rs564605612

chr22-28694042-G-Achr22-28694042-G-Cchr22-28694042-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_007194.4(CHEK2):c.1451C>T(p.Pro484Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000119 in 1,593,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. P484S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00037 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000092 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:14 B:1
• Conservation: PhyloP100: 7.00

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08254403).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.1451C>T	p.Pro484Leu	missense_variant	13/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.1451C>T	p.Pro484Leu	missense_variant	13/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.000375 AC: 57 AN: 152140 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00295

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000956

GnomAD3 exomes AF: 0.0000770 AC: 18 AN: 233788 Hom.: 0 AF XY: 0.0000935 AC XY: 12 AN XY: 128360

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000233

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000330

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000828

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000916 AC: 132 AN: 1441408 Hom.: 0 Cov.: 30 AF XY: 0.0000920 AC XY: 66 AN XY: 717600

Gnomad4 AFR exome AF: 0.0000600

Gnomad4 AMR exome AF: 0.000358

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000802

Gnomad4 OTH exome AF: 0.000367

GnomAD4 genome AF: 0.000374 AC: 57 AN: 152258 Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30 AN XY: 74436

Gnomad4 AFR AF: 0.0000722

Gnomad4 AMR AF: 0.00294

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.000277 Hom.: 0

Bravo AF: 0.000657

ExAC AF: 0.000112 AC: 13

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:14 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial cancer of breast Uncertain:3 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 484 of the CHEK2 protein (p.Pro484Leu). This variant is present in population databases (rs564605612, gnomAD 0.03%). This missense change has been observed in individual(s) with breast cancer and/or mesothelioma (PMID: 21244692, 25186627, 31206626, 31780696, 34008015). ClinVar contains an entry for this variant (Variation ID: 140938). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 30851065, 31780696). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Feb 26, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 17, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 09, 2023	This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. -

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 10, 2023	In the published literature, the variant has been reported in individuals with breast cancer (PMIDs: 33471991 (2021) see also LOVD https://databases.lovd.nl/shared/variants/CHEK2), 31742824 (2020), 31206626 (2019), 31780696 (2019), 25186627 (2015), and 21244692 (2011)). This variant has been reported to have no effect on CHEK2 DNA damage response (PMID: 30851065 (2019)), however additional studies are required to determine the global effect of this variant on CHEK2 protein function. The frequency of this variant in the general population, 0.000081 (10/124182 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 07, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 30, 2023	Observed in individuals with a personal or family history of breast and/or ovarian cancer, as well as in controls (Le Calvez-Kelm et al., 2011; Tung et al., 2015; Capriotti et al., 2017; Yadav et al., 2017; Dutil et al., 2019; Dorling et al., 2021); Published functional studies are conflicting: DNA damage response and cell growth comparable to wildtype in a yeast-based assay (Delimitsou et al., 2019), but reduced stability and decreased kinase activity, with retained autophosphorylation, in a human cell line (Dutil et al., 2019); 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; This variant is associated with the following publications: (PMID: 25186627, 21244692, 26787654, 27878467, 28102005, 31106920, 30851065, 31780696, 32310333, 31742824, 34008015, 22419737, 19782031, 33471991) -

Hereditary cancer-predisposing syndrome Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 31, 2023	The p.P484L variant (also known as c.1451C>T), located in coding exon 12 of the CHEK2 gene, results from a C to T substitution at nucleotide position 1451. The proline at codon 484 is replaced by leucine, an amino acid with similar properties. This alteration has been reported in 1/1303 breast cancer patients and was absent from 1109 healthy controls (Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13:R6). This variant was observed in 1/3251 individuals who met eligibility criteria for hereditary breast and ovarian cancer syndrome (Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). This alteration was detected in 1/1054 Hispanic BRCA1/2-negative probands with hereditary breast cancer and 0/1189 controls (Weitzel JN et al. Cancer, 2019 Aug;125:2829-2836). This variant was reported in 5/60,466 breast cancer cases and in 1/53,461 controls in another study (Dorling et al. N Engl J Med. 2021 02;384:428-439). In addition, this alteration has been detected in a cohort of 122 patients who underwent multi-gene panel testing for hereditary cancer after having previously tested negative for mutations in BRCA1 and BRCA2 (Yadav S et al. Fam. Cancer. 2017 07;16:319-328). This alteration behaved as functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum. Mutat. 2019 05;40(5):631-648). However, another in vitro kinase assay showed p.P484L to be damaging (Dutil J et al. Sci. Rep. 2019 11;9(1):17769). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Nov 23, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 15, 2023	This missense variant replaces proline with leucine at codon 484 of the CHEK2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study has demonstrated this variant to be benign in a yeast-based DNA damage repair assay (PMID: 30851065). This variant has been reported in individuals affected with breast cancer (PMID: 21244692, 25186627, 31780696, Lovejoy 2018, 33471991), prostate cancer (PMID: 31214711), or had a personal or family history of breast and/or ovarian cancer (PMID: 31742824). This variant has also been identified in 22/265184 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. -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 30, 2023	Variant summary: CHEK2 c.1451C>T (p.Pro484Leu) results in a non-conservative amino acid change located in the protein kinase domain (IPR000719) 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 8.2e-05 in 267402 control chromosomesm (gnomAD, Calvez-Kelm_2011). This frequency is not significantly higher than estimated for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome (8.2e-05 vs 0.00031), allowing no conclusion about variant significance. c.1451C>T has been reported in the literature in individuals affected with breast and other cancers (e.g. Young_2016, Calvez-Kelm_2011, Tung_2014, Yadav_2016, Dutil_2019, Shao_2019, Weitzel_2019, Dorling_2021, Cheung_2021), but have also been seen in individuals over age 70 with no history of cancer (FLOSSIES database). These data do not allow any conclusion about variant significance. Several publications report experimental evidence evaluating an impact on protein function, with conflicting results. The variant was classified as benign following assessment in a yeast-based assay (Delimitsou_2019), but was shown to significantly reduce kinase activity when expressed in HEK293T cells (Duhl_2019). The following publications have been ascertained in the context of this evaluation (PMID: 21244692, 25186627, 26787654, 27878467, 30851065, 31206626, 31742824, 31780696, 33471991, 34008015). Ten ClinVar submitters have assessed the variant since 2014: all have classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 16, 2020	DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.1451C>T, in exon 13 that results in an amino acid change, p.Pro484Leu. This sequence change has been described in the gnomAD database with a frequency of 0.03% in the Latino sub-population (dbSNP rs564605612). The p.Pro484Leu change has been reported in individuals with breast cancer (PMIDs: 21244692, 25186627, 31780696). Functional studies have demonstrated conflicting results; Dutil et al., 2019 reported dramatically decreased levels of protein expression compared to wild type, while Delimitsou et al., 2019 reported that this variant did not have a substantial impact on protein function (PMIDs: 31780696, 30851065). The p.Pro484Leu change affects a highly conserved amino acid residue located in a domain of the CHEK2 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Pro484Leu substitution. Due to these contrasting evidences, the clinical significance of the p.Pro484Leu change remains unknown at this time. -

Breast and/or ovarian cancer Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Jan 08, 2021

- -

CHEK2-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 02, 2024

The CHEK2 c.1451C>T variant is predicted to result in the amino acid substitution p.Pro484Leu. This variant has been observed in individuals with breast cancer, but its pathogenicity was not established (Le Calvez-Kelm et al. 2011. PubMed ID: 21244692; Tung et al. 2014. PubMed ID: 25186627; Yadav et al. 2017. PubMed ID: 27878467; Shao et al. 2020. PubMed ID: 31742824). An in vitro functional assay showed that this variant leads to decreased kinase activity (Dutil et al. 2019. PubMed ID: 31780696). This variant is reported in 0.026% of alleles in individuals of Latino descent in gnomAD and is interpreted as uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/140938/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Familial cancer of breast;C0346629:Colorectal cancer;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C1836482:Li-Fraumeni syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 25, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.0026	T
BayesDel_noAF	Uncertain	0.050
Cadd	Pathogenic	30
Dann	Uncertain	1.0
DEOGEN2	Benign	0.35	T;.;T;.;T;.;T;.;.
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.97	D
M_CAP	Benign	0.066	D
MetaRNN	Benign	0.083	T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.12	D
MutationAssessor	Pathogenic	3.3	M;.;M;.;M;.;M;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.56	T
PROVEAN	Pathogenic	-6.8	D;D;D;.;D;D;.;D;D
REVEL	Uncertain	0.52
Sift	Uncertain	0.0080	D;D;D;.;D;D;.;D;D
Sift4G	Uncertain	0.0070	D;D;D;.;D;D;.;D;D
Polyphen		1.0	D;D;D;.;D;D;D;D;D
Vest4		0.81
MutPred		0.77		Loss of disorder (P = 0.037);.;Loss of disorder (P = 0.037);.;Loss of disorder (P = 0.037);.;Loss of disorder (P = 0.037);.;.;
MVP		0.70
MPC		0.11
ClinPred		0.88	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.78
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs564605612; hg19: chr22-29090030;