ClinVar Genomic variation as it relates to human health

This sequence change replaces isoleucine with threonine at codon 157 of the CHEK2 protein (p.Ile157Thr). The isoleucine residue is moderately conserved and there is a moderate physiochemical difference between isoleucine and threonine.This variant is present in population databases (rs17879961, 2.6%) and has been reported in the literature. ClinVar contains entries for this variant (RC000116018, RC000144596).In large meta-analyses involving several thousand cases and controls, patients who carried this variant had a slightly increased risk of breast cancer (OR=1.48-1.58) (PMID: 22799331, 23713947), and colorectal cancer (OR=1.48-1.67) (PMID: 22901170, 23713947). The risk was found to be more pronounced for lobular breast tumors (OR=4.17) (PMID: 22799331).Smaller case-control studies suggest this variant may also lead to increased risk of additional cancers, including kidney, prostate, thyroid, and gastric cancer (PMID: 15492928, 23296741, 24599715).Experimental studies find that this missense change reduces the binding of the CHEK2 protein to Cdc25A, BRCA1 and p53 proteins in vitro and may have a dominant-negative effect in cells, although it does not have an effect on CHEK2 protein kinase activity (PMID: 11298456, 11571648, 15239132, 12049740, 22419737). The relationship between these experimental findings and the cancer risk is unclear. In summary, this variant is reported to cause an increased risk for cancer, however, since this variant is associated with a much lower risk than other Pathogenic alleles in the CHEK2 gene, it has been classified as Likely Pathogenic (low penetrance).

DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.470T>C, in exon 4 that results in an amino acid change, p.Ile157Thr. This sequence change has been identified by previous testing performed at the Molecular Pathology laboratory on DNA derived from a bone marrow sample on this patient. This sequence change has been described in the gnomAD database with a population frequency of 0.49% in general population and a frequency of 2.5% in European Finnish population (dbSNP rs17879961). This sequence change has been described in patients with prostate cancer, CLL, breast cancer, colorectal cancer and other cancers and has been considered to be a susceptibility risk allele to cancer (PMIDs: 16574953, 15492928, 22799331, 23713947, 26506619). The p.Ile157Thr change affects a poorly conserved amino acid residue located in the FHA domain of the CHEK2 protein. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Ile157Thr substitution. Functional studies have demonstrated that the p.Ile157Thr fails to bind to checkpoint proteins and inability to autophosphorylate (PMIDs: 11571648; 22419737). These collective evidence suggests that p.Ile157Thr is a risk allele. Clinical correlation is recommended.

The CHEK2 c.470T>C variant is predicted to result in the amino acid substitution p.Ile157Thr. This variant has been observed in ~0.5% of individuals in the gnomAD database, and is particularly prevalent within the Finnish European subpopulation (~2.5% of individuals, 10 homozygotes) (http://gnomad.broadinstitute.org/variant/22-29121087-A-G). However, this variant has repeatedly been associated with an increased risk for several cancers, including breast cancer, uterine serous carcinoma, and colorectal cancer (Kilpivaara et al. 2004. PubMed ID: 15239132; Roeb et al. 2012. PubMed ID: 22419737; Liu et al. 2012. PubMed ID: 22799331; Pennington et al. 2013. PubMed ID: 22811390; Han et al. 2013. PubMed ID: 23713947). This variant negatively affects CHEK2 function through a possible dominant-negative mechanism (Kilpivaara et al. 2004. PubMed ID: 15239132; Roeb et al. 2012. PubMed ID: 22419737). In ClinVar, it is reported as a variant of uncertain significance, risk factor, likely pathogenic, and pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/5591/). Taken together, we classify this variant as likely pathogenic.

The CHEK2 c.470T>C variant is classified as Pathogenic (PS3, PS4) The CHEK2 c.470T>C variant is a single nucleotide change in exon Missing Exon of the CHEK2 gene, which is predicted to change the amino acid isoleucine at position 157 in the protein to threonine. The variant has been reported in probands with a clinical presentation of colorectal cancer (PS4). Well-established functional studies show a deleterious effect of this variant (PS3). The variant has been reported in dbSNP (rs17879961) and has been reported with Conflicting interpretations of pathogenicity, Risk factor by other diagnostic laboratories (ClinVar Variation ID: 5591). It has not been reported in HGMD.

