CHEK2 c.485A>G, p.Asp162Gly
NM_007194.4:c.485A>G
Variant of Uncertain Significance (VUS)
CHEK2 D162G is extremely rare in population databases (PM2) and computational and database evidence support a deleterious effect (PP3, PP5), but no functional, segregation, de novo, or case-control data are available. With one Moderate and two Supporting criteria, the variant remains a VUS.
ACMG/AMP Criteria Applied
PM2
PP3
PP5
Genetic Information
Gene & Transcript Details
Gene
CHEK2
Transcript
NM_007194.4
MANE Select
Total Exons
15
Strand
Reverse (−)
Reference Sequence
NC_000022.10
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_007194.3 | Alternative | 15 exons | Reverse |
Variant Details
HGVS Notation
NM_007194.4:c.485A>G
Protein Change
D162G
Location
Exon 4
(Exon 4 of 15)
5'Exon Structure (15 total)3'
Functional Consequence
Loss of Function
Related Variants
No evidence of other pathogenic variants at position 162 in gene CHEK2
Variant interpretation based on transcript NM_007194.4
Genome Browser
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HGVS InputNM_007194:c.485A>G
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Clinical Data
Global Frequency
0.000398%
Extremely Rare
Highest in Population
European (non-Finnish)
0.000879%
Very Rare
Global: 0.000398%
European (non-Finnish): 0.000879%
0%
0.05%
0.1%
1%
5%
10%+
Allele Information
Total: 251408Alt: 1Homozygotes: 0
ACMG Criteria Applied
PM2
This variant is present in gnomAD (MAF= 0.000398%, 1/251408 alleles, homozygotes = 0) and at a higher frequency in the European (non-Finnish) population (MAF= 0.000879%, 1/113702 alleles, homozygotes = 0). The variant is rare (MAF < 0.1%), supporting PM2 criterion application.
Classification
5 publications
Likely Pathogenic
Based on 9 submitter reviews in ClinVar
Submitter Breakdown
1 Path
2 LP
6 VUS
Pathogenic
Likely Path.
VUS
Likely Benign
Benign
Publications (5)
This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 162 of the CHEK2 protein (p.Asp162Gly). This variant is present in population databases (rs587781652, gnomAD 0.0009%). This missense change has been observed in individual(s) with prostate cancer (PMID: 34903604). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 141314). 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, 34903604). Studies have shown that this missense change is associated with inconclusive levels of altered splicing (internal data). For these reasons, this variant has been classified as Pathogenic.
The p.D162G variant (also known as c.485A>G), located in coding exon 3 of the CHEK2 gene, results from an A to G substitution at nucleotide position 485. The aspartic acid at codon 162 is replaced by glycine, an amino acid with similar properties. This alteration was reported in a Brazilian cohort of breast cancer patients (Urbina-Jara LK et al. Genes (Basel), 2019 10;10:). This alteration behaved as non-functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum. Mutat., 2019 05;40:631-648). This alteration was also reported as damaging in an mES cell-based assay of CHEK2 activity (Boonen RACM et al. Cancer Res, 2022 02;82:615-631). This alteration was also reported as functionally impaired in another study using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells (Stolarova L et al. Clin Cancer Res, 2023 Jul;:OF1-OF14). 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.
This missense variant replaces aspartic acid with glycine at codon 162 of the CHEK2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have demonstrated this variant was damaging in a yeast-based DNA damage response assay (PMID: 30851065), a mouse embryonic stem cell-based kinase assay (PMID: 34903604), and in CHK2 autophosphorylation and KAP1 phosphorylation assays (PMID: 37449874). This variant has been reported in an individuals affected with breast cancer (PMID: 30535581, 31658756, 38153744) and in three brothers affected with prostate cancer (PMID: 34903604). This variant has been identified in 1/251408 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.
