rs142763740

chr22-28694066-G-Achr22-28694066-G-Cchr22-28694066-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5 BP4

The NM_007194.4(CHEK2):c.1427C>T(p.Thr476Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000404 in 1,595,894 control chromosomes in the GnomAD database, including 1 homozygotes. 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. T476K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00031 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00041 (1 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:21 U:24 B:1 O:1
• Conservation: PhyloP100: 3.15

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 0 ACMG points.

• PP5: Variant 22-28694066-G-A is Pathogenic according to our data. Variant chr22-28694066-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 128060.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Established_risk_allele=1, Likely_benign=1, Likely_pathogenic=16, Uncertain_significance=17, not_provided=1}. Variant chr22-28694066-G-A is described in Lovd as [Pathogenic]. Variant chr22-28694066-G-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.34246725).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.1427C>T	p.Thr476Met	missense_variant	13/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.1427C>T	p.Thr476Met	missense_variant	13/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes AF: 0.000309 AC: 47 AN: 152112 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

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: 0.000529

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000329 AC: 77 AN: 233796 Hom.: 0 AF XY: 0.000335 AC XY: 43 AN XY: 128358

Gnomad AFR exome AF: 0.000204

Gnomad AMR exome AF: 0.000175

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: 0.000542

Gnomad OTH exome AF: 0.00151

GnomAD4 exome AF: 0.000414 AC: 597 AN: 1443664 Hom.: 1 Cov.: 30 AF XY: 0.000408 AC XY: 293 AN XY: 718628

Gnomad4 AFR exome AF: 0.000180

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000696

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000487

Gnomad4 OTH exome AF: 0.000300

GnomAD4 genome AF: 0.000309 AC: 47 AN: 152230 Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15 AN XY: 74420

Gnomad4 AFR AF: 0.000217

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000529

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000684 Hom.: 0

Bravo AF: 0.000355

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000639 AC: 3

ExAC AF: 0.000372 AC: 43

EpiCase AF: 0.000273

EpiControl AF: 0.000711

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:21 Uncertain:24 Benign:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:6 Uncertain:8

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 30, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Jan 21, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 22, 2023	In the published literature, this variant has been reported in individuals with hereditary breast and/or ovarian cancer (PMIDs: 32658311 (2021), 33030641 (2020), 32906215 (2020), 31050813 (2019), 30287823 (2018), 28008555 (2017), 22862163 (2012), 21244692 (2011)), endometrial cancer (PMID: 27443514 (2016)), pancreatic cancer (PMID: 26845104 (2016)), colorectal cancer (PMIDs: 32658311 (2021), 28944238 (2017)), and prostate cancer (PMIDs: 32832836 (2020), 29520813 (2018)). This variant has also been reported in unaffected individuals (PMIDs: 32658311 (2021), 31050813 (2019), 30287823 (2018)). Additionally, experimental studies have reported conflicting results in this variant's impact on CHEK2 protein functions (PMIDs: 31050813 (2019), 30851065 (2019), 22419737 (2012)), 22114986 (2011)). The frequency of this variant in the general population, 0.0005 (62/124190 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Based on the available information, we are unable to determine the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	CHEK2: PM1, PS3:Moderate, BP4 -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Uncertain significance, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 16, 2022	The CHEK2 c.1427C>T; p.Thr476Met variant (rs142763740) is reported in numerous individuals with CHEK2-associated cancers (Classen 2013, Girard 2019, Hu 2018, Kamihara 2022, Le Calvez-Kelm 2011, Lilyquist 2017, Rizzolo 2019, Sutcliffe 2020), but is also reported in individuals without cancer suggesting reduced penetrance (Girard 2019). The overall lifetime breast cancer risk for CHEK2 pathogenic variants in general is 20-30% (Slavin 2015). In vitro kinase assays and in vivo DNA damage response assays with the variant protein showed a loss of kinase activity and impaired function (Delimitsou 2019, Desrichard 2011, Kleiblova 2019, Roeb 2012). However, one CHEK2-cell based assay showed no effect of the variant on protein function (Kleiblova 2019). This variant is reported by multiple laboratories in ClinVar (Variation ID: 128060). It is found in the general population with an overall allele frequency of 0.03% (83/265178 alleles) in the Genome Aggregation Database. The threonine at codon 476 is moderately conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.445). Based on the currently available information, this variant is considered to be likely pathogenic. References: Classen CF et al. Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis. Hum Genet. 2013 Jul;132(7):825-41. PMID: 23552953. Delimitsou A et al. Functional characterization of CHEK2 variants in a Saccharomyces cerevisiae system. Hum Mutat. 2019 May;40(5):631-648. PMID: 30851065. Desrichard A et al. CHEK2 contribution to hereditary breast cancer in non-BRCA families. Breast Cancer Res. 2011;13(6):R119. PMID: 22114986. Girard E et al. Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. Int J Cancer. 2019 Apr 15;144(8):1962-1974. PMID: 30303537. Hu C et al. Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer. JAMA. 2018 Jun 19;319(23):2401-2409. PMID: 29922827. Kamihara J et al. Germline pathogenic variants in cancer risk genes among patients with thyroid cancer and suspected predisposition. Cancer Med. 2022 Apr;11(8):1745-1752. PMID: 35174967. Kleiblova P et al. Identification of deleterious germline CHEK2 mutations and their association with breast and ovarian cancer. Int J Cancer. 2019 Oct 1;145(7):1782-1797. PMID: 31050813. Le Calvez-Kelm F et al. Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study. Breast Cancer Res. 2011 Jan 18;13(1):R6. PMID: 21244692. Lilyquist J et al. Frequency of mutations in a large series of clinically ascertained ovarian cancer cases tested on multi-gene panels compared to reference controls. Gynecol Oncol. 2017 Nov;147(2):375-380. PMID: 28888541. Rizzolo P et al. Insight into genetic susceptibility to male breast cancer by multigene panel testing: Results from a multicenter study in Italy. Int J Cancer. 2019 Jul 15;145(2):390-400. PMID: 30613976. Roeb W et al. Response to DNA damage of CHEK2 missense mutations in familial breast cancer. Hum Mol Genet. 2012 Jun 15;21(12):2738-44. PMID: 22419737. Slavin TP et al. Clinical Application of Multigene Panels: Challenges of Next-Generation Counseling and Cancer Risk Management. Front Oncol. 2015 5:208. PMID: 26484312. Sutcliffe EG et al. Differences in cancer prevalence among CHEK2 carriers identified via multi-gene panel testing. Cancer Genet. 2020 Aug;246-247:12-17. PMID: 32805687. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2020	Published functional studies demonstrate a damaging effect: most show reduced or absent kinase activity and DNA damage response (Desrichard 2011, Roeb 2012, Delimitsou 2019, Kleiblova 2019); Observed in many individuals with personal and/or family history of CHEK2-related cancers (Desrichard 2011, Le Calvez-Kelm 2011, Hu 2015, Leedom 2016, Pritzlaff 2016, Shirts 2016, Frey 2017, Isaacsson Velho 2018, Schubert 2018, Wu 2018); 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: 26681312, 29368341, 21244692, 29945567, 28944238, 25186627, 26845104, 22862163, 23552953, 28008555, no PMID, 10617473, 22419737, 22114986, 26787654, 26483394, 27751358, 21901162, 28495237, 27621404, 26022348, 27443514, 15095295, 29478780, 29520813, 30128536, 31050813, 30613976, 30851065, 30426508, 24595525, 30322717, 31159747, 31784482, 30303537, 31447099, 32832836, 31263571, 31948886) -
Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Familial cancer of breast Pathogenic:3 Uncertain:7 Benign:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 30, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Apr 25, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 476 of the CHEK2 protein (p.Thr476Met). This variant is present in population databases (rs142763740, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with breast cancer, colorectal cancer, endometrial cancer, ovarian cancer, and/or prostate cancer (PMID: 21244692, 27443514, 28008555, 28944238, 29368341, 29520813, 31050813). ClinVar contains an entry for this variant (Variation ID: 128060). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a low probability of being pathogenic (external communication). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 22114986, 22419737, 30851065, 31050813). 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	Genetics and Molecular Pathology, SA Pathology	Aug 11, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Oct 06, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Heidelberg University	Apr 14, 2022	reported as secondary finding -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Feb 13, 2024	Criteria applied: PS4_MOD,PP3 -
Uncertain significance, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Apr 16, 2018	- -
Likely benign, flagged submission	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]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Department of Molecular Diagnostics, Institute of Oncology Ljubljana	Apr 12, 2020	- -

Hereditary cancer-predisposing syndrome Pathogenic:5 Uncertain:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Feb 14, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 17, 2024	This missense variant replaces threonine with methionine at codon 476 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have demonstrated inconsistent results. The mutant protein has shown significantly reduced kinase activity in vitro using bacteria produced protein (PMID: 22114986, 31050813), but displayed normal kinase activity in a human cell assay (PMID: 31050813, 37449874). DNA damage repair assays in yeast have shown the mutant protein to exhibit partial to complete loss of function (PMID: 22419737, 30851065). This variant has been reported in individuals affected with breast cancer (PMID: 15095295, 21244692, 22114986, 22862163, 24595525, 25186627, 26681312, 28008555, 28495237 30426508, 32658311, 32805687, 32906215, 33030641, 36315097, 37628581), prostate cancer (PMID: 29368341, 29520813), colorectal cancer (PMID: 28008555, 28135145, 28944238, 32658311), pancreatic cancer (PMID: 26483394, 26845104 29945567), and endometrial cancer (PMID: 27443514), as well as in individuals unaffected with cancer (PMID: 32658311). A history weighting algorithm score was inconsistent with that expected for CHEK2 pathogenic mutations (Mundt, et al. poster #154, ACMG 2017). This variant has been identified in 83/265178 chromosomes in the general population by the Genome Aggregation Database (gnomAD). This variant has been reported in two large case-control meta analyses; this variant has been identified in 83/60383 cases and 45/53416 controls (OR=1.632, 95%CI [1.135 to 2.346]) (PMID: 33471991) and 101/73048 BC cases and 60/88658 controls (OR=2.043, 95%Ci [1.4841 to 2.8125]) (PMID: 37449874). In summary, functional studies have been inconclusive regarding the impact of this variant on protein function, and this variant has been observed in individuals affected with breast cancer as well as in the general population. 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	curation	Sema4, Sema4	Feb 05, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneID Lab - Advanced Molecular Diagnostics	Sep 07, 2017	- -
Established risk allele, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 04, 2022	The p.T476M variant (also known as c.1427C>T), located in coding exon 12 of the CHEK2 gene, results from a C to T substitution at nucleotide position 1427. The threonine at codon 476 is replaced by methionine, an amino acid with similar properties. Recent case-control studies have reported association with breast cancer risk with odds ratios ranging from 1.35 to 1.63 (Dorling et al. N Engl J Med. 2021 02;384:428-439; Bychkovsky BL et al. JAMA Oncol. 2022 Sep). Functional studies of this alteration have reported conflicting findings. In one in vivo, yeast-based growth rate assay, this variant was indicated to be semi-functional (Delimitsou A. Hum Mutat. 2019 05;40(5):631-648). However, several other studies have reported the variant as deleterious based on kinase and DNA damage response activity (Desrichard A et al. Breast Cancer Res. 2011 Nov;13:R119; Roeb W et al. Hum. Mol. Genet. 2012 Jun;21:2738-44). Another study reported this alteration as deleterious in an in vitro assay of kinase activity using bacterially expressed CHEK2, but neutral in an assay conducted in a human cell line (Kleiblova P et al Int J Cancer. 2019 10;145(7):1782-1797). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is interpreted as a moderate risk mutation, also referred to as an established risk allele. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 09, 2021	This variation detected results in the substitution of the amino acid Threonine with Methionine at codon 476 of the CHEK2 protein. The threonine residue is highly conserved among species in the Protein kinase domain of the protein and there is physiochemical difference between threonine and methionine (Grantham Score 81). This variant has been described in the international literature in individuals affected with breast and endometrial cancers (PMID: 21244692, PMID: 27443514).This variant is present in mutation databases at a low frequency (rs142763740, ExAC 0.07%). The mutation database ClinVar contains entries for this variant (Variation ID: 128060). Algorithms developed to predict the effect of missense changes on protein structure and function suggest that this variant is likely to be damaging to the protein, a prediction supported also by experimental studies. (PMID: 22114986, PMID: 22419737). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Mar 12, 2019	- -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 09, 2021	DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.1427C>T, in exon 13 that results in an amino acid change, p.Thr476Met. This sequence change has been described in the gnomAD population databases with a global population frequency of 0.03% (dbSNP rs142763740); however, this variant is present in a homologous region of the CHEK2 gene and therefore population data for this region may not be reliable. The p.Thr476Met change affects a highly conserved amino acid residue located in a domain of the CHEK2 protein that is known to be functional. The p.Thr476Met substitution appears to be possibly damaging using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). The p.Thr476Met change has been identified in patients with a personal and/or family history of breast cancer colorectal cancer, prostate cancer, and pancreatic cancer (PMIDs: 21244692, 27443514, 28944238, 29368341, 29520813, 28008555). Additionally, a different sequence change affecting the same amino acid residue (p.Thr476Lys) has been reported in an individual affected with prostate cancer (PMID: 16835864).. Experimental studies have shown that this missense change disrupts CHEK2 kinase activity in vitro and impairs DNA damage response (PMID: 22114986, 22419737). -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 29, 2024	Variant summary: CHEK2 c.1427C>T (p.Thr476Met) results in a non-conservative amino acid change located in the Protein kinase domain 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 0.00032 in 238040 control chromosomes. The observed variant frequency is approximately the same as the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (0.00031), strongly suggesting that the variant is benign. Additionally, this variant has been observed in 8 individuals who are reportedly cancer free at age 70 in the FLOSSIES database. In addition, co-occurrences with other pathogenic variants have been observed at our laboratory (BRCA2 c.8677C>T, p.Gln2893*; PMS2 c.2444C>T, p.Ser815Leu), providing additional supporting evidence for a benign role. c.1427C>T has been reported in the literature in individuals affected with a variety of cancers such as Breast, Ovarian, Colorectal, and Pancreatic cancers (example, Le Calvez-Kelm_2011, Angelova_2012, Susswein_2015, Hu_2016, Schuber_2019, Henn_2019, Bertelsen_2019, Lerner-Ellis_2019). For some of these cases multigenic panel screening was performed, however, in most cases, the co-occurrence information was not provided and segregation studies were not performed. In addition, Leedom_2016 reported similar frequencies for the variant in their affected (at risk) population of European descent (0.07%; 46/62392 chromosomes tested). This variant was identified in an individual who tested positive for a large deletion encompassing exon 9-15 of CHEK2 in trans in an internal specimen.These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Several publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in disruption of CHEK2 kinase activity in vitro and impairs DNA damage response in a yeast assay (example, Desrichard_2011; Roeb_2012, Delimitsou_2019), suggesting a deleterious outcome or at least a possible modifying role of the variant in carcinogenesis. The following publications have been ascertained in the context of this evaluation (PMID: 22862163, 31341520, 31398194, 27621404, 31263571, 35643632, 28944238, 30851065, 22114986, 15095295, 28495237, 30680046, 26483394, 29922827, 29368341, 21244692, 27751358, 31784482, 30128536, 28008555, 27443514, 22419737, 30426508, 26845104, 26681312, 26787654, 29945567, 28135145, Young_2016). Multiple clinical diagnostic laboratories and other submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as uncertain significance until more definitive data becomes available. -