Variant summary: CHEK2 c.470T>C (p.Ile157Thr) results in a non-conservative amino acid change located in the Forkhead-associated (FHA) domain that is a phosphopeptide recognition domain (IPR000253) 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 0.0042 in 253524 control chromosomes in the gnomAD database, including 11 homozygotes. The observed variant frequency is approximately 14 fold of 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. In certain subpopulations the variant was found with even higher frequencies, e.g. within the Finnish (2.5%, gnomAD), Estonian (4.6%, gnomAD) and Polish (4-6%; e.g. Cybulski_2004, Lukomska_2021). The variant has also been reported in 47/7325 European American women (including 1 homozygote), who are older than age 70 and cancer free (FLOSSIES database). However, c.470T>C has been reported in the literature in several individuals affected with breast- and/or ovarian cancer. In families with this variant, transmissions of the variant allele, as well as the reference allele to affected individuals were reported, in addition to unaffected individuals who harbored the variant (e.g. Allinen_2001, Dong_2003, Roeb_2012, Bak_2014, Cragun_2014, Stradella_2018). These data indicate that the variant is likely to be associated with disease, but also suggests incomplete segregation and low penetrance. Co-occurrences with other pathogenic variants have been reported in CHEK2, as well as in other genes associated with cancer (e.g. BRCA2 c.6468_6469delTC [p.Gln2157fsX18]; NBN c.657_661delACAAA [p.Lys219fsX16]; BRCA1 c.3700_3704delGTAAA [p.Val1234fsX8]; CHEK2 c.444+1G>A; CHEK2 1100delC [p.Thr367fsX15]; CHEK2 c.433C>T [p.Arg145Trp]), providing supporting evidence for a benign role, though in some of these cases the observed phenotype (earlier onset), could also suggest an additive effect (Stradella_2018). Multiple association studies have produced conflicting results, with an overall consensus for the variant being associated with a moderate risk for breast cancer, based on a large meta-analysis by Liu_2012 that included a total of fifteen case-control studies (19,621 cases and 27,001 controls), showing a significant association for (unselected) breast cancer (OR = 1.48, 95% CI = 1.31-1.66, P < 0.0001). Another study indicated a lack of risk association with ovarian cancer (Lukomska_2021), and a large study found no statistically significant difference in overall- or breast cancer-specific survival between carriers of this variant and non-carriers (Muranen_2016). Multiple functional studies reported experimental evidence evaluating an impact on protein function, and demonstrated retained kinase activity (Lee_2001, Chrisanthar_2008), decreased interaction with p53 and BRCA1 (Falck_2001, Li_2002, Bazinet_2021) and impaired CHEK2 oligomerization with reduced autophosphorylation (Schwarz_2003). A recent study assigned a "benign" functional classification to the variant based on its DNA repair-ability after chemically induced DNA damage (Delimitsou_2019), while another study classified it as an "intermediate" function variant with decreased catalytic activity (Kleiblova_2019). The following publications have been ascertained in the context of this evaluation (PMID: 21356067, 18085035, 22419737, 21778326, 12533788, 10617473, 11719428, 33986034, 22799331, 15810020, 26083025, 18725978, 25798211, 15492928, 15239132, 18281249, 25503501, 11571648, 15095295, 11461078, 12805407, 24713400, 12049740, 19782031, 17517688, 27878467, 27716369, 16816021, 30851065, 30580288, 31159747, 31050813, 31844177, 32255556, 32243226, 24506336, 30441849, 33670479, 31447099). ClinVar contains an entry for this variant (Variation ID: 5591). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic, due to the probability of this variant for being a possible moderate risk factor for HBOC.

This c.470T>C (p.Ile157Thr) variant in the CHEK2 gene has been reported to be associated with cancer susceptibility, including significant association with increased risk of breast and colon cancer in large meta-analysis studies [odds ratios ~1.5, PMID: 22901170, 22799331, 23713947]. Co-segregation in families is variable: while families have been reported with complete penetrance, others show incomplete penetrance [PMID 22419737]. In vitro and in vivo studies have shown that the mutant allele does not affect the kinase activity of the protein [PMID 11719428] but does affect the dimerization of the protein in a dominant negative manner, resulting in the lack of autophosphosphorylation [PMID 12805407]. The mutant protein also impaired the binding of CHEK2 to check point proteins including CDC25A in response to DNA damage [PMID 11298456]. This variant was reported in 497 heterozygous and 6 homozygous individuals in the ExAC population database (http://exac.broadinstitute.org/variant/22-29121087-A-G). Isoleucine at amino acid position 157 of the CHEK2 protein is conserved in mammals. While not validated for clinical use, computer-based algorithms (SIFT and Polyphen-2) predict this p.Ile157Thr change to be deleterious. It is thus classified as a pathogenic variant.

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 33986034) - PS3_supporting. The c.470T>C;p.(Ile157Thr) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 5591; PMID: 33986034; 33670479; 32243226; 23713947; 31844177; 31159747; 31050813; 30851065; 30441849; 22058216; 30580288)-PS4. Pathogenic missense variant in this residue have been reported (Clinvar ID: 265327) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 22058216; 30580288)PP1.and allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is likely pathogenic

CHEK2 NM_007194.4 exon 4 p.Ile157Thr (c.470T>C): This variant has been reported in the literature in numerous individuals with a history of cancer; meta-analyses have shown that patients with this variant have a slightly increased risk of breast cancer (OR=1.48-1.58) (Liu 2012 PMID:22799331; Han 2013 PMID:23713947) and colorectal cancer (OR=1.48-1.67) (Liu 2012 PMID: 22901170; Han 2013 PMID:23713947). This variant has also been found to confer an increased risk of additional cancers including kidney, prostate, thyroid, and gastric cancer (Cybulski 2004 PMID:15492928; Teodorczyk 2013 PMID:23296741; Wójcicka 2014 PMID:24599715). This variant is present in 2.5% (627/25118) of Finnish alleles, and in 18 homozygotes, in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/22-29121087-A-G?dataset=gnomad_r2_1), and is present in ClinVar, with classifications ranging from Uncertain significance to Pathogenic; one lab classified it as a Risk Factor (Variation ID:5591). Evoluationary conservation and computational predictive tools for this variant are unclear. There is conflicting functional evidence in the literature but the majority of studies suggest that this variant impairs the CHEK2 protein's ability to bind and phosphorylate certain substrates and impacts the cellular response to DNA damage, with some suggesting a potential dominant negative effect (Selected publications: Falck 2001 PMID:11298456; Falck 2001 PMID:11571648; Li 2002 PMID:12049740; Schwarz 2003 PMID:12805407; Roeb 2012 PMID:22419737). However, these studies may not accurately represent biological function in humans and it is unclear how these findings may relate to cancer risk. This variant has also been referred to in the literature as a "risk allele" (Senal-Cosar 2019 PMID:31147632; Vargas-Parra 2020 PMID:32906215). In summary, based on the well-defined moderate increase in cancer risk and functional evidence suggesting a deleterious impact, this variant is classified as Likely Pathogenic; however, because of the relatively low increased risk of cancer associated with this variant, it may instead be more accurately described as a risk allele.

The CHEK2 c.470T>C (p.Ile157Thr) missense change has an overall frequency of 0.49% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/22-29121087-A-G?dataset=gnomad_r2_1). The variant has been widely reported to be associated with cancer susceptibility, including significant associations with increased risk of breast and colon cancer in large meta-analysis studies (odds ratios ~1.5, PMID: 15239132, 15810020, 15492928, 22901170, 22799331, 23713947). Co-segregation in families is variable, with some families exhibiting complete penetrance and others exhibiting incomplete penetrance (PMID: 22419737). In silico tools and functional assays are not in agreement about the effect of this variant on protein function. Functional assays have reported that this variant affects the dimerization of the protein in a dominant negative manner resulting in a lack of autophosphorylation (PMID 12805407). In addition, functional assays have shown that the variant does not affect the kinase activity of the protein (PMID: 11719428), but it does impair the binding of CHEK2 to other proteins (PMID: 11298456, 12049740). In summary, this variant meets criteria to be classified as likely pathogenic with evidence indicating lower penetrance.

I157T has a reduced penetrance compared to the pathogenic CHEK2 mutation, c.1100delC.