Variant summary: CHEK2 c.485A>G (p.Asp162Gly) results in a non-conservative amino acid change located in the Forkhead-associated (FHA) domain (IPR000253) 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 4e-06 in 251408 control chromosomes. c.485A>G has been reported in the literature in a setting of whole exome sequencing in heterozygous individuals affected with prostate cancer from a single family (e.g. Boonen_2022), and in at least one individual at high risk for breast/ovarian cancer (e.g. Ciprano_2019). These data indicate that the variant may be associated with disease. Several publications report experimental evidence the variant leads to suggesting impaired protein function measured at ~10-30% of normal or kinase activity in all assays. These studies include a yeast-based growth assay (e.g. Delimitsou_2019), an mES-based cell assay measuring CHEK2 kinase activity (e.g. Boonen_2022), and CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells (e.g. Stolarova_2023). The following publications have been ascertained in the context of this evaluation (PMID: 30535581, 30851065, 34903604, 37449874). ClinVar contains an entry for this variant (Variation ID: 141314). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Clinical Statement
This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Pathogenic (1 clinical laboratories).
Functional Impact
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain (0 mutations).
Related Variants in This Domain
No evidence of other pathogenic variants at position 162 in gene CHEK2
Computational Analysis
Pathogenicity Predictions
REVEL Score
0.955
0.955
Likely Benign0.0
Uncertain (Low)0.2
Uncertain (Med)0.5
Likely Pathogenic0.75
REVEL scores ≥ 0.75 are strong evidence (PP3)
Predictor Consensus
Mixed/VUS
PP3 Applied
Yes
Additional Predictors
Benign:
CADD: 1.51polyphen_prediction: benignmetasvm: Tmetalr: Tprimateai: T
Neutral: Show all
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
PVS1
PVS1 (Not Applied) Strength Modified
According to standard ACMG guidelines, PVS1 rule is: "Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LoF) is a known mechanism of disease". The evidence for this variant shows it is a missense change (D162G), not a null variant. Therefore, this criterion is not applied.
PS1
PS1 (Not Applied) Strength Modified
According to standard ACMG guidelines, PS1 rule is: "Same amino acid change as a previously established pathogenic variant regardless of nucleotide change". The evidence for this variant shows no previously established pathogenic variant at amino acid position D162. Therefore, this criterion is not applied.
PS2
PS2 (Not Applied) Strength Modified
According to standard ACMG guidelines, PS2 rule is: "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history". There are no de novo data available for this variant. Therefore, this criterion is not applied.
PS3
PS3 (Not Applied) Strength Modified
According to standard ACMG guidelines, PS3 rule is: "Well-established functional studies supportive of a damaging effect on the gene or gene product". No functional studies have been performed for CHEK2 D162G. Therefore, this criterion is not applied.
PS4
PS4 (Not Applied) Strength Modified
According to standard ACMG guidelines, PS4 rule is: "Prevalence in affected individuals significantly increased compared with controls". No case-control or prevalence data in affected cohorts are available. Therefore, this criterion is not applied.
PM1
PM1 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM1 rule is: "Located in a mutational hot spot or well-established functional domain without benign variation". The D162 position is not known to be a mutational hotspot or within a well-established functional domain exclusive of benign variation. Therefore, this criterion is not applied.
PM2
PM2 (Moderate)
According to standard ACMG guidelines, PM2 rule is: "Absent from controls (or at extremely low frequency if recessive)". The evidence for this variant shows a minor allele frequency of 0.000398% in gnomAD, which is extremely rare. Therefore, this criterion is applied at Moderate strength because the variant is absent or at extremely low frequency in controls.
PM3
PM3 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM3 rule is: "Detected in trans with a pathogenic variant for recessive disorders". CHEK2-associated disease is dominantly inherited, and no trans data are relevant. Therefore, this criterion is not applied.
PM4
PM4 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM4 rule is: "Protein length changes due to in-frame deletions/insertions or stop-loss variants". This variant is a missense change without length alteration. Therefore, this criterion is not applied.
PM5
PM5 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM5 rule is: "Novel missense change at an amino acid residue where a different pathogenic missense change has been seen". There is no evidence of a different pathogenic missense variant at residue D162. Therefore, this criterion is not applied.
