22-28725265-T-G

Position:

• chr22-28725265-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PP3

The NM_007194.4(CHEK2):​c.422A>C​(p.Lys141Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,824 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 Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts P:1 U:9
• Conservation: PhyloP100: 6.12

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 5 ACMG points.

• PM1: In a domain FHA (size 62) in uniprot entity CHK2_HUMAN there are 10 pathogenic changes around while only 2 benign (83%) in NM_007194.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.811

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.422A>C	p.Lys141Thr	missense_variant	3/15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.422A>C	p.Lys141Thr	missense_variant	3/15	1	NM_007194.4	ENSP00000385747	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461824 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727214

Gnomad4 AFR exome AF: 0.00

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: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Pathogenic:1 Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 08, 2023	This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk. -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 07, 2024	This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 141 of the CHEK2 protein (p.Lys141Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 25186627, 26976419, 27616075, 33558524). ClinVar contains an entry for this variant (Variation ID: 186751). 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: 34903604). 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 12, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Apr 20, 2017	- -
Likely pathogenic, no assertion criteria provided	research	Center of Medical Genetics and Primary Health Care	Apr 08, 2020	ACMG Guidelines 2015 criteria This variant is in exon 3 of the CHEK2 gene in the forkhead-associated (FHA) domain (aa 113-175); it functions as a phosphopeptide recognition domain found in many regulatory proteins. It is in a mutation hotspot of 16 pathogenic variants (source ClinVar) (PM1 Pathogenic Moderate). This variant is not found in GnomAD exomes neither in GnomAD genomes (PM2 Pathogenic Moderate). This variant has been reported in the literature in individuals affected with breast cancer (PMID: 26976419, 27616075). 12 pathogenic predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL, SIFT, PolyPhen-2 and Align-GVGD versus 1 benign prediction from PrimateAI support its deleterious effect (PP3 Pathogenic Supporting). In our study this variant was found in a 45-year-old female with unilateral breast cancer and a strong family history. This patient also had a VUS in the SLX4 gene. Although this variant has been reported in ClinVar as a VUS, based on the evidence provided above, we classified this variant as a Likely Pathogenic. -

not provided Uncertain:3

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, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The CHEK2 p.Lys141Thr variant was identified in 1 of 976 proband chromosomes (frequency: 0.001) from individuals or families with stage I to stage III breast cancer (Tung 2016). The variant was also identified in dbSNP (ID: rs786203192) as “with uncertain significance allele” and in the ClinVar and Clinvitae databases as uncertain significance by Ambry Genetics, GeneDx and Invitae. The variant was not identified in Cosmic, MutDB, or the Zhejiang Colon Cancer Databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Lys141 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Thr 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 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing; this is not very 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 07, 2018	This variant is denoted CHEK2 c.422A>C at the cDNA level, p.Lys141Thr (K141T) at the protein level, and results in the change of a Lysine to a Threonine (AAG>ACG). This variant was observed in at least three individuals with breast cancer (Tung 2015, Tung 2016, Kraus 2017). CHEK2 Lys141Thr was not observed in large population cohorts (Lek 2016). This variant is located in the FHA domain (Cai 2009, Roeb 2012). In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. Based on currently available evidence, it is unclear whether CHEK2 Lys141Thr is a pathogenic or benign variant. We consider it to be a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 18, 2023	The p.K141T variant (also known as c.422A>C), located in coding exon 2 of the CHEK2 gene, results from an A to C substitution at nucleotide position 422. The lysine at codon 141 is replaced by threonine, an amino acid with similar properties. This alteration has been identified in individuals with personal and/or family histories of breast cancer (Tung N et al. J. Clin. Oncol. 2016 May;34:1460-8; Kraus C et al. Int J Cancer, 2017 Jan;140:95-102; Hauke J et al. Cancer Med. 2018 Apr;7:1349-1358; Akcay IM et al. Int J Cancer, 2021 Jan;148:285-295; Moradian MM et al. Hum Genome Var, 2021 Feb;8:9; Güleç Ceylan G et al. Tohoku J Exp Med, 2022 Nov;258:319-325). This alteration was reported as intermediate in an mES cell-based assay of CHEK2 activity (Boonen RACM et al. Cancer Res, 2022 Feb;82:615-631). 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	Aug 08, 2023	This missense variant replaces lysine with threonine at codon 141 in the FHA domain 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). One functional study has shown this variant to have intermediate impact on CHEK2 auto-phosphorylation and phosphorylation of CHEK2 substrate KAP1 in a mouse embryonic stem cell based assay (PMID: 34903604), while another similar kinase activity study in a CHEK2-deficient human cell based assay has shown this variant to have no significant impact on kinase activity (PMID: 37449874). This variant has been reported in at least four individuals affected with breast cancer (PMID: 26976419, 27616075, 25186627, 33558524, 33980423). In a large breast cancer case-control meta analysis conducted by the BRIDGES consortium, this variant has shown an inconclusive association with breast cancer (4/60466 cases and 0/53461 controls; p-value=0.128) (PMID: 33471991; Leiden Open Variation Database DB-ID CHEK2_000536). At Color, this variant has been observed in multiple individuals lacking personal or family history of breast cancer. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may have a pathogenic role, the available functional evidence is conflicting, and clinical evidence is insufficient to determine the association of this variant with breast cancer conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.14
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.56	D;.;D;D;.;D;.;.;.;D;.;T
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.97	.;D;.;.;D;D;.;D;D;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Pathogenic	0.81	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.76	D
MutationAssessor	Uncertain	2.3	M;M;M;M;.;M;M;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.70	T
PROVEAN	Pathogenic	-4.4	D;D;D;D;D;.;D;D;D;.;.;N
REVEL	Pathogenic	0.74
Sift	Benign	0.042	D;D;D;D;D;.;D;D;D;.;.;T
Sift4G	Uncertain	0.050	T;T;T;T;D;.;T;T;D;D;.;.
Polyphen		0.94	P;P;P;P;D;P;P;.;.;.;.;.
Vest4		0.63
MutPred		0.52		Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);.;Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);.;Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);Gain of phosphorylation at K141 (P = 0.0351);
MVP		0.97
MPC		0.15
ClinPred		0.98	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.88
gMVP		0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs786203192; hg19: chr22-29121253;