Case control studies suggest this variant is associated with several types of cancer, including breast, colon, prostate, gastric, renal, and thyroid cancers, though some odds ratios are only modestly elevated (Seppala 2003, Cybulski 2004, Kilpivaara 2006, Suchy 2010, Desrichard 2011, Liu 2012, Roeb 2012, Han 2013, Teodorczyk 2013, Kaczmarek-Rys 2015, Siolek 2015, Carlo 2018); Published functional studies demonstrate a damaging effect with respect to autophosphorylation, binding of downstream targets, and DNA damage response, and may exhibit a dominant-negative effect, while studies assessing kinase activity have varied results (Falck 2001a, Falck 2001b, Lee 2001, Wu 2001, Li 2002, Schwarz 2003, Kilpivaara 2004, Roeb 2012, Delimitsou 2019, Kleiblova 2019, Boonen 2021); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 19876921, 24880342, 30851065, 15087378, 14612911, 28040716, 26681312, 28680382, 28779002, 28503720, 28152038, 29520813, 30152102, 20643596, 18058223, 22799331, 22901170, 25583358, 23713947, 15810020, 22114986, 24728327, 20658728, 12610780, 18996005, 11461078, 22811390, 19782031, 10617473, 24557336, 19030985, 12805407, 22058216, 25798211, 16574953, 18281249, 18725978, 24599715, 23296741, 16816021, 28135136, 27488870, 27696107, 27595995, 27616075, 27878467, 27249685, 27632928, 28008555, 27751358, 27716369, 26084796, 26264438, 27153395, 28709830, 26991782, 28657667, 15492928, 29368341, 29356917, 29458332, 29682443, 28837162, 26556299, 28724667, 29902706, 21876083, 12049740, 15239132, 16835864, 11571648, 29978187, 30067863, 15095295, 30425093, 29506128, 29445900, 29961768, 18930998, 30322717, 31050813, 29607586, 31159747, 30676620, 29723101, 30612635, 31360903, 31206626, 11298456, 11053450, 22419737, 11719428, 30672594, 30306255, 32255556, 31447099, 32081490, 31980526, 33986034, 34347074, 34308366, 33466343, 34570182, 33057200, 33144682, 33558524, 32504211, 32906215, 34903604)

ACMG classification criteria: PS3 supporting, PP1 supporting

This variant has been reported in the literature in numerous individuals with a history of cancer; meta-analyses have shown that patients with this variant have a slightly increased risk of breast cancer (OR=1.48-1.58) (Liu 2012 PMID:22799331; Han 2013 PMID:23713947) and colorectal cancer (OR=1.48-1.67) (Liu 2012 PMID: 22901170; Han 2013 PMID:23713947). This variant has also been found to confer an increased risk of additional cancers including kidney, prostate, thyroid, and gastric cancer (Cybulski 2004 PMID:15492928; Teodorczyk 2013 PMID:23296741; Wójcicka 2014 PMID:24599715). This variant is present in 2.5% (627/25118) of Finnish alleles, and in 18 homozygotes, in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/22-29121087-A-G?dataset=gnomad_r2_1), and is present in ClinVar, with classifications ranging from VUS to Pathogenic; one lab classified it as a Risk Factor (Variation ID:5591). Evoluationary conservation and computational predictive tools for this variant are unclear. There is conflicting functional evidence in the literature but the majority of studies suggest that this variant impairs the CHEK2 protein's ability to bind and phosphorylate certain substrates and impacts the cellular response to DNA damage, with some suggesting a potential dominant negative effect (Selected publications: Falck 2001 PMID:11298456; Falck 2001 PMID:11571648; Li 2002 PMID:12049740; Schwarz 2003 PMID:12805407; Roeb 2012 PMID:22419737). However, these studies may not accurately represent biological function in humans and it is unclear how these findings may relate to cancer risk. This variant has also been referred to in the literature as a "risk allele" (Senal-Cosar 2019 PMID:31147632; Vargas-Parra 2020 PMID:32906215). In summary, based on the well-defined moderate increase in cancer risk and functional evidence suggesting a deleterious impact, this variant is classified as Likely Pathogenic; however, because of the relatively low increased risk of cancer associated with this variant, it may instead be more accurately described as a risk allele.