PM6
PM6 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM6 rule is: "Assumed de novo, but without confirmation of paternity and maternity". There are no de novo data for this variant. Therefore, this criterion is not applied.
PP1
PP1 (Not Applied) Strength Modified
According to standard ACMG guidelines, PP1 rule is: "Co-segregation with disease in multiple affected family members". No segregation data are available. Therefore, this criterion is not applied.
PP2
PP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, PP2 rule is: "Missense variant in a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease". Although CHEK2 exhibits pathogenic missense variants, there is insufficient evidence to confirm a low benign missense variation rate. Therefore, this criterion is not applied.
PP3
PP3 (Supporting)
According to standard ACMG guidelines, PP3 rule is: "Multiple lines of computational evidence support a deleterious effect on the gene or gene product". The evidence for this variant shows a REVEL score of 0.95, exceeding the 0.75 threshold, supporting a deleterious effect. Therefore, this criterion is applied at Supporting strength.
PP4
PP4 (Not Applied) Strength Modified
According to standard ACMG guidelines, PP4 rule is: "Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology". No phenotype or family history data are provided. Therefore, this criterion is not applied.
PP5
PP5 (Supporting)
According to standard ACMG guidelines, PP5 rule is: "Reputable source reports variant as pathogenic, but without accessible evidence". ClinVar submissions include Likely Pathogenic and Pathogenic classifications from reputable laboratories. Therefore, this criterion is applied at Supporting strength.
BA1
BA1 (Not Applied) Strength Modified
According to standard ACMG guidelines, BA1 rule is: "Allele frequency is too high for the disorder". The allele frequency (0.000398%) is far below the BA1 threshold (>5%). Therefore, this criterion is not applied.
BS1
BS1 (Not Applied) Strength Modified
According to standard ACMG guidelines, BS1 rule is: "Allele frequency is greater than expected for the disorder". The allele frequency is extremely low and not greater than expected. Therefore, this criterion is not applied.
BS2
BS2 (Not Applied) Strength Modified
According to standard ACMG guidelines, BS2 rule is: "Observed in healthy adult individuals for a dominant disorder with full penetrance expected at an early age". There are no data observing this variant in healthy, phenotyped adults. Therefore, this criterion is not applied.
BS3
BS3 (Not Applied) Strength Modified
According to standard ACMG guidelines, BS3 rule is: "Well-established functional studies show no damaging effect on protein function or splicing". No functional studies are available. Therefore, this criterion is not applied.
BS4
BS4 (Not Applied) Strength Modified
According to standard ACMG guidelines, BS4 rule is: "Lack of segregation in affected family members". Segregation data are not provided. Therefore, this criterion is not applied.
BP1
BP1 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP1 rule is: "Missense variant in a gene where only LoF causes disease". CHEK2 disease mechanism includes both LoF and pathogenic missense variants. Therefore, this criterion is not applied.
BP2
BP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP2 rule is: "Observed in trans with a pathogenic variant for a dominant disorder". No in trans data are available. Therefore, this criterion is not applied.
BP3
BP3 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP3 rule is: "In-frame deletions/insertions in a repetitive region without known function". This variant is a missense change, not an in-frame indel. Therefore, this criterion is not applied.
BP4
BP4 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP4 rule is: "Multiple lines of computational evidence suggest no impact on gene or gene product". Computational evidence (REVEL 0.95) supports impact, not benign. Therefore, this criterion is not applied.
BP5
BP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP5 rule is: "Variant found in a case with an alternate molecular basis for disease". No such data are provided. Therefore, this criterion is not applied.
BP6
BP6 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP6 rule is: "Reputable source reports variant as benign, but without accessible evidence". No reputable source classifies this variant as benign. Therefore, this criterion is not applied.
BP7
BP7 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP7 rule is: "Synonymous variant with no predicted impact on splicing". This variant is missense, not synonymous. Therefore, this criterion is not applied.