AtlasGene
CHEK2
checkpoint kinase 2
- HGNC 16627↗(opens in a new tab)
- Ensembl gene ENSG00000183765↗(opens in a new tab)
- NCBI Gene 11200↗(opens in a new tab)
Summary
- Cytogenetic location
- 22q12.1
- Coordinates
- Chromosome 22: 28,687,743–28,741,820 (GRCh38)
- Exons
- 15 exons across 54.1 kb
- Protein
- 543 amino acids, 60.9 kDa
- Also known as
- CDS1, CHK2, HuCds1, PP1425, bA444G7
- Previous symbols
- RAD53
- MANE Select transcript
- ENST00000404276.6NM_007194.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Breast and Ovarian Cancer Genes Beyond BRCA1/2
- CHEK2-related cancer predispositionAutosomal dominant
Variants in CHEK2 that moderately raise the risk of breast cancer and possibly some other cancers.
- ClinGen definitiveClinGen rates the link definitive
- GenCC 22 GenCC submitters rate it definitive or strong
▶Actionability
Enhanced breast screening, often including annual MRI, is generally recommended.
- Hereditary breast cancerAutosomal dominant
Inherited susceptibility to breast cancer caused by variants in one of several genes.
- GenCC 11 GenCC submitter rates it definitive or strong
▶Actionability
Earlier and more intensive breast screening, including MRI, may be recommended depending on the gene.
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Get my Genome TestHow CHEK2 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
- Variants with a page
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 1.8 kb of the gene's 54.1 kb; 1,632 of those bases code for the protein.
Sequencing CHEK2
51Hard
How hard CHEK2 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Much of CHEK2 sits where short reads can miss or misplace a change.
What adds to it: the share of CHEK2's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. On its own, a gene wholly in this kind of region would score 100.35%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. On its own, a gene wholly in this kind of region would score 60.37%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so a read from one may be placed on the other. On its own, a gene wholly in this kind of region would score 60.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. On its own, a gene wholly in this kind of region would score 50.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. On its own, a gene wholly in this kind of region would score 30.3.5%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. On its own, a gene wholly in this kind of region would score 20.5.6%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of CHEK2's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
731
positions in CHEK2 where ClinVar classes a change as pathogenic or likely pathogenic
212 of them (29%) fall in regions short reads find hard.
- Low mappabilityRegions where 100 bp or 250 bp reads cannot be placed uniquely. (187 sites)
- Segmental duplicationsCopies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy. (212 sites)
A whole genome covers all 54.1 kb of CHEK2, introns included, not only the 1.8 kb of exons.
Variants with a page (323)
The CHEK2 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| A91Cfs*17 | c.269dup | Exon 2 | 28,734,452 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| A98Pfs*12 | c.292del | Exon 2 | 28,734,429 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.98C>G | Exon 2 | 28,734,624 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.276del | Exon 2 | 28,734,445 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.278G>A | Exon 2 | 28,734,444 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.319+1G>A | Intron 2 | 28,734,402 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.319+1G>C | Intron 2 | 28,734,402 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.319+1G>T | Intron 2 | 28,734,402 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.319+2T>A | Intron 2 | 28,734,401 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.320-1G>T | Intron 2 | 28,725,368 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
ClinVar pathogenic variants (1,043)
The CHEK2 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 741
- Pathogenic/likely pathogenic 63
- Likely pathogenic 239
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_007194.4(CHEK2):c.1502_1503dup (p.Glu502fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1486C>T (p.Gln496Ter) | hereditary breast carcinoma and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1465G>T (p.Glu489Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1459C>T (p.Gln487Ter) | CHEK2-related cancer predisposition and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1455dup (p.Leu486fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1454G>A (p.Trp485Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1451del (p.Pro484fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1442T>G (p.Leu481Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1434del (p.Glu479fs) | breast cancer and 2 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1435G>T (p.Glu479Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1432G>T (p.Glu478Ter) | hereditary breast carcinoma | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1415del (p.Lys472fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1400del (p.Leu467fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1400T>A (p.Leu467Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1393A>T (p.Lys465Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1371_1372del (p.Lys458fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1368dup (p.Glu457fs) | CHEK2-related cancer predisposition and 4 others | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1369G>T (p.Glu457Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1367C>G (p.Ser456Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1356G>A (p.Trp452Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1355G>A (p.Trp452Ter) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1348G>T (p.Glu450Ter) | hereditary breast carcinoma | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1344del (p.Pro449fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1341del (p.Phe447fs) | hereditary breast carcinoma | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_007194.4(CHEK2):c.1337del (p.Asn446fs) | hereditary breast carcinoma and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
See all 1,043 with every other CHEK2 variant in ClinVar → (opens in a new tab)
Genes linked to the same conditions
Traits linked to CHEK2
The Human Phenotype Ontology lists these as features of the rare conditions CHEK2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Glioblastoma multiforme
- Anxiety
- Attention deficit
- Behavioral abnormality
- Depression
- Epilepsy
- Irritability
- Migraine
Show 22 more traits
- Rise in pressure inside skull
- Abnormal gait
- Abnormal pyramidal sign
- Abnormal speech pattern
- Astrocytoma
- Benign neoplasm of the central nervous system
- Cancer of early nerve cells
- Choroid plexus carcinoma
- Difficulty articulating speech
- Disorder of involuntary muscle movements
- Disturbed sensory perception
- Dysgraphia
- Ependymoma
- Hallucinations
- Loss of developmental milestones
- Memory impairment
- Paralysis or weakness of one side of body
- Pins and needles feeling
- Tumors of the central nervous system
- Medulloblastoma
- Glioma
- Noncancerous growth of membranes covering brain
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-21: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- AlphaFold DB model AF-O96017-F1, version 6, from Google DeepMind and EMBL-EBI (CC BY 4.0): the protein's structure as AlphaFold predicts it, not as measured, and its confidence in each part.
- Data release 2026.10.21-c791e85a.
Cite this page
Dante Labs. (n.d.). CHEK2 gene: checkpoint kinase 2. Retrieved 23 October 2026, from https://dantelabs.com/genes/chek2
Dante Labs. CHEK2 gene: checkpoint kinase 2 [Internet]. [cited 23 October 2026]. Available from: https://dantelabs.com/genes/chek2
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