CAMK2D
protein-codingcalcium/calmodulin dependent protein kinase II delta, the group of Calmodulin dependent protein kinases
Gene summary
The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a delta chain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Distinct isoforms of this chain have different expression patterns.[provided by RefSeq, Nov 2008]
- CAMKD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~343.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0100038
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:1040008
Submitter: ClinGen
*CAMK2D* was first reported in relation to autosomal dominant *CAMK2D*-related neurodevelopmental disorder and dilated cardiomyopathy in 2024 (Rigter et al., PMID: 38272033). *CAMK2D* encodes a member of the family of type II multifunctional calcium- and calmodulin-dependent protein kinases, which play a central role in synaptic plasticity, learning, and memory. *CAMK2D* is the major CAMK2 isozyme present in the heart and plays an important role in cardiac function. Affected individuals present with speech and motor delays, intellectual disability (mild to profound), dysmorphic facial features, behavioral abnormalities (including autism spectrum disorder), skeletal abnormalities, brain MRI anomalies, and dilated cardiomyopathy often requiring cardiac transplantation (PMIDs: 37372357, 38272033). Additional features in a subset of individuals can include seizures, visual abnormalities, digestive problems (including tube feeding), and kidney abnormalities. Six missense variants reported in 8 probands in 3 publications (PMIDs: 27479843, 37372357, 38272033) are included in this curation, with most variants arising *de novo*. One recurrent variant, p.Arg275His, has been reported in at least 3 families, 2 of which are scored in this curation (PMIDs: 27479843, 37372357, 38272033). The third family includes a set of 3 siblings with dilated cardiomyopathy; 2 of these siblings also have neurodevelopmental disorders and a 16p11.2 microdeletion (PMID: 38272033). Their father, deceased at the time of the report (and therefore unavailable for testing), also had a history of dilated cardiomyopathy. While not scored due to the compounding 16p11.2 microdeletion, the presence of dilated cardiomyopathy within this family lends additional support to the assertion that variation in this gene causes cardiac phenotypes in addition to neurodevelopmental disorders. Functional assays assessing protein levels, kinase activity, and impact on neuronal migration of these patient-specific *CAMK2D* missense variants demonstrated both gain-of-function and loss-of-function effects, with only gain-of-function variants proposed to be associated with the cardiac phenotype (PMID: 38272033). However, more evidence is needed to determine a specific phenotype correlation with disease mechanism. *CAMK2D* is constrained for missense (Z = 3.41, gnomAD v4.1.1) but not loss-of-function variants (pLI = 0.02, LOEUF = 0.58). One individual with a *de novo* splice variant predicted to lead to a frameshift was not scored for this reason. This gene-disease relationship is also supported by experimental evidence, including biochemical function, protein interactions, and mouse knockdown, overexpression and rescue models (PMID: 38272033). The 3 other members of the CAMK2 family, *CAMK2A*, *CAMK2B*, and *CAMK2G*, are also involved in neurodevelopmental disorders (PMID: 39631163), and form homo- and hetero-oligomeric complexes with CAMK2D. In summary, there is strong evidence supporting the relationship between *CAMK2D* and autosomal dominant *CAMK2D*-related neurodevelopmental disorder and dilated cardiomyopathy. Three years must elapse from the first proposal of the assertion to reach a definitive classification without any valid contradictory evidence. We will re-evaluate this gene-disease relationship at that time to determine if an upgraded classification of definitive is warranted. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on October 15, 2025 (SOP Version 12).
Inheritance Pattern: AD
Disease ID:MONDO:1040008
Submitter: G2P
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CAMK2D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001321571.2. 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 | 1 | 3 | 4 | |||
| missense | 5 | 3 | 45 | 3 | 56 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 11 | 11 | ||||
| Total | 5 | 3 | 61 | 6 | 0 | 75 |
Highest pathogenic variant AF is 6.994768e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001308500.1 | 20 | MANE Select | |
| Ensembl | ENSP00000425824.1 | 20 | MANE Select | |
| RefSeq | NP_001212.2 | 18 | Standard | |
| RefSeq | NP_001308495.1 | 19 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
- Aldosterone synthesis and secretion - Homo sapiens (human)
- Oxytocin signaling pathway - Homo sapiens (human)
- Long-term potentiation - Homo sapiens (human)
- Neurotrophin signaling pathway - Homo sapiens (human)
Biological Process
- MAPK cascade
- regulation of cell growth
- regulation of the force of heart contraction
- regulation of membrane depolarization
- regulation of transcription by RNA polymerase II
Molecular Function
- protein serine/threonine kinase activity
- calmodulin-dependent protein kinase activity
- Ras guanyl-nucleotide exchange factor activity
- protein binding
- calmodulin binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000342666
- Coding exons
- 18
- Length
- 310896
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125745
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.11 | 124 | 267 | 0.465 | 0.0000133 | 3286 |
| Missense (PolyPhen) | 56 | 160.78 | 0.34829 | 2031 | ||
| Synonymous | 1.65 | 68 | 87.7 | 0.775 | 0.00000422 | 904 |
| Loss of Function | 3.63 | 11 | 33.8 | 0.325 | 0.00000170 | 416 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium/calmodulin-dependent protein kinase involved in the regulation of Ca(2+) homeostatis and excitation-contraction coupling (ECC) in heart by targeting ion channels, transporters and accessory proteins involved in Ca(2+) influx into the myocyte, Ca(2+) release from the sarcoplasmic reticulum (SR), SR Ca(2+) uptake and Na(+) and K(+) channel transport. Targets also transcription factors and signaling molecules to regulate heart function. In its activated form, is involved in the pathogenesis of dilated cardiomyopathy and heart failure. Contributes to cardiac decompensation and heart failure by regulating SR Ca(2+) release via direct phosphorylation of RYR2 Ca(2+) channel on 'Ser- 2808'. In the nucleus, phosphorylates the MEF2 repressor HDAC4, promoting its nuclear export and binding to 14-3-3 protein, and expression of MEF2 and genes involved in the hypertrophic program. Is essential for left ventricular remodeling responses to myocardial infarction. In pathological myocardial remodeling acts downstream of the beta adrenergic receptor signaling cascade to regulate key proteins involved in ECC. Regulates Ca(2+) influx to myocytes by binding and phosphorylating the L-type Ca(2+) channel subunit beta-2 CACNB2. In addition to Ca(2+) channels, can target and regulate the cardiac sarcolemmal Na(+) channel Nav1.5/SCN5A and the K+ channel Kv4.3/KCND3, which contribute to arrhythmogenesis in heart failure. Phosphorylates phospholamban (PLN/PLB), an endogenous inhibitor of SERCA2A/ATP2A2, contributing to the enhancement of SR Ca(2+) uptake that may be important in frequency-dependent acceleration of relaxation (FDAR) and maintenance of contractile function during acidosis. May participate in the modulation of skeletal muscle function in response to exercise, by regulating SR Ca(2+) transport through phosphorylation of PLN/PLB and triadin, a ryanodine receptor- coupling factor. {ECO:0000269|PubMed:16690701, ECO:0000269|PubMed:17179159}.;
Recessive Scores
- pRec
- 0.240
Intolerance Scores
- LoFtool
- 0.921
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |