rs373073383

Positions:

• chr22-28695794-G-A
• chr22-28695794-G-C
• chr22-28695794-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1 PP3_Moderate

The NM_007194.4(CHEK2):​c.1175C>T​(p.Ala392Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,584 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. A392E) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000051 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:13
• Conservation: PhyloP100: 8.67

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 Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 16 uncertain in NM_007194.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.86

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.1175C>T	p.Ala392Val	missense_variant	11/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.1175C>T	p.Ala392Val	missense_variant	11/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152156 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

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: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000358 AC: 9 AN: 251060 Hom.: 0 AF XY: 0.0000368 AC XY: 5 AN XY: 135722

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.0000617

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000513 AC: 75 AN: 1461428 Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31 AN XY: 727028

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000374

Gnomad4 NFE exome AF: 0.0000630

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152156 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74336

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000189

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000576 AC: 7

EpiCase AF: 0.000164

EpiControl AF: 0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:13

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 29, 2022	The frequency of this variant in the general population, 0.000062 (7/113398 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: 35127508 (2021), 34011307 (2021), 29752822 (2018), 28779002 (2017), 19656415 (2009)) and in unaffected individuals (PMID: 28779002 (2017)). In a large breast cancer association study, the variant was found in both affected and unaffected individuals (PMID: 33471991 (2021), https://databases.lovd.nl/shared/variants/CHEK2). Functional studies on yeast and mouse models show this variant has a damaging effect on protein function (PMID: 34903604 (2021), 30851065 (2019)). 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	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 22, 2021	Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with breast cancer in published literature (Soumittra 2009, Decker 2017, Hauke 2018, Li 2019); Published functional studies demonstrate damaged protein function in vivo (Delimitsou 2019); This variant is associated with the following publications: (PMID: 19656415, 22920209, 26466571, 28743916, 29522266, 29752822, 31398194, 30851065, 28779002, 29021619) -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2022	CHEK2: PS3, BP1 -

Familial cancer of breast Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jun 13, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 27, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 392 of the CHEK2 protein (p.Ala392Val). This variant is present in population databases (rs373073383, gnomAD 0.008%). This missense change has been observed in individual(s) with breast cancer (PMID: 19656415, 29752822, 34011307, 34326862). ClinVar contains an entry for this variant (Variation ID: 141136). 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: 28743916, 30851065). 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	Institute of Human Genetics, University of Leipzig Medical Center	Apr 08, 2019	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 10, 2019	Variant summary: CHEK2 c.1175C>T (p.Ala392Val) results in a non-conservative amino acid change in 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 3.6e-05 in 251060 control chromosomes. c.1175C>T has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer, lung cancer, melanoma (Soumittra_2009, Guauque-Olarte_2016, Riaz_2017, Li_2018). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. At least one publication reports experimental evidence evaluating an impact on protein function and showed that this variant had damaging effect (Delimitsou_2019). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS. -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 11, 2024	The p.A392V variant (also known as c.1175C>T), located in coding exon 10 of the CHEK2 gene, results from a C to T substitution at nucleotide position 1175. The alanine at codon 392 is replaced by valine, an amino acid with similar properties. Across studies, this alteration has been identified in both breast cancer cases and unaffected controls (Soumittra N et al. Hered. Cancer Clin. Pract. 2009 Aug;7:13; Decker B et al. J. Med. Genet., 2017 11;54:732-741; Li JY et al. Int. J. Cancer, 2019 01;144:281-289; Zografos E et al. Genes (Basel), 2022 Jul;13; Zografos E et al. BMC Cancer, 2021 May;21:572; Andrikopoulou A et al. Front Oncol, 2021 Jan;11:797505; Hauke J et al. Cancer Med. 2018 Apr;7(4):1349-1358). In a large study, this variant was reported in 15/60,466 breast cancer cases and in 4/53,461 controls (Dorling et al. N Engl J Med 2021 02;384:428-439). This alteration was reported as damaging in an mES cell-based assay of CHEK2 activity (Boonen RACM et al. Cancer Res, 2022 02;82:615-631) and 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 functionally impaired in a study assessing CHEK2-complementation through quantification of KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells (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. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 04, 2023	This missense variant replaces alanine with valine at codon 392 of the CHEK2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental functional studies have demonstrated this variant to be damaging in a yeast DNA damage repair assay (PMID: 30851065), deficient in Ser516 autophosphorylation (PMID: 28743916, 37449874) and Kap1 p.S473 phosphorylation in cell-based kinase assays (PMID: 34903604, 37449874). This variant has been reported in individuals affected with breast cancer (PMID: 19656415, 29522266, 29752822, 33471991, 34011307) and was associated with a risk of breast cancer in a case-control study (PMID: 33471991; observed in 15/60,466 women with breast cancer and 4/53,461 controls). This variant has also been identified in 9/251060 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and has been observed in an individual over 70 with no personal history of cancer (FLOSSIES; https://whi.color.com/). 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. -