This missense variant replaces isoleucine with threonine at codon 157 in the FHA domain 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). Functional studies have shown that this variant does not significantly impact phosphorylation of a downstream target protein (PMID: 31050813, 34903604) and results in a reduced binding of the CHEK2 protein to BRCA1, CDC25A and TP53 proteins in vitro and may have a dominant-negative effect on CHEK2 function (PMID: 11571648, 12049740, 15239132, 22419737). These observations do not directly prove that this results in an increased cancer risk. Multiple large case-control studies and meta analyses have shown that this variant is associated with slightly increased risk of breast cancer (OR=1.43-1.90) (PMID: 15239132, 18930998, 22799331, 23713947, 27751358) and colorectal cancer (OR=1.48-1.67) (PMID: 22901170, 23713947). One study has reported no significant association of this variant with breast cancer relapse or breast cancer-associated death (PMID: 27716369). This variant is common in the population and has been identified in 1391/282816 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. Please note that the breast cancer risk associated with this variant is much lower than other known pathogenic CHEK2 variants, such as c.1100delC (ClinVar variation ID: 128042).

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 157 of the CHEK2 protein (p.Ile157Thr). This variant is present in population databases (rs17879961, gnomAD 2.5%), and has an allele count higher than expected for a pathogenic variant. This variant has been reported in the literature in large meta-analyses involving several thousand cases and controls. Individuals who carried the Ile157Thr variant had a slightly increased risk of breast cancer (OR=1.48-1.58) (PMID: 22799331, 23713947), and colorectal cancer (OR=1.48-1.67) (PMID: 22901170, 23713947). The risk was found to be more pronounced for lobular type breast tumors (OR=4.17) (PMID: 22799331). In addition, smaller case-control studies suggest this variant may also lead to increased risk of additional cancers, including kidney, prostate, thyroid, and gastric cancer (PMID: 15492928, 23296741, 24599715). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5591). 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 find that this missense change reduces the binding of the CHEK2 protein to Cdc25A, BRCA1 and p53 proteins in vitro and may have a dominant-negative effect in cells, although it does not have an effect on CHEK2 protein kinase activity (PMID: 11298456, 11571648, 15239132, 12049740, 22419737). The relationship between these experimental findings and cancer risk is unclear. In summary, this variant is reported to cause disease. However, as this variant is associated with a lower penetrance than other pathogenic alleles in the CHEK2 gene, it has been classified as Pathogenic (low penetrance).

The CHEK2 c.470T>C; p.Ile157Thr variant (rs17879961) is reported in the medical literature in large case-controlled meta-analyses as associated with a slightly increased risk of breast cancer, colon cancer, kidney cancer, prostate cancer, thyroid cancer, gastric, and pancreatic cancer (Cybulski 2004, Han 2013, Obazee 2019, Teodorczyk 2013). In vitro assays suggest the variant protein has wildtype kinase activity but fails to interact with normal binding partners (Falck 2001, Li 2002, Wu 2001). The p.Ile157Thr variant is listed as pathogenic or likely pathogenic by numerous laboratories in ClinVar (Variation ID: 5591), though it is found in the general population with an overall allele frequency of 0.49% (1391/282816 alleles) in the Genome Aggregation Database. Due to the small but statistically significant increased risk of cancer, this variant is classified as a low penetrance likely pathogenic variant. References: Cybulski C et al. CHEK2 is a multiorgan cancer susceptibility gene. Am J Hum Genet. 2004 Dec;75(6):1131-5. PMID: 15492928. Falck J et al. Functional impact of concomitant versus alternative defects in the Chk2-p53 tumour suppressor pathway. Oncogene. 2001 Sep 6;20(39):5503-10. PMID: 11571648. Han FF et al. The effect of CHEK2 variant I157T on cancer susceptibility: evidence from a meta-analysis. DNA Cell Biol. 2013 Jun;32(6):329-35. PMID: 23713947. Li J et al. Structural and functional versatility of the FHA domain in DNA-damage signaling by the tumor suppressor kinase Chk2. Mol Cell. 2002 May;9(5):1045-54. PMID: 12049740. Obazee O et al. Germline BRCA2 K3326X and CHEK2 I157T mutations increase risk for sporadic pancreatic ductal adenocarcinoma. Int J Cancer. 2019 Aug 1;145(3):686-693. PMID: 30672594. Teodorczyk U et al. The risk of gastric cancer in carriers of CHEK2 mutations. Fam Cancer. 2013 Sep;12(3):473-8. PMID: 23296741. Wu X et al. Characterization of tumor-associated Chk2 mutations. J Biol Chem. 2001 Jan 26;276(4):2971-4. PMID: 11053450.

