CHEK2
checkpoint kinase 2
Basic information
Region (hg38): 22:28687743-28742422
Previous symbols: [ "RAD53" ]
Links
Phenotypes
GenCC
Source:
- acute myeloid leukemia (Moderate), mode of inheritance: AD
- Li-Fraumeni syndrome 2 (Definitive), mode of inheritance: AR
- hereditary breast carcinoma (Definitive), mode of inheritance: AD
- Li-Fraumeni syndrome 2 (Strong), mode of inheritance: AD
- colorectal cancer (Moderate), mode of inheritance: AD
- Li-Fraumeni syndrome (Definitive), mode of inheritance: AD
- hereditary breast carcinoma (Strong), mode of inheritance: AD
- hereditary breast carcinoma (Definitive), mode of inheritance: AD
- familial ovarian cancer (Disputed Evidence), mode of inheritance: AD
- hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Tumor predisposition syndrome 4 | AD/AR | Oncologic | Surveillance for neoplasms (eg, breast cancer screening with MRI) may allow preventive measures (eg, with tamoxifen chemoprevention in the case of breast cancer) and early treatment, resulting in improved outcome of malignancies | Oncologic | 10617473; 11719428; 11479205; 11967536; 12094328; 12533788; 12690581; 15122511; 15492928; 15087378; 15466005; 15239132; 16257342; 12690581; 17085682; 16551709; 16835864; 18178638; 22058428; 22114986; 21787115; 22006311; 21807500; 22201027; 22072393; 21956126 |
| Variants may be associated with susceptibility to a number of different cancer types |
ClinVar
This is a list of variants' phenotypes submitted to
- Familial cancer of breast (477 variants)
- Hereditary cancer-predisposing syndrome (182 variants)
- not provided (32 variants)
- Hereditary breast ovarian cancer syndrome (8 variants)
- Colorectal cancer (4 variants)
- Malignant tumor of breast (4 variants)
- Gastric cancer (4 variants)
- Li-Fraumeni syndrome 2 (4 variants)
- CHEK2-related cancer predisposition (4 variants)
- Breast and/or ovarian cancer (3 variants)
- CHEK2-related disorder (2 variants)
- Predisposition to cancer (2 variants)
- Malignant tumor of prostate (2 variants)
- Breast neoplasm (2 variants)
- Li-Fraumeni syndrome (2 variants)
- Familial cancer of breast;Li-Fraumeni syndrome 2;Malignant tumor of prostate;Bone osteosarcoma (1 variants)
- Carcinoma of pancreas (1 variants)
- not specified (1 variants)
- TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL (1 variants)
- Breast neoplasm;Leiomyosarcoma (1 variants)
- Li-Fraumeni syndrome 2;Bone osteosarcoma;Malignant tumor of prostate;Familial cancer of breast (1 variants)
- Breast cancer, susceptibility to (1 variants)
- Breast carcinoma (1 variants)
- Inherited breast cancer and ovarian cancer (1 variants)
- Li-Fraumeni syndrome 2;Familial cancer of breast;Malignant tumor of prostate;Bone osteosarcoma (1 variants)
- Li-Fraumeni syndrome 1 (1 variants)
- Astrocytoma (1 variants)
- Malignant tumor of prostate;Familial cancer of breast;Colorectal cancer (1 variants)
- Bone osteosarcoma (1 variants)
- Inflammation of the large intestine;Colitis;Hematochezia;Thrombocytopenia (1 variants)
- Sarcoma (1 variants)
- Breast and colorectal cancer, susceptibility to (1 variants)
- Malignant tumor of prostate;Familial cancer of breast;Li-Fraumeni syndrome 2;Bone osteosarcoma (1 variants)
- Neoplasm of ovary (1 variants)
- Congenital heart defects, multiple types, 3 (1 variants)
- Malignant tumor of prostate;Familial cancer of breast;Li-Fraumeni syndrome 2;Colorectal cancer;Bone osteosarcoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHEK2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 429 | 437 | ||||
| missense | 1636 | 1649 | ||||
| nonsense | 122 | 37 | 164 | |||
| start loss | 7 | |||||
| frameshift | 412 | 91 | 21 | 525 | ||
| inframe indel | 64 | 65 | ||||
| splice donor/acceptor (+/-2bp) | 146 | 152 | ||||
| splice region | 1 | 18 | 118 | 82 | 219 | |
| non coding | 43 | 319 | 40 | 408 | ||
| Total | 538 | 289 | 1785 | 754 | 41 |
Highest pathogenic variant AF is 0.00172
Variants in CHEK2
This is a list of pathogenic ClinVar variants found in the CHEK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-28687820-T-TA | Hereditary breast ovarian cancer syndrome | Uncertain significance (Apr 19, 2022) | ||
| 22-28687838-G-A | CHEK2-related cancer predisposition | Uncertain significance (Jan 12, 2018) | ||
| 22-28687849-T-A | CHEK2-related cancer predisposition | Uncertain significance (Jan 12, 2018) | ||
| 22-28687871-T-C | CHEK2-related cancer predisposition | Uncertain significance (Jan 12, 2018) | ||
| 22-28687878-C-T | not specified | Likely benign (Aug 01, 2016) | ||
| 22-28687879-G-A | not specified • Familial cancer of breast • Hereditary cancer-predisposing syndrome • CHEK2-related cancer predisposition • Breast and/or ovarian cancer | Conflicting classifications of pathogenicity (Aug 01, 2024) | ||
