22-28699879-T-G

Position:

• chr22-28699879-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_007194.4(CHEK2):​c.967A>C​(p.Thr323Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,848 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 (★★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CHEK2 NM_007194.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:7
• Conservation: PhyloP100: 4.78

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 Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.947

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHEK2	NM_007194.4	c.967A>C	p.Thr323Pro	missense_variant	9/15	ENST00000404276.6	NP_009125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHEK2	ENST00000404276.6	c.967A>C	p.Thr323Pro	missense_variant	9/15	1	NM_007194.4	ENSP00000385747	P2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461848 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 727230

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 08, 2023	This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk. -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 06, 2023	This missense change has been observed in individual(s) with prostate and breast cancer (PMID: 16835864, 21244692, 22419737). ClinVar contains an entry for this variant (Variation ID: 420003). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 16835864, 22419737). 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. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 323 of the CHEK2 protein (p.Thr323Pro). -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	May 25, 2018	- -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 01, 2023	The p.T323P variant (also known as c.967A>C), located in coding exon 8 of the CHEK2 gene, results from an A to C substitution at nucleotide position 967. The threonine at codon 323 is replaced by proline, an amino acid with highly similar properties. This alteration has been reported in both breast and prostate cancer cases (Wu X et al. Hum. Mutat. 2006 Aug;27(8):742-; Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13(1):R6; 7; Young EL et al. J Med Genet, 2016 06;53:366-76). Functional analysis of this alteration revealed CHEK2-mediated DNA damage response is similar to wild-type; however, this alteration has also been reported to result in partially reduced CHEK2 kinase activity (Wu X et al. Hum. Mutat. 2006 Aug;27(8):742-7; Roeb W, Higgens J, and King MC. Hum. Mol. Genet. 2012 Jun;21(12):2738-44). This residue is located in the alpha-helix of the kinase c-lobe domain; proline substitutions are typically destabilizing to the protein structure in alpha-helix regions (Le Calvez-Kelm F et al. Breast Cancer Res. 2011 Jan;13(1):R6). This amino acid position is well 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 19, 2021	This missense variant replaces threonine with proline at codon 323 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 shown that this variant causes a partial loss of CHEK2 kinase activity (PMID: 16835864) but does not affect DNA damage response of the CHEK2 protein (PMID: 22419737). This variant has been observed in individuals affected with early-onset breast caner (PMID: 21244692), familial breast cancer (PMID: 22419737) and prostate cancer (PMID: 16835864). This variant has not been identified 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. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jul 25, 2016

This variant is denoted CHEK2 c.967A>C at the cDNA level, p.Thr323Pro (T323P) at the protein level, and results in the change of a Threonine to a Proline (ACC>CCC). This variant was observed in an individual with early-onset breast cancer as well as in both tumor and adjacent normal tissues from an individual with prostate cancer (Dong 2003, Le Calvez-Kelm 2011). In a yeast-based assay CHEK2 Thr323Pro demonstrated DNA damage response comparable to wild-type, but led to partially reduced kinase activity in mammalian cells (Wu 2006, Roeb 2012). CHEK2 Thr323Pro was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Threonine and Proline differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CHEK2 Thr323Pro occurs at a position that is conserved in mammals and is located in the kinase domain (Desrichard 2011, Roeb 2012). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether CHEK2 Thr323Pro is pathogenic or benign. We consider it to be a variant of uncertain significance. -

Familial cancer of breast;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C5882668:Li-Fraumeni syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.19
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.28	T;.;T;.;T;.;T;.;.;.;.;.
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.61
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.91	.;D;.;D;.;D;D;D;.;D;D;D
M_CAP	Benign	0.036	D
MetaRNN	Pathogenic	0.95	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.44	T
MutationAssessor	Benign	1.3	L;L;L;.;L;.;L;.;L;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-2.7	D;D;D;.;D;D;.;D;D;D;.;D
REVEL	Uncertain	0.49
Sift	Benign	0.20	T;T;T;.;T;T;.;T;T;T;.;T
Sift4G	Benign	0.21	T;T;T;.;T;T;.;T;T;T;.;.
Polyphen		0.99	D;D;D;.;D;D;D;D;D;.;.;.
Vest4		0.79
MutPred		0.90		Gain of catalytic residue at T323 (P = 0.1184);Gain of catalytic residue at T323 (P = 0.1184);Gain of catalytic residue at T323 (P = 0.1184);.;Gain of catalytic residue at T323 (P = 0.1184);.;Gain of catalytic residue at T323 (P = 0.1184);.;Gain of catalytic residue at T323 (P = 0.1184);.;.;.;
MVP		0.77
MPC		0.14
ClinPred		0.96	D
GERP RS		5.7
Varity_R		0.97
gMVP		0.77

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: rs750984976; hg19: chr22-29095867;