The CHEK2 c.470T>C(p.(Ile157Thr) missense variant, also known as c.599T>C p.(Ile200Thr), is a recurrent variant evaluated in multiple epidemiological studies. A meta-analysis of 15 different studies (including 19,621 cases and 27,001 controls) by Liu et al. (2012a) found a statistically significant association between carrying the p.Ile157Thr variant and increase in the risk of breast cancer overall (OR=1.48), familial breast cancer (OR=1.48), early-onset breast cancer (OR=1.47) and lobular breast cancer (OR = 4.17). The association of the p.Ile157Thr variant and increased risk of breast cancer was also supported by Han et al. (2013) (OR = 1.58). A similar meta-analysis of seven different studies (including 4,029 cases and 13,844 controls), also by Liu et al. (2012b) found a statistically significant association between carrying the p.Ile157Thr variant and increase in the risk of colon cancer overall (OR = 1.61), sporadic colon cancer (OR = 1.48) and familial colon cancer (OR=1.97). The association of the p.Ile157Thr variant and increased risk of colon cancer was also supported by Han et al. (2013) (OR = 1.67). The p.Ile157Thr variant has also been associated with the risk of developing other cancers including prostate cancer in several studies including Cybulski et al. (2006) with odds ratios of up to 2.7, and thyroid cancer with odds ratios of up to 2.8 (Siolek et al. 2015). The p.Ile157Thr variant is localized in the functionally important FHA domain of the CHEK2 gene. Functional studies by Kilpivaara et al. (2004) demonstrated the variant protein was stable but dimerized with the normal CHEK2 protein when co-expressed in human cells, suggesting a dominant negative effect on the amount of normal CHEK2 protein in carriers of the variant. The p.Ile157Thr variant protein has also been shown to be defective in its ability to bind and phosphorylate Cdc25A and to bind p53 and BRCA1 (Falck et al. 2001a; Falck et al. 2001b; Li et al. 2002). The highest frequency of this allele in the Genome Aggregation Database is 0.02496 in the European (Finnish) population (version 2.1.1). In the literature, the allele frequency has been estimated at approximately 5% some northern and eastern European populations, where it is considered as a founder variant (Desrichard et. al 2016). Based on the collective evidence, the p.Ile157Thr variant is classified as pathogenic for CHEK2-related cancer susceptibility. It should be noted that while this increased risk for various cancers is widely reported in association with the p.Ile157Thr variant, this additional risk is low to moderate in magnitude.

The c.470T>C (p.I157T) alteration is located in exon 4 (coding exon 3) of the CHEK2 gene. This alteration results from a T to C substitution at nucleotide position 470, causing the isoleucine (I) at amino acid position 157 to be replaced by a threonine (T). Several large case-control studies and meta-analyses have estimated a 1.5-fold increased risk of breast cancer (4-fold risk for lobular breast cancer), up to a 2-fold increased risk of colorectal cancer, and an increased risk for prostate cancer and thyroid cancer (precise risk unknown) associated with the p.I157T mutation (Zhang, 2011; Liu, 2012; Han, 2013; Liu, 2012; Cybulski, 2004; Kaczmarek-Ry, 2015; Sioek, 2015). Incomplete segregation of p.I157T with disease has been reported in familial breast cancer kindreds and has also been observed at high frequencies in general population databases, consistent with previous observations of intermediate cancer risk and reduced penetrance (Roeb, 2012). This amino acid position is well conserved in available vertebrate species. This alteration is located in the FHA protein domain and although there are some conflicting functional studies (Wu, 2001; Schwarz, 2003; Lee, 2001; Lee and Chung, 2001; Ahn, 2002; Kilpivaara, 2004; Cai, 2009), the majority agree that this alteration confers impaired phosphoprotein binding and kinase activities on some CHK2 substrates, which could contribute to defective DNA damage repair and delay the cell cycle checkpoint mechanism (Falck; 2001; Falck, 2001; Li, 2002; Roeb, 2012). The in silico prediction for this alteration is inconclusive. Roeb et al., 2012 speculate that fewer alignable sequences in the FHA domain may limit the predictive value of in silico models for alterations in this region. Based on the available evidence, this alteration is classified as pathogenic.

