22-28725338-T-C
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1PP3_StrongPP5_Very_Strong
The NM_007194.4(CHEK2):c.349A>G(p.Arg117Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,613,986 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 Likely pathogenic (★★).
Frequency
Consequence
NM_007194.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251236Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135772
GnomAD4 exome AF: 0.000193 AC: 282AN: 1461792Hom.: 0 Cov.: 32 AF XY: 0.000183 AC XY: 133AN XY: 727192
GnomAD4 genome 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not provided Pathogenic:14Other:1
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In the published literature, the variant has been reported in individuals with breast cancer (PMIDs: 31263054 (2019), 31206626 (2019), 31090900 (2019), 30303537 (2019), 30426508 (2018), 30128536 (2018), 28709830 (2017), 28503720 (2017), 27553368 (2016), 25503501 (2015)), prostate cancer (PMIDs: 29659569 (2018), 29439820 (2018)), and pancreatic cancer (PMIDs: 29945567 (2018), 29922827 (2018)). In addition, families show evidence of co-segregation with breast cancer (PMID: 12610780 (2003)). Functional studies in the published literature report this variant causes loss of CHEK2 activity (PMIDs: 30851065 (2019), 22419737 (2012), 18725978 (2008), 16982735 (2006), 16835864 (2006)). The frequency of this variant in the general population, 0.00019 (24/128958 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
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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. -
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CHEK2: PP1:Strong, PS4, PP3, PS3:Supporting, BP1 -
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Published functional studies demonstrate a damaging effect: reduced auto-phosphorylation, protein instability, impaired kinase activity, and loss of CHEK2-mediated DNA damage response (Wu 2006, Sodha 2006, Chrisanthar 2008, Roeb 2012, Delimitsou 2019); Case control study in Europeans suggests this variant is associated with female breast cancer (Southey 2016); Observed in many individuals with CHEK2-related cancers (Sodha 2002, Kleibl 2008, Desrichard 2011, Le Calvez-Kelm 2011, Roeb 2012, Castera 2014, Moran 2017, Pinto 2016, Lu 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at a significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 12454775, 18058223, 22114986, 21244692, 22419737, 24549055, 27798748, 27553368, 30128536, 27595995, 16835864, 16982735, 18725978, 30851065, 33158149, 31447099, 31206626, 31263054, 30303537, 30676620, 31090900, 30322717, 29922827, 15095295, 12610780, 30666157, 30426508, 29659569, 29945567, 30067863, 30256826, 28125075, 29439820, 28553140, 28709830, 28503720, 28008555, 28452373, 27498913, 28082821, 26681312, 23555315, 27751358, 15488637, 15385111, 23960188, 15818573) -
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Familial cancer of breast Pathogenic:9
This variant is considered likely pathogenic. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. -
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This CHEK2 variant was identified in a female patient diagnosed with breast cancer at 38 years old, and whose mother also have had bilateral breast cancer at ages 40 and 42 years old. Mutation screening in BRCA1 and BRCA2 genes gave negative results. -
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PS3, PS4_STR -
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This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 117 of the CHEK2 protein (p.Arg117Gly). This variant is present in population databases (rs28909982, gnomAD 0.02%). This missense change has been observed in individual(s) with CHEK2-related cancers (PMID: 12454775, 12610780, 21244692, 28503720). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 128071). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CHEK2 function (PMID: 16982735, 18725878, 22419737). For these reasons, this variant has been classified as Pathogenic. -
Hereditary cancer-predisposing syndrome Pathogenic:6
PS3, PS4_Moderate, PP3_Moderate c.349A>G, located in exon 3 of the CHEK2 gene, replaces arginine with glycine at codon 117 of the CHEK2 protein, p.(Arg117Gly). This amino acid position is highly conserved in available vertebrate species, FHA-domain (115-175 aa). This variant is found in 22/117950 with a filtering allele frequency of 0.01% in the gnomAD v2.1.1 database (European non-Finnish non-cancer data set). The SpliceAI algorithm predicts no significant impact on splicing. The REVEL meta-predictor score for this variant (0.93) suggests a deleterious effect on protein function according to Pejaver 2022 thresholds (PMID: 36413997)(PP3_Moderate). Functional studies have shown that this variant causes reduced kinase activity, reduced protein stability, incomplete phosphorylation of CHEK2 protein, defective DNA damage repair in a yeast based assay (PMID: 16835864, PMID: 16982735, PMID: 18725978, PMID: 22419737, PMID: 30851065). Also, a recent CHEK2-complementation assay quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1–CHEK2-knockout cells has shown a deleterious effect (PMID: 37449874)(PS3). Southey 2016 (PMID: 27595995) reported that CHEK2 c.349A>G variant is associated with breast cancer risk (OR 2.26 (95% CI 1.29 to 3.95)(PS4_Moderate). It has been reported in the ClinVar (10x pathogenic, 31x likely pathogenic) and the LOVD (8x likely pathogenic, 2x not provided) databases. Based on currently available information, c.349A>G is classified as a likely pathogenic variant according to ACMG guidelines. -
