22-28696905-A-G

Position:

• chr22-28696905-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1 PP3_Moderate

The NM_007194.4(CHEK2):​c.1091T>C​(p.Ile364Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 1,454,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I364K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000023 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:9
• Conservation: PhyloP100: 7.31

Genes affected

CHEK2 (HGNC:16627): (checkpoint kinase 2) In response to DNA damage and replication blocks, cell cycle progression is halted through the control of critical cell cycle regulators. The protein encoded by this gene is a cell cycle checkpoint regulator and putative tumor suppressor. It contains a forkhead-associated protein interaction domain essential for activation in response to DNA damage and is rapidly phosphorylated in response to replication blocks and DNA damage. When activated, the encoded protein is known to inhibit CDC25C phosphatase, preventing entry into mitosis, and has been shown to stabilize the tumor suppressor protein p53, leading to cell cycle arrest in G1. In addition, this protein interacts with and phosphorylates BRCA1, allowing BRCA1 to restore survival after DNA damage. Mutations in this gene have been linked with Li-Fraumeni syndrome, a highly penetrant familial cancer phenotype usually associated with inherited mutations in TP53. Also, mutations in this gene are thought to confer a predisposition to sarcomas, breast cancer, and brain tumors. This nuclear protein is a member of the CDS1 subfamily of serine/threonine protein kinases. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 17 uncertain in NM_007194.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.914

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHEK2	NM_007194.4	c.1091T>C	p.Ile364Thr	missense_variant	10/15	ENST00000404276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHEK2	ENST00000404276.6	c.1091T>C	p.Ile364Thr	missense_variant	10/15	1	NM_007194.4	P2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000239 AC: 6 AN: 251208 Hom.: 0 AF XY: 0.0000295 AC XY: 4 AN XY: 135808

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000463

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000234 AC: 34 AN: 1454162 Hom.: 0 Cov.: 29 AF XY: 0.0000318 AC XY: 23 AN XY: 723930

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.0000271

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000312 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.0000330 AC: 4

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 23, 2020	DNA sequence analysis of the CHEK2 gene demonstrated a sequence change, c.1091T>C, in exon 10 that results in an amino acid change, p.Ile364Thr. This sequence change has been described in the gnomAD database in six individuals with a low overall population frequency of 0.0024% (dbSNP rs774179198). The p.Ile364Thr change has been reported in individuals with breast cancer, rectal cancer, and with suspected Lynch syndrome (PMIDs: 18725978, 27978560, 25980754, 31050813). The p.Ile364Thr change affects a moderately conserved amino acid residue located in a domain of the CHEK2 protein that is known to be functional. The p.Ile364Thr substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Functional studies have provided conflicting results regarding CHEK2 protein function in the presence of this sequence change (PMIDs: 18725978, 31050813, 30851065). Due to these contrasting evidences, the clinical significance of the p.Ile364Thr change remains unknown at this time. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 21, 2023	This missense variant replaces isoleucine with threonine at codon 364 of the CHEK2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported the mutant protein to exhibit normal dimerization and only mildly reduced kinase activity in human cells (PMID: 18725978, 31050813) and intermediate function in yeast complementation assay (PMID: 30851065). Loss of kinase activity observed in in vitro assays using bacterially expressed recombinant protein may be attributed to the lack of appropriate post-translational modifications that can modulate CHEK2 activity in vivo (PMID: 31050813). This variant has been reported in individuals affected with breast cancer without strong family history (PMID: 18725978, 31050813), as well as in individuals affected with diffuse large B cell lymphoma (PMID 23960188), colorectal cancer (PMID: 27978560) and polyps and/or Lynch syndrome-associated cancers (PMID: 25980754). This variant has been identified in 6/251208 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	May 08, 2023	The p.I364T variant (also known as c.1091T>C), located in coding exon 9 of the CHEK2 gene, results from a T to C substitution at nucleotide position 1091. The isoleucine at codon 364 is replaced by threonine, an amino acid with similar properties. This alteration has been identified in cohorts of breast and colorectal cancer patients (Chrisanthar R et al. PLoS ONE. 2008 Aug;3:e3062; Pearlman R et al. JAMA Oncol. 2017 Apr;3:464-471; Hauke J et al. Cancer Med. 2018 04;7:1349-1358). This variant was also observed in 1/3251 individuals who met eligibility criteria for hereditary breast and ovarian cancer syndrome (Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). Functional data for this variant are conflicting with some studies reflecting intermediate activity in an in vitro kinase assay and a yeast-based cell growth, while another in vitro kinase assay found this variant non-functional and yet another human-cell-based trans-phosphorylation assay found this variant functional (Chrisanthar R et al. PLoS ONE. 2008 Aug;3:e3062; Delimitsou A et al. Hum Mutat. 2019 05;40:631-648; Kleiblova P et al. Int J Cancer. 2019 10;145:1782-1797). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Familial cancer of breast Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 364 of the CHEK2 protein (p.Ile364Thr). This variant is present in population databases (rs774179198, gnomAD 0.004%). This missense change has been observed in individual(s) with breast cancer, rectal cancer, or undergoing genetic testing for Lynch syndrome (PMID: 18725978, 25980754, 27978560, 31050813). ClinVar contains an entry for this variant (Variation ID: 185975). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 18725978, 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	Baylor Genetics	Mar 04, 2024	- -