Li-Fraumeni syndrome 2 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Oct 30, 2023	PS3, PM2, PM5 -
Likely pathogenic, no assertion criteria provided	clinical testing	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	Nov 24, 2023	- -

CHEK2-related cancer predisposition Pathogenic:1 Other:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The CHEK2 c.1427C>T (p.Thr476Met) missense variant, also referred to as c.1556C>T (p.Thr519Met), was reported in five of 1,955 breast cancer patients (Le Calvez-Kelm et al. 2011; Desrichard et al. 2011; Angelova et al. 2012). The variant was absent from a total of 1,622 controls, but is reported at a frequency of 0.00068 in the European (non-Finnish) population of the Exome Aggregation Consortium. Desrichard et al. (2011) developed an in vitro kinase activity assay to assess the activity of missense variants in CHEK2. In this assay the p.Thr476Met variant demonstrated no kinase activity and was similar to a known non-functional kinase variant of CHEK2. In addition, Roeb et al. (2012) developed a yeast-based in-vivo functional assay to assess the effect of CHEK2 variants on the repair of DNA damage. Cells with wild type CHEK2 repaired the DNA damage while cells with a known non-functional variant of CHEK2 did not. The p.Thr476Met variant was shown to have loss of function by this DNA damage response assay. Based on the evidence, the p.Thr476Met variant is classified as pathogenic for CHEK2-related cancer susceptibility. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
not provided, no classification provided	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	Variant interpreted as Uncertain significance and reported on 11-27-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -

CHEK2-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 13, 2023

The CHEK2 c.1427C>T variant is predicted to result in the amino acid substitution p.Thr476Met. This variant has been reported in many individuals with breast cancer with a recent study reporting an odds ratio of 1.35 (95% CI=1.03-1.77, P-value=0.03) (Table S1, Le Calvez-Kelm et al. 2011. PubMed ID: 21244692; Desrichard et al. 2011. PubMed ID: 22114986; Roeb et al. 2012. PubMed ID: 22419737; Angelova et al. 2012. PubMed ID: 22862163; Table S1, Susswein et al. 2016. PubMed ID: 26681312; Schubert et al. 2019. PubMed ID: 30426508; Lerner-Ellis et al. 2020. PubMed ID: 31784482; Figure 2, Bychkovsky et al. 2022. PubMed ID: 36136322). This variant has also been reported in individuals with ovarian cancer, prostate cancer, pancreatic cancer, and colorectal cancer (Table S1, Hu et al. 2016. PubMed ID: 26483394; Table S1, Susswein et al. 2016. PubMed ID: 26681312; Table 1, Isaacsson Velho et al. 2018. PubMed ID: 29368341; Table 1, Young et al. 2018. PubMed ID: 29945567; Table S4, Bertelsen et al. 2019. PubMed ID: 31263571; Table S3, Arvai et al. 2019. PubMed ID: 31341520). In vitro and vivo experimental studies suggest this variant results in reduced or absent kinase activity and DNA damage response (Desrichard et al. 2011. PubMed ID: 22114986; Table 1, Roeb et al. 2012. PubMed ID: 22419737; Figure 1, Kleiblova et al. 2019. PubMed ID: 31050813). An additional functional study using protein expression in yeast found that his variant results in semi-functional kinase activity (Delimitsou et al. 2019. PubMed ID: 30851065). In the gnomAD public population database this variant has been reported in up to ~0.05% of alleles in a subpopulation (http://gnomad.broadinstitute.org/variant/22-29090054-G-A) and has conflicting interpretations of uncertain, risk allele, and likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/128060/). Taken together, we interpret c.1427C>T (p.Thr476Met) as likely pathogenic. -

Breast neoplasm Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

Across three studies, the c.1427C>T (p.Thr476Met), was reported in five of 1,955 breast cancer patients (Le Calvez-Kelm et al. 2011; Desrichard et al. 2011; Angelova et al. 2012). The variant was absent from a total of 1,622 controls, but is reported at a frequency of 0.00068 in the European (Non-Finnish) population of the Exome Aggregation Consortium. Desrichard et al. (2011) developed an in vitro kinase activity assay to assess the activity of missense variants in CHEK2. In this assay the p.Thr476Met variant demonstrated no kinase activity and was similar to a known non-functional kinase variant of CHEK2. In addition, Roeb et al. (2012) developed a yeast-based in-vivo functional assay to assess the effect of CHEK2 variants on the repair of DNA damage. Cells with wild-type CHEK2 repaired the DNA damage while cells with a known non-functional variant of CHEK2 did not. The p.Thr476Met variant was shown to have loss of function by this DNA damage response assay. Based on the evidence, the p.Thr476Met variant is classified as likely pathogenic for breast cancer. -