The p.R117G variant (also known as c.349A>G), located in coding exon 2 of the CHEK2 gene, results from an A to G substitution at nucleotide position 349. The arginine at codon 117 is replaced by glycine, an amino acid with dissimilar properties. This alteration has been identified in many cancer cases including familial breast/ovarian, pancreatic and colorectal and prostate cancer cohorts (Sodha N et al. Br. J. Cancer. 2002 Dec;87:1445-8; Kleibl Z et al. Breast Cancer Res. Treat. 2008 Nov;112:159-64; Desrichard A et al. Breast Cancer Res. 2011 Nov;13:R119; Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13:R6; Moran O et al. Breast Cancer Res. Treat. 2017 Jan;161:135-142; Pinto P et al. Breast Cancer Res. Treat. 2016 Sep;159:245-56; Schutte M et al. Am. J. Hum. Genet. 2003 Apr;72:1023-8). This variant has also been reported to be a possible European founder variant leading to a significant increase in prostate cancer risk (Brandão A et al. Cancers (Basel). 2020 Nov;12(11)). Multiple functional studies have found that this variant is abnormal with respect to protein stability and kinase activity (Sodha N et al. Cancer Res. 2006 Sep;66:8966-70; Chrisanthar R et al. PLoS One. 2008 Aug;3:e3062; Roeb W et al. Hum. Mol. Genet. 2012 Jun;21:2738-44; Wu X et al. Hum. Mutat. 2006 Aug;27:742-7; Delimitsou A et al. Hum. Mutat. 2019 May;40(5):631-648; Boonen RACM et al. Cancer Res, 2022 Feb;82:615-631). This alteration was also more frequent in breast cancer cases than controls in a study from the Breast Cancer Association Consortium (BCAC) (Southey MC et al. J. Med. Genet., 2016 12;53:800-811). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
This missense variant replaces arginine with glycine at codon 117 in the FHA domain of the CHEK2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown that this variant causes reduced kinase activity, reduced protein stability, incomplete phosphorylation of CHEK2 protein and defective DNA damage repair (PMID: 16835864, 16982735, 18725978, 22419737, 30851065, 34903604, 37449874). This variant has been reported in individuals affected with breast cancer (PMID: 12454775, 12610780, 18058223, 21244692, 22114986, 23555315, 25503501, 27553368, 27798748, 28503720, 30128536, 31263054, 33030641, 33326660, 33803639, 35264596, 36315097), colorectal cancer (PMID: 30256826), prostate cancer (PMID: 33158149), and pancreatic cancer (PMID: 29922827, 29945567). Large case-control studies have shown that this variant is associated with an increased risk of breast cancer (OR 2.26, 95% CI [1.29 to 3.95], PMID: 27595995; OR=2.936, 95%CI [1.823 to 4.73], PMID: 33471991; OR=2.83, 95% CI [2.35 to 3.41], PMID: 37449874). This variant has been identified in 32/282632 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this variant has been shown to cause partial loss of CHEK2 protein function and is associated with an increased risk of breast cancer. Based on the available evidence, this variant is classified as Likely Pathogenic. -
PP3; PS3_SUP; PS4 -
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Li-Fraumeni syndrome 2 Pathogenic:3
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This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
This variant has been identified by standard clinical testing. -
CHEK2-related cancer predisposition Pathogenic:2Other:1
Variant interpreted as Likely pathogenic and reported on 03-13-2018 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. -
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 18725978; 16982735; 22419737) - PS3_moderate. The c.349A>G;p.(Arg117Gly) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 128071; PMID: 12454775; PMID: 12610780; PMID: 21244692; PMID: 28503720) -PS4. The variant is present at low allele frequencies population databases (rs28909982 – gnomAD 0.001132%; ABraOM 0.001281 frequency - http://abraom.ib.usp.br.) - PM2_supporting. In summary, the currently available evidence indicates that the variant is likely pathogenic -
