CAMK2N1
protein-codingcalcium/calmodulin dependent protein kinase II inhibitor 1
Gene summary
Predicted to enable calcium-dependent protein kinase inhibitor activity and protein kinase binding activity. Predicted to be involved in long-term memory and positive regulation of inflammatory response. Predicted to be located in neuronal cell body and synapse. Implicated in ovarian cancer; ovarian carcinoma; and prostate adenocarcinoma. Biomarker of hepatocellular carcinoma; oral squamous cell carcinoma; papillary thyroid carcinoma; and prostate cancer. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CAMK2N1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018584.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 2 | 2 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 | 2 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061054.2 | 2 | MANE Select | |
| Ensembl | ENSP00000364219.3 | 2 | MANE Select | |
| Ensembl | ENSP00000611561.1 | 2 | Standard | |
| Ensembl | ENSP00000611561.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| camk2n1a | Danio rerio | Structure: ventricular system Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of protein kinase activity
- negative regulation of cell population proliferation
- positive regulation of gene expression
- negative regulation of cell cycle
- negative regulation of proteolysis
Molecular Function
- calcium-dependent protein kinase inhibitor activity
- protein kinase binding
Cellular Component
- cellular_component
- postsynaptic density
- cell junction
- dendrite
- neuronal cell body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375078
- Coding exons
- 2
- Length
- 3830
- Individuals with no LoFs
- 124777
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 124778
- p
- 0.00000401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.44 | 14 | 39.5 | 0.354 | 0.00000191 | 501 |
| Missense (PolyPhen) | 3 | 8.7525 | 0.34276 | 100 | ||
| Synonymous | 1.05 | 12 | 17.6 | 0.682 | 9.34e-7 | 146 |
| Loss of Function | 0.798 | 1 | 2.31 | 0.433 | 9.90e-8 | 29 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Potent and specific inhibitor of CaM-kinase II (CAMK2). {ECO:0000250, ECO:0000269|PubMed:18305109}.;
Intolerance Scores
- LoFtool
- 0.333
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 60.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231