CHEK2

Chr 22

checkpoint kinase 2

Also known as: CDS1, CHK2, HuCds1, LFS2, PP1425, RAD53, TPDS4, hCds1

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]

Primary Disease Associations & Inheritance

Osteosarcoma, somaticMIM #259500
Prostate cancer, somaticMIM #176807
Tumor predisposition syndrome 4, breast/prostate/colorectalMIM #609265
UniProtOsteogenic sarcoma
UniProtBreast cancer
4725
ClinVar variants
144
Pathogenic / LP
0.00
pLI score
12
Active trials
Clinical SummaryCHEK2
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
144 Pathogenic / Likely Pathogenic· 131 VUS of 4725 total submissions
💊
Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.53LOEUF
pLI 0.000
Z-score -0.76
OE 1.15 (0.871.53)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.45Z-score
OE missense 1.07 (0.981.18)
327 obs / 304.9 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.15 (0.871.53)
00.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.07 (0.981.18)
00.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.86
01.21.6
LoF obs/exp: 34 / 29.6Missense obs/exp: 327 / 304.9Syn Z: 1.14

ClinVar Variant Classifications

4725 submitted variants in ClinVar

Classification Summary

Pathogenic109
Likely Pathogenic35
VUS131
Likely Benign150
Benign59
Conflicting3
109
Pathogenic
35
Likely Pathogenic
131
VUS
150
Likely Benign
59
Benign
3
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
83
0
26
0
109
Likely Pathogenic
28
2
5
0
35
VUS
9
103
18
1
131
Likely Benign
0
0
113
37
150
Benign
1
0
8
50
59
Conflicting
3
Total12110517088487

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CHEK2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

CHEK2-related cancer predisposition

definitive
ARLoss Of FunctionAbsent Gene Product, Altered Gene Product Structure
Cancer
G2P ↗
stop gainedmissense variantintron variant

CHEK2-related cancer

definitive
ADLoss Of FunctionAbsent Gene Product
Cancer
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

Osteosarcoma, somatic

MIM #259500

Molecular basis of disorder known

Prostate cancer, somatic

MIM #176807

Molecular basis of disorder known

Tumor predisposition syndrome 4, breast/prostate/colorectal

MIM #609265

Molecular basis of disorder known

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Homologous Recombination Deficiencies and Hereditary Tumors.
Yamamoto H et al.·Int J Mol Sci
2021Review
Top 10 resultsSearch PubMed ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

BRCA1 MutationPOLD1 Gene MutationCDKN2A Mutation

An Intervention to Increase Genetic Testing in Families Who May Share a Gene Mutation Related to Cancer Risk and An Intervention to Help Patients and Their Primary Care Providers Stay Up-to-date About Uncertain Genetic Test Results

RECRUITING
NCT05420064Phase NAMemorial Sloan Kettering Cancer CenterStarted 2022-12-01
Intervention Arm At-risk Relative/ARR ContactsMyGene PortalStandard of Care
Prostate CancerBRCA MutationMismatch Repair Gene Mutation

The GENPET Study - An Imaging Study of FCH-PET-CT in Men With Prostate Cancer and a DNA Repair Gene Mutation.

RECRUITING
NCT05097274Institute of Cancer Research, United KingdomStarted 2015-10-15
MRI pelvis or CT imaging under clinical management for Pr CaWhole body bone scan imagingPET-CT imaging
Pancreatic Cancer

Pancreatic Cancer Genetics

RECRUITING
NCT01102569Columbia UniversityStarted 2008-01
Metastatic Breast CancerInvasive Breast CancerSomatic Mutation Breast Cancer (BRCA1)

Olaparib In Metastatic Breast Cancer

ACTIVE NOT RECRUITING
NCT03344965Phase PHASE2Beth Israel Deaconess Medical CenterStarted 2018-04-01
Olaparib
BRCA1 MutationBRCA2 MutationBRCA Mutation

Olaparib and ASTX727 in BRCA1/2- and Homologous Recombination Deficient (HRD)-Mutated Tumors

RECRUITING
NCT06177171Phase PHASE1Pamela MunsterStarted 2024-02-07
OlaparibASTX727
Lynch SyndromeLi Fraumeni SyndromePTEN Hamartoma Syndrome

Video Capsule Examination in Patients With Lynch Syndrome

RECRUITING
NCT06712095Phase NARoyal Marsden NHS Foundation TrustStarted 2024-03-04
Video capsule investigation
Renal Cell CarcinomaMetastatic Renal Cell CarcinomaKidney Cancer

Study of Olaparib in Metastatic Renal Cell Carcinoma Patients With DNA Repair Gene Mutations

RECRUITING
NCT03786796Phase PHASE2Sidney Kimmel Comprehensive Cancer Center at Johns HopkinsStarted 2019-06-03
Olaparib
Gastric CancerGastroEsophageal Cancer

Study of SBRT/Olaparib Followed by Pembrolizumab/Olaparib in Gastric Cancers

ACTIVE NOT RECRUITING
NCT05379972Phase PHASE2University of Colorado, DenverStarted 2023-01-12
PembrolizumabOlaparibStereotactic Body Radiation Therapy
BRCA MutationPALB2 Gene MutationDuctal Carcinoma in Situ

Low Dose TamOxifen and LifestylE Changes for bReast cANcer prevenTion

ACTIVE NOT RECRUITING
NCT06033092Phase PHASE2European Institute of OncologyStarted 2024-06-21
Tamoxifen 10 mg TabletIntermittent caloric restrictionStep counter Device
Uveal Melanoma

Identification of New Candidate Genes for Hereditary Predisposition to Uveal Melanoma

ACTIVE NOT RECRUITING
NCT06550674Phase NACentre Jean PerrinStarted 2024-10-29
Constitutional exome analysis
Advanced or Metastatic Solid TumorsBreast CancerOvarian Cancer

A Study of PARG Inhibitor IDE161 in Participants With Advanced Solid Tumors

RECRUITING
NCT05787587Phase PHASE1IDEAYA BiosciencesStarted 2023-04-18
IDE-161Pembrolizumab
Prostate CancerProstate BiopsyGenetic Counselling

The PROFILE Study: Germline Genetic Profiling: Correlation With Targeted Prostate Cancer Screening and Treatment

RECRUITING
NCT02543905Institute of Cancer Research, United KingdomStarted 2015-03-09
Prostate MRI and Biopsy