The CHEK2 c.349A>G p.(Arg117Gly), also referred to c.478A>G (Arg160Gly), missense variant has been identified in individuals with a phenotype consistent with CHEK2-related cancer susceptibility. In two individuals, other pathogenic BRCA2 and CHEK2 variants were also identified (Sodha et al. 2002; Schutte et al. 2003; Le Calvez-Kelm et al. 2011; Southey et al. 2016; Susswein et al. 2016). In a large case-control study, Southey et al. (2016) showed that the p.(Arg117Gly) variant was significantly associated with breast cancer in European women (odds ratio of 2.26). In this study, odd ratios were not statistically significant for prostate cancer or ovarian cancer. The variant segregated with breast cancer in one family whereas in two families incomplete segregation was observed whereby two affected individuals did not carry the variant (Schutte et al. 2003). The highest frequency of this allele in the Genome Aggregation Database is 0.000186 in the European (non-Finnish) population (version 2.1.1). Functional studies in cells lines demonstrated reduced protein expression and stability, and impaired phosphorylation and kinase activity of the variant protein when compared to wildtype protein. However, the variant protein dimerized efficiently to wildtype CHEK2 (Sodha et al. 2006; Wu et al. 2006; Chrisanthar et al. 2008). Multiple lines of computational evidence suggest the variant may impact the gene or gene product. Based on the available evidence, the c.349A>G p.(Arg117Gly) variant is classified as likely pathogenic for CHEK2-related breast cancer susceptibility. -
CHEK2-related disorder Pathogenic:2
The CHEK2 c.349A>G variant is predicted to result in the amino acid substitution p.Arg117Gly. This is a well-documented variant reported in multiple individuals with cancers of breasts, colon, skin, kidneys, thyroid, ovaries and prostate gland (Table S1, Susswein et al. 2016. PubMed ID: 26681312; Southey et al. 2016. PubMed ID: 27595995). Earlier, Schutte and colleagues had described this variant as having no major contribution to susceptibility to breast cancer (Schutte et al. 2003. PubMed ID: 12610780). However, more recently the authors reported it to be associated with increased risk for breast cancer, but not for prostate and ovarian cancers (Southey et al. 2016. PubMed ID: 27595995). Several functional studies on this variant have indicated impaired CHEK2 functions, specifically the kinase activity and DNA damage response (Chrisanthar et al. 2008. PubMed ID: 18725978; Roeb et al. 2012. PubMed ID: 22419737). The Arg117 residue, located within the forkhead-associated domain of the CHEK2 protein, has been highly conserved during evolution (http://www.uniprot.org/uniprot/O96017). This variant is listed in the ClinVar database with interpretations of likely pathogenic and pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/128071/). This variant is reported in 0.019% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely pathogenic. -
PS3, PS4, PP3 -
Malignant tumor of breast Pathogenic:2
Variant summary: CHEK2 c.349A>G (p.Arg117Gly) results in a non-conservative amino acid change located in the Forkhead-associated (FHA) domain (IPR000253) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. This variant allele was found in 33/265114 control chromosomes at a frequency of 0.00012 (gnomAD and publications). This frequency is not higher than expected for a pathogenic variant in CHEK2 causing Breast Cancer (0.00012 vs 0.00031), allowing no conclusion about variant significance. The variant, c.349A>G, has been reported in the literature in multiple individuals affected with cancer including breast cancer, pancreatic cancer, colorectal cancer and prostate cancer (but also in controls) (Hu_2018, Lu_2018, Martin-Morales_2018, Paulo_2018, Rummel_2017, Pinto_2016, Southey_2016), with limited cosegregation information. In one study, in 3 families, 8 transmissions of the variant allele and 2 transmissions of the reference allele to affected individuals was reported (Schutte_2003). The variant has also been reported in studies that included cohorts of comprehensively genotyped patients with early onset breast cancer meeting the NCCN guidelines (Rummel_2017), and a family history of breast cancer (Pinto_2016; Moran_2017, Lu_2018). A case-control study showed evidence of association with breast cancer (OR = 2.03; Southey_2016) but no association with prostate and ovarian cancer, suggesting this might be a risk variant. FLOSSIES database reports the variant in 2 women older than age 70 years who have never had cancer. In addition, co-occurrences with other pathogenic variants have been reported (BRCA2 c.891_899delAACAGTTGTinsGATACTTCAG, p.Thr298Ilefs; CHEK2 c.1100delC, p.Thr367fsX15 (Susswein_2015); APC c.426_427delAT, p.Leu143AlafsX4 at our laboratory). However, as co-occurrence with other pathogenic variants is not mutually exclusive in cancer probands, this is not entirely supportive of a benign role of this variant. Functional in vitro and in vivo studies showed that p.R117G is incompletely phosphorylated and is not efficiently activated in response to DNA damage, showing minimal kinase activity when studied in isolation, however, it can dimerize efficiently to CHEK2 wild-type without strongly affecting the wild-type CHEK2 activity (Roeb_2012, Chrisanthar_2008, Sodha_2006, Wu_2006). Twenty ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely pathogenic (n=16) and pathogenic (n=4). Several submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic. -
