rs878854922

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_007194.4(CHEK2):​c.762G>T​(p.Arg254Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

CHEK2
NM_007194.4 missense

Scores

1
4
14

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:2

Conservation

PhyloP100: 2.28
Variant links:
Genes affected
CHEK2 (HGNC:16627): (checkpoint kinase 2) In response to DNA damage and replication blocks, cell cycle progression is halted through the control of critical cell cycle regulators. The protein encoded by this gene is a cell cycle checkpoint regulator and putative tumor suppressor. It contains a forkhead-associated protein interaction domain essential for activation in response to DNA damage and is rapidly phosphorylated in response to replication blocks and DNA damage. When activated, the encoded protein is known to inhibit CDC25C phosphatase, preventing entry into mitosis, and has been shown to stabilize the tumor suppressor protein p53, leading to cell cycle arrest in G1. In addition, this protein interacts with and phosphorylates BRCA1, allowing BRCA1 to restore survival after DNA damage. Mutations in this gene have been linked with Li-Fraumeni syndrome, a highly penetrant familial cancer phenotype usually associated with inherited mutations in TP53. Also, mutations in this gene are thought to confer a predisposition to sarcomas, breast cancer, and brain tumors. This nuclear protein is a member of the CDS1 subfamily of serine/threonine protein kinases. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 22-28711939-C-A is Pathogenic according to our data. Variant chr22-28711939-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 240753.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Likely_pathogenic=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHEK2NM_007194.4 linkuse as main transcriptc.762G>T p.Arg254Ser missense_variant 6/15 ENST00000404276.6 NP_009125.1 O96017-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHEK2ENST00000404276.6 linkuse as main transcriptc.762G>T p.Arg254Ser missense_variant 6/151 NM_007194.4 ENSP00000385747.1 O96017-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Familial cancer of breast Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 20, 2023In 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 tolerated. ClinVar contains an entry for this variant (Variation ID: 240753). This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 254 of the CHEK2 protein (p.Arg254Ser). -
Likely pathogenic, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Jun 26, 2023This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. -
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 21, 2024The p.R254S variant (also known as c.762G>T), located in coding exon 5 of the CHEK2 gene, results from a G to T substitution at nucleotide position 762. The arginine at codon 254 is replaced by serine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). In addition, the in silico prediction for this missense impact of this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.58
BayesDel_addAF
Uncertain
0.10
D
BayesDel_noAF
Benign
-0.090
CADD
Pathogenic
34
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
T;.;T;.;T;.;T;.;.;.;.;.;.
Eigen
Benign
0.067
Eigen_PC
Benign
0.20
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.85
.;T;.;D;.;D;D;T;.;D;D;D;D
M_CAP
Benign
0.021
T
MetaRNN
Benign
0.28
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.73
T
MutationAssessor
Benign
0.89
L;L;L;.;L;.;L;.;L;.;.;.;.
PrimateAI
Uncertain
0.64
T
PROVEAN
Benign
-1.6
N;N;N;.;N;N;.;N;N;N;.;N;N
REVEL
Benign
0.18
Sift
Benign
0.36
T;T;T;.;T;T;.;T;T;T;.;T;T
Sift4G
Benign
0.62
T;T;T;.;T;T;.;T;T;T;.;.;D
Polyphen
0.0060
B;D;B;.;B;B;B;P;D;.;.;.;.
Vest4
0.61
MutPred
0.55
Loss of solvent accessibility (P = 0.0193);Loss of solvent accessibility (P = 0.0193);Loss of solvent accessibility (P = 0.0193);.;Loss of solvent accessibility (P = 0.0193);.;Loss of solvent accessibility (P = 0.0193);.;Loss of solvent accessibility (P = 0.0193);.;.;.;.;
MVP
0.74
MPC
0.022
ClinPred
0.75
D
GERP RS
5.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.45
gMVP
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.97
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.97
Position offset: 2
DS_DL_spliceai
0.61
Position offset: -30

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs878854922; hg19: chr22-29107927; API