CHEK2: PS3:Supporting, PS4:Supporting, BP2

ACMG Guidelines 2015 criteria The CHEK2 variant p.Ile157Thr was observed in the kinase domain in a tight region between amino acid 407-499 and in a mutation hotspot of 13 pathogenic variants (PM1 Pathogenic Moderate). 4 functional studies (PMID: 12049740, 15239132, 11298456, & 11571648) confirmed the likely pathogenic effect of this variant (PS3 Pathogenic Strong). An alternative variant (chr22:29121087 A>C (Ile157Ser)) at the same amino acid residue is classified as likely pathogenic (PM5 Pathogenic Moderate). Meantime, majority of missense variants detected in CHEK2 are pathogenic and known cause of disease (PP2 Pathogenic Supporting). The homozygous allele count in GnomAD exomes is 11 which is greater the threshold 3 for dominant and recessive gene CHEK2 (BS2 Benign Strong). In our study the variant p.Ile157Thr was found in a 46-year-old female with family history of cancer. In summary, based on the evidence and given the previous reports of the variant in association with increased risk of breast cancer, we classified this variant as a Likely Pathogenic.

The CHEK2 c.470T>C (p.Ile157Thr) variant was identified in 634 of 21,958 proband chromosomes (frequency: 0.03) from individuals or families with Li-Fraumeni Syndrome, colorectal, endometrial, and breast cancer and was present in 497 of 21,838 control chromosomes (frequency: 0.02) from healthy individuals (Cybulski 2006, Kilpivaara 2004, Lee 2001, Schutte 2003, Kilpivaara 2006, Konstantinova 2009, Kuusisto 2011, Serrano-Fernandez 2008, Bak 2014, Kleibl 2009, Lener 2016). The variant was also identified in dbSNP (rs17879961) with likely pathogenic, pathogenic allele; and ClinVar (classified as pathogenic by Ambry Genetics, Baylor, Invitae, Color, Quest Diagnostics Nichols Institute San Juan Capistrano, Mayo Clinic, True Health Diagnostics; likely pathogenic by GeneDx, PreventionGenetics, Counsyl, Pathway Genomics and 4 other submitters, uncertain significance by Integrated Genetics and 2 other submitters and risk factor/pathogenic by OMIM). The variant was identified in control databases in 1309 of 268,296 chromosomes (18 homozygous) at a frequency of 0.005 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Finnish in 627 of 25,102 chromosomes (freq: 0.02), Other in 55 of 6706 chromosomes (freq: 0.008), European in 608 of 118,138 chromosomes (freq: 0.005), Ashkenazi Jewish in 14 of 9860 chromosomes (freq: 0.001), African in 2 of 23,612 chromosomes (freq: 0.00009), Latino in 2 of 35,108 chromosomes (freq: 0.00006), South Asian in 1 of 30,522 chromosomes (freq: 0.00003); the variant was not observed in the East Asian population. The p.Ile157Thr variant has been observed in our laboratory in multiple cases and described extensively in the literature. The variant was identified in our laboratory in a case with a co-occurring PALB2 pathogenic variant (c.424A>T; p.Lys142*) and in the literature with the high risk pathogenic CHEK2 c.1100delC variant (Kuusisto 2011). In multiple case-control studies, the presence of the variant was determined to significantly increase the risk of breast and colorectal cancer in Polish and Finnish populations (Kilpivaara 2004, Kilpivaara 2006, Cybulski 2006). The functional role of the variant remains uncertain as several studies have yielded confounding observations. In vitro expression of the variant altered the ability of CHEK2 to bind p53 and also impaired CHEK2 oligomerization (Falck 2001, Schwarz 2003). The consequences on phosphorylation varied as p.Ile157Thr did not alter CHEK2 kinase activity, however in a different study, the variant reduced the CHEK2 autophosphorylation activity (Lee 2001, Schwarz 2003). The p.Ile157 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 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) do not predict a difference in splicing. The p.Ile157Thr has been the subject of discussion regarding discordant results between clinical laboratories with discrepancies based on the weight of evidences used in each analysis (Mundt 2017, Balmana 2016). The combination of conflicting functional data and high allele frequencies in control populations highlight the challenge of interpreting low penetrance alleles in a format designed for high-penetrance alleles. Studies have identified a modest odds ratio displaying that the variant is more likely to be found in patients with cancer then in healthy controls and this seems to be consistent with functional studies displaying only modest decreases in protein function. However it remains unclear whether other factors contribute to disease in affected patients with this variant and at this time we cannot determine whether the variant plays a definitive pathogenic role in disease. 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. However, this variant may be a risk factor for hereditary cancer.

The CHEK2 c.470T>C (p.Ile157Thr) variant was identified in 634 of 21,958 proband chromosomes (frequency: 0.03) from individuals or families with Li-Fraumeni Syndrome, colorectal, endometrial, and breast cancer and was present in 497 of 21,838 control chromosomes (frequency: 0.02) from healthy individuals (Cybulski 2006, Kilpivaara 2004, Lee 2001, Schutte 2003, Kilpivaara 2006, Konstantinova 2009, Kuusisto 2011, Serrano-Fernandez 2008, Bak 2014, Kleibl 2009, Lener 2016). The variant was also identified in dbSNP (rs17879961) with likely pathogenic, pathogenic allele; and ClinVar (classified as pathogenic by Ambry Genetics, Baylor, Invitae, Color, Quest Diagnostics Nichols Institute San Juan Capistrano, Mayo Clinic, True Health Diagnostics; likely pathogenic by GeneDx, PreventionGenetics, Counsyl, Pathway Genomics and 4 other submitters, uncertain significance by Integrated Genetics and 2 other submitters and risk factor/pathogenic by OMIM). The variant was identified in control databases in 1309 of 268,296 chromosomes (18 homozygous) at a frequency of 0.005 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Finnish in 627 of 25,102 chromosomes (freq: 0.02), Other in 55 of 6706 chromosomes (freq: 0.008), European in 608 of 118,138 chromosomes (freq: 0.005), Ashkenazi Jewish in 14 of 9860 chromosomes (freq: 0.001), African in 2 of 23,612 chromosomes (freq: 0.00009), Latino in 2 of 35,108 chromosomes (freq: 0.00006), South Asian in 1 of 30,522 chromosomes (freq: 0.00003); the variant was not observed in the East Asian population. The p.Ile157Thr variant has been observed in our laboratory in multiple cases and described extensively in the literature. The variant was identified in our laboratory in a case with a co-occurring PALB2 pathogenic variant (c.424A>T; p.Lys142*) and in the literature with the high risk pathogenic CHEK2 c.1100delC variant (Kuusisto 2011). In multiple case-control studies, the presence of the variant was determined to significantly increase the risk of breast and colorectal cancer in Polish and Finnish populations (Kilpivaara 2004, Kilpivaara 2006, Cybulski 2006). The functional role of the variant remains uncertain as several studies have yielded confounding observations. In vitro expression of the variant altered the ability of CHEK2 to bind p53 and also impaired CHEK2 oligomerization (Falck 2001, Schwarz 2003). The consequences on phosphorylation varied as p.Ile157Thr did not alter CHEK2 kinase activity, however in a different study, the variant reduced the CHEK2 autophosphorylation activity (Lee 2001, Schwarz 2003). The p.Ile157 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 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) do not predict a difference in splicing. The p.Ile157Thr has been the subject of discussion regarding discordant results between clinical laboratories with discrepancies based on the weight of evidences used in each analysis (Mundt 2017, Balmana 2016). The combination of conflicting functional data and high allele frequencies in control populations highlight the challenge of interpreting low penetrance alleles in a format designed for high-penetrance alleles. Studies have identified a modest odds ratio displaying that the variant is more likely to be found in patients with cancer then in healthy controls and this seems to be consistent with functional studies displaying only modest decreases in protein function. However it remains unclear whether other factors contribute to disease in affected patients with this variant and at this time we cannot determine whether the variant plays a definitive pathogenic role in disease. 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. However, this variant may be a risk factor for hereditary cancer.

Variant reported in multiple Invitae PIN participants. Variant interpreted as Pathogenic and reported most recently on 12/10/20 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.

Variant identified in multiple GenomeConnect participants. Variant classified as Likely pathogenic and reported on 11-27-2021 by Lab or GTR ID 506138. Variant classified as Pathogenic and reported on 05-09-2018 by Lab or GTR ID 61756. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.