Breast carcinoma Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Aug 19, 2021

Invasive Ductal Carcinoma Estrogen Receptor: Positive Progesterone Receptor: Positive HER2 Receptor: Negative -

Colon cancer Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Aug 16, 2021

Colon Carcinoma -

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

May 26, 2023

- -

Breast and colorectal cancer, susceptibility to Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

University of Washington Department of Laboratory Medicine, University of Washington

Nov 20, 2015

- -

Colorectal cancer Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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.Thr476Met variant was identified in 5 of 3910 proband chromosomes (frequency: 0.001) from individuals or families with breast cancer and non-BRCA hereditary breast cancer cases of Bulgarian and French ethnicity, and was not identified in 3244 control chromosomes from healthy individuals (Angelova 2012, Desrichard 2011, Le Calvez-Kelm 2011). However among these studies, the frequencies were not consistent and ranged from 0.01 to 0.0004. An additional large study identified the variant in 67 of 91758 proband chromsomes (freq. 0.0007) from individuals who underwent panel testing that including CHEK2 (Leedom 2016 27751358). The variant was also identified in dbSNP (ID: rs142763740) as “with likely pathogenic allele”, in ClinVar and Clinvitae databases (as likely pathogenic by GeneDx, Ambry Genetics, Illumina clinical Services, Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C, Quest Diagnostics Nichols Institute San Juan Capistrano as uncertain significance by Invitae, University of Washington Department of Laboratory Medicine and Genetic Services Laboratory, University of Chicago). The variant is further listed in the Zhejiang University database with no classification. The variant was not identified in Cosmic and MutDB databases. The same amino acid change but different nucleotide change (c.1427C>A) was observed in a patient with a clinical diagnosis of Li-Fraumeni syndrome (Sardi 2014). The variant is identified in the 1000 Genomes Project in 1 of 5000 chromosomes (frequency: 0.0002) and the NHLBI GO Exome Sequencing Project in 3 of 4698 European American alleles. In addition, the variant was identified in control databases in 84 of 260146 chromosomes at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 6 of 22580 chromosomes (freq: 0.0003), “other” in 7 of 6276 chromosomes (freq: 0.001), Latino in 6 of 34216 chromosomes (freq: 0.0002), European Non-Finnish in 65 of 122014 chromosomes (freq: 0.0005); it was not observed in the Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. In order to evaluate mutations in all parts of the CHEK2 gene with a single biological test, an assay to evaluate CHEK2-mediated response to DNA damage was developed based on complementation of S. cerevisiae rad53 by human CHEK2. Based on growth of the strain after DNA damage, the p.Thr476Met variant was found to be damaging (Roeb 2012). The p.Thr476Met variant, which maps to the kinase domain of CHEK2, is likely to disrupt the protein function (Angelova 2012). In one study, the p.Thr476Met variant did not display kinase activity consistently and was classified as probably deleterious (Desrichard 2011). However additional functional studies are needed to determine that the p.Thr476Met variant disrupts the biological function of CHEK2. The p.Thr476 residue is conserved in 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 p.Thr476Met 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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	Benign	0.20
BayesDel_addAF	Benign	-0.016	T
BayesDel_noAF	Uncertain	0.10
Cadd	Pathogenic	32
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.43	T;.;T;.;T;.;T;.;.
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.83	D
M_CAP	Benign	0.057	D
MetaRNN	Benign	0.34	T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.066	D
MutationAssessor	Pathogenic	3.4	M;.;M;.;M;.;M;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Benign	0.48	T
PROVEAN	Pathogenic	-4.7	D;D;D;.;D;D;.;D;D
REVEL	Uncertain	0.45
Sift	Uncertain	0.0010	D;D;D;.;D;D;.;D;D
Sift4G	Pathogenic	0.0010	D;D;D;.;D;D;.;D;D
Polyphen		1.0	D;D;D;.;D;D;D;D;D
Vest4		0.54
MVP		0.81
MPC		0.16
ClinPred		0.59	D
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.81
gMVP		0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs142763740; hg19: chr22-29090054; COSMIC: COSV105899907; COSMIC: COSV105899907;