The CHEK2 p.Arg117Gly variant was identified in 55 of 88752 proband chromosomes (frequency: 0.0006) from individuals or families with hereditary breast and ovarian cancer (Desrichard 2011, Kleibl 2008, Moran 2017, Pinto 2016, Schutte 2003, Sodha 2002, Southey 2016, Wu 2006). The variant was also identified in dbSNP (ID: rs28909982) as “With Pathogenic allele”, ClinVar (as pathogenic by GeneDx and Mayo Clinic; and as likely pathogenic by Ambry Genetics, Invitae, Color Genomics, University Hospital of Geneva, and Counsyl), MutDB, and Zhejiang Colon Cancer Database (4x). The variant was not identified in the Cosmic database. The variant was identified in control databases in 31 of 276970 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 2 of 24030 chromosomes (freq: 0.00008), Other in 1 of 6464 chromosomes (freq: 0.0002), Latino in 4 of 34418 chromosomes (freq: 0.0001), European in 22 of 126468 chromosomes (freq: 0.0002), Finnish in 2 of 25792 chromosomes (freq: 0.00008), while the variant was not observed in the Ashkenazi Jewish, East Asian, or South Asian populations. The p.Arg117Gly variant has been extensively studied in the literature. In vitro studies have demonstrated that the Arg117Gly variant has strongly reduced kinase activity (Chrisanthar 2008). Multiple studies found that following DNA damage with ionizing radiation, the variant protein demonstrated greatly reduced CHEK2 kinase activity (Wu 2006, Roeb 2012, Le Calvez-Kelm 2011). In addition, studies have shown that the protein encoded by this allele is phosphorylated by ATM in response to DNA damage, shows slightly to markedly reduced autophosphorylation, probably fails to oligomerize, and has severely compromised kinase activity. Sodha (2006) also concluded through bioinformatic analysis that the variant is likely to be deleterious and functional studies showed that the variant protein is less stable than the wild type protein. The p.Arg117Gly residue is conserved across mammals and other organisms, and 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, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -
Breast and/or ovarian cancer Pathogenic:1
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Inherited breast cancer and ovarian cancer Pathogenic:1
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Breast cancer, susceptibility to;C3469524:Prostate cancer susceptibility Pathogenic:1
The c.349A>G(p.Arg117Gly) variant in the CHEK2 gene (seen 31 times in gnomAD) has been observed in multiple unrelated probands and segregated in one family with BRCA1/2 negative breast cancer (PMID 12454775, 12610780, 18058223, 27595995, 27553368, 27798748). Although not validated for clinical use, the in silico programs predict this variant to be damaging. Experimental studies are consistent with this variant resulting in disruption of CHEK2 function (PMID 16982735, 16835864, 22419737). Therefore, this c.349A>G (p.Arg117Gly) variant in the CHEK2 gene is classified as pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:1
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Bone osteosarcoma;C2931456:Familial prostate cancer;C5882668:Li-Fraumeni syndrome 2 Pathogenic:1
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Predisposition to cancer Pathogenic:1
The CHEK2 c.349A>G (p.Arg117Gly) missense change has a maximum frequency of 0.019% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/22-29121326-T-C?dataset=gnomad_r2_1). Seven of seven in silico tools predict a deleterious effect of this variant on protein function (PP3). Several functional studies suggest that this variant is pathogenic, demonstrating a strongly reduced CHEK2-mediated DNA damage response, impaired kinase activity, and incomplete phosphorylation (PS3; PMID: 18725978, 22419737, 30851065, 16835864, 16982735). This variant has been identified in many cancer cases including familial breast/ovarian, prostate, pancreatic, colorectal, as well as other cancer types (PMID: 12454775, 15095295, 21244692, 26681312, 28125075, 29439820, 29659569, 29439820, 29945567, 30322717, 30256826, 28709830, 30426508, 31090900, 31263054, 31206626, 32906215, 30676620, 32906215). A case-control study showed evidence of association with breast cancer (PS4; OR = 2.26; PMID: 27595995), but no association with prostate and ovarian cancer. In addition, the variant segregated with breast cancer in three families, although it was not identified in all affected family members (PMID: 12610780) This variant is present 2x in the FLOSSIES database which contains genetic variants from women older than 70 years of age who have never had cancer (BS2_supporting; https://whi.color.com/). In summary, this variant meets criteria to be classified as likely pathogenic based on the ACMG/AMP criteria: PS3, PS4, PP3, BS2_supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at