| 22-28687881-G-A | not specified • Hereditary cancer-predisposing syndrome | Likely benign (May 31, 2017) | ||
| 22-28687887-A-C | Hereditary cancer-predisposing syndrome | Uncertain significance (Nov 09, 2018) | ||
| 22-28687890-A-G | not specified • Familial cancer of breast • Hereditary cancer-predisposing syndrome • Malignant tumor of breast | Conflicting classifications of pathogenicity (Feb 06, 2024) | ||
| 22-28687891-C-T | not specified • Hereditary cancer-predisposing syndrome | Likely benign (Feb 21, 2017) | ||
| 22-28687892-G-A | Hereditary cancer-predisposing syndrome | Conflicting classifications of pathogenicity (Jun 20, 2023) | ||
| 22-28687894-A-AG | Hereditary cancer-predisposing syndrome • not specified | Conflicting classifications of pathogenicity (Feb 03, 2023) | ||
| 22-28687895-G-A | Hereditary cancer-predisposing syndrome | Uncertain significance (Aug 10, 2016) | ||
| 22-28687895-G-T | Hereditary cancer-predisposing syndrome | Likely benign (Jul 26, 2021) | ||
| 22-28687897-T-A | Familial cancer of breast | Uncertain significance (Sep 22, 2023) | ||
| 22-28687899-A-C | Familial cancer of breast | Uncertain significance (Sep 27, 2022) | ||
| 22-28687899-A-G | Familial cancer of breast • Hereditary cancer-predisposing syndrome | Uncertain significance (Aug 27, 2021) | ||
| 22-28687900-C-T | Familial cancer of breast | Likely benign (Mar 16, 2023) | ||
| 22-28687901-A-G | Familial cancer of breast • Hereditary cancer-predisposing syndrome | Conflicting classifications of pathogenicity (Apr 16, 2024) | ||
| 22-28687901-A-T | Familial cancer of breast | Uncertain significance (Oct 23, 2023) | ||
| 22-28687902-A-C | Familial cancer of breast | Uncertain significance (Apr 06, 2019) | ||
| 22-28687901-A-AACACAGCAGCAC | Familial cancer of breast • Hereditary cancer-predisposing syndrome | Uncertain significance (May 28, 2019) | ||
| 22-28687903-C-T | Familial cancer of breast | Likely benign (Nov 29, 2021) | ||
| 22-28687904-A-G | Familial cancer of breast | Uncertain significance (May 08, 2021) | ||
| 22-28687905-C-T | Hereditary cancer-predisposing syndrome • Familial cancer of breast | Uncertain significance (Oct 24, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHEK2 | protein_coding | protein_coding | ENST00000382580 | 15 | 54680 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.21e-24 | 0.0000764 | 125047 | 0 | 701 | 125748 | 0.00279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.450 | 327 | 305 | 1.07 | 0.0000161 | 3793 |
| Missense in Polyphen | 128 | 107.9 | 1.1863 | 1383 | ||
| Synonymous | 1.14 | 95 | 110 | 0.862 | 0.00000564 | 1129 |
| Loss of Function | -0.755 | 34 | 29.6 | 1.15 | 0.00000140 | 394 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00142 | 0.00139 |
| Ashkenazi Jewish | 0.00181 | 0.00179 |
| East Asian | 0.000389 | 0.000381 |
| Finnish | 0.00993 | 0.00993 |
| European (Non-Finnish) | 0.00330 | 0.00327 |
| Middle Eastern | 0.000389 | 0.000381 |
| South Asian | 0.00137 | 0.00137 |
| Other | 0.00230 | 0.00228 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest, activation of DNA repair and apoptosis in response to the presence of DNA double-strand breaks. May also negatively regulate cell cycle progression during unperturbed cell cycles. Following activation, phosphorylates numerous effectors preferentially at the consensus sequence [L-X- R-X-X-S/T]. Regulates cell cycle checkpoint arrest through phosphorylation of CDC25A, CDC25B and CDC25C, inhibiting their activity. Inhibition of CDC25 phosphatase activity leads to increased inhibitory tyrosine phosphorylation of CDK-cyclin complexes and blocks cell cycle progression. May also phosphorylate NEK6 which is involved in G2/M cell cycle arrest. Regulates DNA repair through phosphorylation of BRCA2, enhancing the association of RAD51 with chromatin which promotes DNA repair by homologous recombination. Also stimulates the transcription of genes involved in DNA repair (including BRCA2) through the phosphorylation and activation of the transcription factor FOXM1. Regulates apoptosis through the phosphorylation of p53/TP53, MDM4 and PML. Phosphorylation of p53/TP53 at 'Ser-20' by CHEK2 may alleviate inhibition by MDM2, leading to accumulation of active p53/TP53. Phosphorylation of MDM4 may also reduce degradation of p53/TP53. Also controls the transcription of pro-apoptotic genes through phosphorylation of the transcription factor E2F1. Tumor suppressor, it may also have a DNA damage-independent function in mitotic spindle assembly by phosphorylating BRCA1. Its absence may be a cause of