chr22-28699838-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_007194.4(CHEK2):​c.1008G>C​(p.Gln336His) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Consequence

CHEK2
NM_007194.4 missense, splice_region

Scores

5
14
Splicing: ADA: 1.000
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.91
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHEK2NM_007194.4 linkuse as main transcriptc.1008G>C p.Gln336His missense_variant, splice_region_variant 9/15 ENST00000404276.6 NP_009125.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHEK2ENST00000404276.6 linkuse as main transcriptc.1008G>C p.Gln336His missense_variant, splice_region_variant 9/151 NM_007194.4 ENSP00000385747 P2O96017-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 29, 2019The c.1008G>C variant (also known as p.Q336H), located in coding exon 8 of the CHEK2 gene, results from a G to C substitution at nucleotide position 1008. The amino acid change results in glutamine to histidine at codon 336, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 8, which makes it likely to have some effect on normal mRNA splicing. This amino acid position is not well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.027
T
BayesDel_noAF
Benign
-0.28
CADD
Uncertain
25
DANN
Benign
0.97
DEOGEN2
Benign
0.13
T;.;T;.;T;.;T;.;.;.;.;.
Eigen
Uncertain
0.39
Eigen_PC
Uncertain
0.39
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.80
.;T;.;D;.;D;D;D;.;D;T;D
M_CAP
Benign
0.042
D
MetaRNN
Uncertain
0.45
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.030
N;N;N;.;N;.;N;.;N;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D;N;N
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-1.7
N;N;N;.;N;N;.;N;N;N;.;N
REVEL
Benign
0.13
Sift
Benign
0.13
T;D;T;.;T;T;.;T;D;T;.;T
Sift4G
Benign
0.13
T;D;T;.;T;T;.;T;D;T;.;.
Polyphen
0.081
B;D;B;.;B;B;B;D;D;.;.;.
Vest4
0.44
MutPred
0.55
Loss of catalytic residue at Q336 (P = 0.1169);Loss of catalytic residue at Q336 (P = 0.1169);Loss of catalytic residue at Q336 (P = 0.1169);.;Loss of catalytic residue at Q336 (P = 0.1169);.;Loss of catalytic residue at Q336 (P = 0.1169);.;Loss of catalytic residue at Q336 (P = 0.1169);.;.;.;
MVP
0.91
MPC
0.031
ClinPred
0.76
D
GERP RS
5.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.45
gMVP
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.98
SpliceAI score (max)
0.78
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.78
Position offset: 0

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-29095826; API