Li-Fraumeni syndrome 2 Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Department of Genetics, HCU Lozano Blesa

May 01, 2023

Variant summary: CHEK2 c.1175C>T results in the replacement of Ala392 by a Val residue (p.Ala392Val). 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 38 years (luminal-B tumor phenotype). Two second-degree relatives were also diagnosed with BC, although a co-segregation study could not be performed. Ala392 is located in the kinase domain, is part of the conserved APE motif (Ala392–Pro393–Glu394) located in the long T-loop. The substitution of Ala392 by valine introduces a bulkier residue at a spot where Ala392 appears to be in close contact with some residues at the dimerization interface, particularly with Arg474. It may affect the protein integrity and thus its function. The variant is reported in gnomAD v4 in 78 cases out of 1613584 alleles analysed (freq=4.8x10-3 %). In ClinVar more than a dozen of reports appear classifying the variant as of Uncertain significance. Other replacements found at this position (A392G, A392T, A392P, and A392E) are also 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 Ala392Val as Pathogenic, whereas the ACMG classification tool Franklin suggests this variant as VUS (Uncertain Significance). Our in-silico study on the protein stability based on relaxation molecular dynamics simulations (doi: 10.3389/fgene.2023.1274108) indicates that Ala392Val induces conformational unstability on CHEK2 protein. Moreover, Stolarova L. et al’s functional study on KAP1 phosphorylation and CHEK2 autophosphorylation protein capability reports this variant as functionally impaired (PMID: 37449874). With all this information, we believe this variant have more chances of being Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

curation

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Jan 09, 2024

. According to the ACMG standard criteria we chose these criteria: PS3 (strong pathogenic): Delimitsou (2019): damaging in yeast assay Stolarova (2023): damaging in CHK2 & KAP1 assay Boonen (2022): damaing in KAP1 assay , PS4 (supporting pathogenic): OR in Stolarova et al. 2.5 but not significant (p=0.07) and CI intervall including 1.0; 18 Families in GC-HBOC only 1X in gnomAD V3.1.2 non Cancer, PP3 (supporting pathogenic): REVEL: 0.825 [cutoff REVEL >0.7333] -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The CHEK2 p.Ala392Val variant was identified in 1 of 182 proband chromosomes (frequency: 0.005) from individuals or families with early onset breast or ovarian cancer (Soumittra 2009 PMID: 19656415). The variant was also identified in dbSNP (ID: rs373073383 as With Uncertain significance allele), ClinVar (5x as a variant of uncertain significance), and Cosmic (1x). The variant was not identified in MutDB or the Zhejiang University Database. The variant was identified in control databases in 11 of 245912 chromosomes at a frequency of 0.00005 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include European Non-Finnish in 9 of 111392 chromosomes (freq: 0.00008), East Asian in 1 of 17248 chromosomes (freq: 0.00006), and Finnish in 1 of 22300 chromosomes (freq: 0.00005), while the variant was not observed in the African, Other, Latino, Ashkenazi Jewish, and South Asian populations. The p.Ala392 residue is conserved across mammals and other organisms, and 4 out of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; however, this is not reliably predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.50	D;.;D;.;D;.;D;.;.
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Uncertain	0.23	D
MetaRNN	Pathogenic	0.86	D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Pathogenic	3.7	H;.;H;.;H;.;H;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.9	D;D;D;.;D;D;.;D;D
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D;D;D;.;D;D;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;.;D;D;.;D;D
Polyphen		1.0	D;D;D;.;D;D;D;D;D
Vest4		0.97
MVP		0.73
MPC		0.16
ClinPred		0.98	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.99
gMVP		0.88

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: rs373073383; hg19: chr22-29091782; COSMIC: COSV60421988; COSMIC: COSV60421988;