the chromosomal instability observed in some cancer cells. Promotes the CCAR2-SIRT1 association and is required for CCAR2-mediated SIRT1 inhibition (PubMed:25361978). {ECO:0000250|UniProtKB:Q9Z265, ECO:0000269|PubMed:10097108, ECO:0000269|PubMed:10724175, ECO:0000269|PubMed:11298456, ECO:0000269|PubMed:12402044, ECO:0000269|PubMed:12607004, ECO:0000269|PubMed:12717439, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:16163388, ECO:0000269|PubMed:17101782, ECO:0000269|PubMed:17380128, ECO:0000269|PubMed:17715138, ECO:0000269|PubMed:18317453, ECO:0000269|PubMed:18644861, ECO:0000269|PubMed:18728393, ECO:0000269|PubMed:20364141, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:25619829, ECO:0000269|PubMed:9836640, ECO:0000269|PubMed:9889122}.;
- Disease
- DISEASE: Li-Fraumeni syndrome 2 (LFS2) [MIM:609265]: A highly penetrant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed (PubMed:8118819 and PubMed:8718514) and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:11719428}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:12533788}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Osteogenic sarcoma (OSRC) [MIM:259500]: A sarcoma originating in bone-forming cells, affecting the ends of long bones. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Breast cancer (BC) [MIM:114480]: A common malignancy originating from breast epithelial tissue. Breast neoplasms can be distinguished by their histologic pattern. Invasive ductal carcinoma is by far the most common type. Breast cancer is etiologically and genetically heterogeneous. Important genetic factors have been indicated by familial occurrence and bilateral involvement. Mutations at more than one locus can be involved in different families or even in the same case. {ECO:0000269|PubMed:12094328, ECO:0000269|PubMed:21618645, ECO:0000269|PubMed:25619829}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. {ECO:0000269|PubMed:12094328}.;
- Pathway
- Cell cycle - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Cell Cycle;miRNA Regulation of DNA Damage Response;ATM Signaling Network in Development and Disease;miRNA regulation of p53 pathway in prostate cancer;DNA Damage Response;DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;role of brca1 brca2 and atr in cancer susceptibility;regulation of cell cycle progression by plk3;Generic Transcription Pathway;Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex;RNA Polymerase II Transcription;Stabilization of p53;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;Ubiquitin Mediated Degradation of Phosphorylated Cdc25A;p53-Independent DNA Damage Response;p53-Independent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;G2/M DNA damage checkpoint;G2/M Checkpoints;Cell Cycle Checkpoints;cell cycle: g2/m checkpoint;atm signaling pathway;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;PLK3 signaling events;FOXM1 transcription factor network;ATM pathway;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.656
Intolerance Scores
- loftool
- 0.356
- rvis_EVS
- -0.13
- rvis_percentile_EVS
- 43.91
Haploinsufficiency Scores
- pHI
- 0.985
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chek2
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- DNA damage checkpoint;G2/M transition of mitotic cell cycle;replicative cell aging;positive regulation of protein phosphorylation;double-strand break repair;regulation of transcription, DNA-templated;protein phosphorylation;cellular response to DNA damage stimulus;DNA damage induced protein phosphorylation;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;intrinsic apoptotic signaling pathway in response to DNA damage;peptidyl-serine phosphorylation;regulation of protein catabolic process;signal transduction in response to DNA damage;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;cellular protein catabolic process;mitotic DNA damage checkpoint;positive regulation of transcription, DNA-templated;protein autophosphorylation;protein stabilization;cell division;negative regulation of cell cycle arrest;cellular response to gamma radiation;signal transduction involved in intra-S DNA damage checkpoint;mitotic spindle assembly;replicative senescence;regulation of signal transduction by p53 class mediator;response to glycoside;cellular response to bisphenol A;negative regulation of DNA damage checkpoint;positive regulation of anoikis
- Cellular component
- chromosome, telomeric region;nucleus;nucleoplasm;cytoplasm;Golgi apparatus;PML body
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;protein kinase binding;ubiquitin protein ligase binding;identical protein binding;protein homodimerization activity;metal ion binding