rs781254437

chr22-28725094-A-Gchr22-28725094-A-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.475T>C(p.Tyr159His) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,613,992 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y159C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts P:1 U:10
• Conservation: PhyloP100: 6.65

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 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 17 uncertain in NM_007194.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.916

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.475T>C	p.Tyr159His	missense_variant	4/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.475T>C	p.Tyr159His	missense_variant	4/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152172 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000294

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.0000159 AC: 4 AN: 251414 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135892

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000752 AC: 11 AN: 1461820 Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7 AN XY: 727212

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: 0.00000899

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152172 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74332

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.000479

Alfa AF: 0.000130 Hom.: 0

Bravo AF: 0.0000151

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Nov 28, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 30, 2023	- -
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	Invitae	Oct 18, 2022	This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 159 of the CHEK2 protein (p.Tyr159His). This variant is present in population databases (rs781254437, gnomAD 0.004%). This missense change has been observed in individual(s) with breast cancer, Hodgkin's lymphoma, myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML) and/or B-cell acute lymphoblastic leukemia (B-ALL) (PMID: 18058223, 21744992, 31300551). ClinVar contains an entry for this variant (Variation ID: 185924). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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, 33986034). 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. -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 21, 2016	This variant is denoted CHEK2 c.475T>C at the cDNA level, p.Tyr159His (Y159H) at the protein level, and results in the change of a Tyrosine to a Histidine (TAC>CAC). This variant was observed in a patient with late-onset breast cancer and another with Hodgkin lymphoma, both of whom were from the Czech Republic (Kleibl 2008, Havranek 2015). CHEK2 Tyr159His was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Tyrosine and Histidine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CHEK2 Tyr159His occurs at a position that is conserved across species and is located in within the FHA domain (Desrichard 2011, Roeb 2012). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether CHEK2 Tyr159His is pathogenic or benign. We consider it to be a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	CHEK2: PM2, PS4:Supporting, BP1 -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 02, 2022	This missense variant replaces tyrosine with histidine at codon 159 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). A functional study has shown the mutant protein to be functional in a yeast complementation assay (PMID: 30851065), while another functional study has shown the mutant protein to exhibit impaired binding to BRCA1 (PMID: 33986034). This variant has been reported in individuals affected with breast cancer and Hodgkin's lymphoma (PMID: 18058223, 21744992, 31300551) and in an individual who sequentially developed myelodysplastic syndrome, chronic myelomonocytic leukemia, and B-cell acute lymphoblastic leukemia (PMID: 33986034). This variant has been identified in 5/282816 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 23, 2023	The p.Y159H variant (also known as c.475T>C), located in coding exon 3 of the CHEK2 gene, results from a T to C substitution at nucleotide position 475. The tyrosine at codon 159 is replaced by histidine, an amino acid with similar properties. This alteration has been identified in multiple individuals diagnosed with breast cancer (Kleibl Z et al. Breast Cancer Res. Treat. 2008 Nov;112:159-64; Fostira F et al. J Med Genet, 2020 01;57:53-61; Guindalini RSC et al. Sci Rep. 2022 Mar;12(1):4190). Additionally, this alteration was identified in an individual diagnosed with Hodgkins lymphoma and in an individual diagnosed with myelomonocytic leukemia and B-cell acute lymphoblastic leukemia (Havranek O et al. Neoplasma. 2011;58:392-5; Bazinet A et al. Cold Spring Harb Mol Case Stud, 2021 Jun;7:), and has been reported in a cohort of individuals with pancreatic cancer undergoing multigene panel testing (Puccini A et al. Cancers (Basel). 2022 Sep;14(18). Several functional studies have reported this alteration as retaining normal levels of activity (Delimitsou A et al. Hum. Mutat. 2019 May;40:631-648; Stolarova L et al. Clin Cancer Res. 2023 Aug;29(16):3037-3050). However, another study reported that this variant impaired association with BRCA1 (Bazinet A et al. Cold Spring Harb Mol Case Stud. 2021 Jun;7(3). 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. -

See cases Pathogenic:1

Likely pathogenic, flagged submission

in vitro;research

Francois Mercier Lab, McGill University

May 12, 2021

The CHEK2 c.475T>C variant leads to the amino acid change Y159H in the functionally important forkhead-associated (FHA) domain. The FHA domain appears to be critical for the binding to downstream BRCA1 (Li 2002). The Y159H variant is rare in population databases and is predicted as likely damaging to protein function by in silico tools. The variant is considered of uncertain significance by most laboratories and this is supported by the ACMG criteria (PM1, PM2, PP3, Richards 2015). We generated in vitro experimental evidence suggesting the Y159H variant disrupts binding to BRCA1, similarly to the I157T variant that is considered to be pathogenic by some. This consists of additional supporting level evidence for pathogenicity (Brnich 2020). These findings require validation by other laboratories but suggest the Y159H may be likely pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 26, 2023

Variant summary: CHEK2 c.475T>C (p.Tyr159His) results in a conservative amino acid change located in the Forkhead-associated (FHA) domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 252780 control chromosomes in gnomAD. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.475T>C has been reported in the literature in individuals affected with Breast Cancer (example: Kleibl_2008, Fostira_2019, Guindalini_2022) and an individual with myelodysplastic syndrome and leukemia (Bazinet_2021). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least two publications report experimental evidence evaluating an impact on protein function and provided discordant results: Delimitsou_2019 suggested no damaging effect of this variant based on a Yeast functional assay, Bazinet_2021 however suggests a loss-of-function effect of this variant by a CHK2-BRCA1 colocalization assay. The following publications have been ascertained in the context of this evaluation (PMID: 33986034, 30851065, 31300551, 35264596, 18058223, 36139606, 33471991). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 (VUS: 7; Likely pathogenic: 1). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.78
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Pathogenic	0.21
Cadd	Pathogenic	27
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.66	D;.;D;D;.;D;.;.;D;.;.
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Uncertain	0.10	D
MetaRNN	Pathogenic	0.92	D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.85	D
MutationAssessor	Uncertain	2.5	M;M;M;M;.;M;M;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.75	T
PROVEAN	Uncertain	-4.2	D;D;D;D;D;.;D;D;.;.;.
REVEL	Pathogenic	0.84
Sift	Uncertain	0.0080	D;D;D;D;D;.;D;D;.;.;.
Sift4G	Pathogenic	0.0	D;D;D;D;D;.;D;D;D;.;.
Polyphen		0.99	D;D;D;D;D;D;D;.;.;.;.
Vest4		0.69
MutPred		0.74		Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);.;Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);.;Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);Gain of disorder (P = 0.0332);
MVP		0.96
MPC		0.17
ClinPred		0.93	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.90
gMVP		0.72

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: rs781254437; hg19: chr22-29121082;