) -
Hereditary nonpolyposis colon cancer Pathogenic:1
- -
not specified Uncertain:1
Variant summary: CHEK2 c.1037G>A (p.Arg346His) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719); Serine/threonine-protein kinase, active site (IPR008271) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 7.7e-06 in 260390 control chromosomes (gnomAD, publications). c.1037G>A has been reported in the literature in individuals affected with Breast And Ovarian Cancer or Bilary tract cancer (examples: Okawa_2023, deOliveira_2021, Dorling_2021, Kleiblova_2019, Lhota_2016, Le Calvez-Kelm_2011), but the variant was also transmitted to unaffected individuals within a family, albeit the age of the unaffected individuals with the variant was early 40s (Kleiblova_2019). These data indicate that the variant may be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function: in vitro assays showed the variant protein had reduced ability to phosphorylate target substrate (Kleiblova_2019), and a functional yeast assay using a DNA repair deficient yeast strain showed the variant protein was incapable of rescuing cell growth and proliferation following MMS induced DNA damage (Delimitsou_2019). The most pronounced variant effect results in <10% of normal activity. The following publications have been ascertained in the context of this evaluation (PMID: 30851065, 33471991, 31050813, 21244692, 26822949, 36243179, 35534704). Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=6) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Predisposition to cancer Uncertain:1
The CHEK2 c.1037G>A (p.Arg346His) missense change has a maximum subpopulation frequency of 0.002% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a deleterious effect on protein function, and functional studies support a deleterious impact (PMID: 30851065, 31050813, 34903604). This variant has been observed in individuals with breast cancer (PMID: 21244692, 26822949, 31050813). In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance. -
CHEK2-related cancer predisposition Other:1
Variant interpreted as Uncertain significance and reported on 12-21-2017 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at