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

Nov 18, 2019

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Feb 12, 2024

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: intermediate response to DNA damage, partially reduced kinase activity in vitro but similar to wildtype in vivo (PMID: 18725978, 30851065, 31050813); Observed in individuals with a personal history of breast and other cancers (PMID: 18725978, 25980754, 27978560, 29522266, 31050813); This variant is associated with the following publications: (PMID: 27708748, 32948195, 18725978, 23960188, 25980754, 22229248, 27978560, 29596542, 29522266, 30851065, 31050813, 31409080, 19782031, 22419737) -

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.Ile364Thr variant was identified in in 1 breast cancer case in a review and compilation of 147 cancer genomic studies in different populations, with CHEK2 mutations found at a greater frequency in breast, colorectal and non-small cell lung cancers overall (Guauque-Olarte 2016), and in another study looking at B cell lymphomas, in one Swedish individual (germline status undetermined, Miranda 2013). A functional study looking at in vitro kinase activity showed partially reduced kinase activity, with the affected individual having no family history of cancer disease (Chrisanthar 2008). The variant was also identified in dbSNP (ID: rs774179198) “With Uncertain significance allele”, ClinVar (classified as uncertain significance in 2017, submitters: Ambry Genetics, GeneDx, Invitae), Clinvitae (3x), and the Zhejiang Colon Cancer Database (1x, co-occurring with a pathogenic CHEK2 variant (c.283C>T/p.Arg95X), and was not identified in Cosmic and MutDB. The variant was identified in control databases in 6 of 246012 chromosomes at a frequency of 0.00002 (Genome Aggregation Consortium Feb 27, 2017), being identified in the following populations: Latino in 1 of 33570 chromosomes (frequency: 0.00003), European Non-Finnish in 4 of 111552 chromosomes (frequency: 0.00004), and European Finnish in 1 of 22260 chromosomes (frequency: 0.00004). The p.Ile364Thr residue is conserved in in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out 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	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Pathogenic	0.19
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.35	T;T;.;T;.;T;.;.
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	.;.;D;.;D;D;D;T
M_CAP	Benign	0.084	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.33	T
MutationAssessor	Benign	1.1	L;L;.;L;.;L;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.78	T
PROVEAN	Uncertain	-3.7	D;D;.;D;D;.;D;D
REVEL	Pathogenic	0.70
Sift	Uncertain	0.0070	D;D;.;D;D;.;D;D
Sift4G	Uncertain	0.028	D;D;.;D;D;.;D;D
Polyphen		1.0	D;D;.;D;D;D;D;.
Vest4		0.89
MutPred		0.84		Loss of stability (P = 0.0019);Loss of stability (P = 0.0019);.;Loss of stability (P = 0.0019);.;Loss of stability (P = 0.0019);.;.;
MVP		0.88
MPC		0.15
ClinPred		0.88	D
GERP RS		5.7
Varity_R		0.80
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs774179198; hg19: chr22-29092893;