KCND2
protein-codingpotassium voltage-gated channel subfamily D member 2, the group of Potassium voltage-gated channels
Gene summary
Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shal-related subfamily, members of which form voltage-activated A-type potassium ion channels and are prominent in the repolarization phase of the action potential. This member mediates a rapidly inactivating, A-type outward potassium current which is not under the control of the N terminus as it is in Shaker channels. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~477.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:1040003
Submitter: ClinGen
*KCND2* encodes Kv4.2, a voltage-dependent potassium channel that produces an A-type potassium current in neurons. This fast-activating channel is crucial for repolarization of the membrane during action potentials. *KCND2* was first reported in relation to autosomal dominant KCND2-related neurodevelopmental disorder with or without seizures in 2014 (Lee et al., PMID: 24501278). This disorder is characterized by significant early-onset global developmental delay, intellectual disability, hypotonia, and, in some cases, epilepsy (including developmental and epileptic encephalopathy), autism, neuroimaging abnormalities, and mild dysmorphic features. Five missense variants that have been reported in 8 probands in 3 publications (PMIDs: 24501278, 34245260, 35510384) are included in this curation. Variants occurred de novo in all instances in which parental DNA was available. The variants affect sites critical for channel gating, and four cluster at residues 402–404, including recurrent variants affecting p.Pro403 and p.Val404. The variants were shown to result in gain-of-function and/or partial loss-of-function effects (PMIDs: 24501278, 29581270, 34245260, 35510384), but more evidence is needed to clarify the mechanism of pathogenicity. This gene-disease relationship is also supported by biochemical function, animal models and in vitro functional assays (PMIDs: 11102480, 32822706, 41188451, 41554648). Electrophysiological studies of patient-associated missense variants demonstrate altered Kv4.2 channel gating, including slowed inactivation and changes in activation kinetics (PMID: 24501278, 29581270, 34245260, 35510384). Knock-in mice with the patient variant *Kcnd2* V404M exhibit epileptiform activity and impaired learning and memory (PMID: 41554648). Multiple voltage-dependent potassium channel genes have been implicated in neurodevelopmental disorders. Another member of the Kv4 family, *KCND3*, which encodes the closely related Kv4.3 channel, is associated with neurodevelopmental disorders with epilepsy. In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on February 4, 2026 (SOP Version 12).
Inheritance Pattern: AD
Disease ID:MONDO:1040003
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0100038
Submitter: Illumina
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KCND2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012281.3. 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 | 3 | 134 | 5 | 142 | ||
| missense | 4 | 7 | 235 | 14 | 1 | 261 |
| nonsense | 9 | 9 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 10 | 10 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 4 | 7 | 262 | 148 | 6 | 427 |
Highest pathogenic variant AF is 6.8450674e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036413.1 | 6 | MANE Select | |
| Ensembl | ENSP00000333496.4 | 6 | MANE Select | |
| Ensembl | ENSP00000415463.1 | 5 | Standard | |
| Ensembl | ENSP00000807435.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Serotonergic synapse - Homo sapiens (human)
- Levomethadyl Acetate Action Action Pathway
- Fluoxetine Action Pathway
- Citalopram Action Pathway
- Escitalopram Action Pathway
Biological Process
- action potential
- chemical synaptic transmission
- neuronal action potential
- sensory perception of pain
- regulation of ion transmembrane transport
Molecular Function
- voltage-gated potassium channel activity
- A-type (transient outward) potassium channel activity
- protein binding
- metal ion binding
- voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential
Cellular Component
- plasma membrane
- integral component of plasma membrane
- voltage-gated potassium channel complex
- postsynaptic density
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000331113
- Coding exons
- 6
- Length
- 476664
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.51 | 189 | 382 | 0.494 | 0.0000244 | 4118 |
| Missense (PolyPhen) | 56 | 181.83 | 0.30799 | 1930 | ||
| Synonymous | 0.452 | 147 | 154 | 0.954 | 0.0000111 | 1281 |
| Loss of Function | 3.17 | 8 | 25.1 | 0.318 | 0.00000155 | 256 |
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 | 0.0 | absent |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes, primarily in the brain. Mediates the major part of the dendritic A-type current I(SA) in brain neurons (By similarity). This current is activated at membrane potentials that are below the threshold for action potentials. It regulates neuronal excitability, prolongs the latency before the first spike in a series of action potentials, regulates the frequency of repetitive action potential firing, shortens the duration of action potentials and regulates the back-propagation of action potentials from the neuronal cell body to the dendrites. Contributes to the regulation of the circadian rhythm of action potential firing in suprachiasmatic nucleus neurons, which regulates the circadian rhythm of locomotor activity (By similarity). Functions downstream of the metabotropic glutamate receptor GRM5 and plays a role in neuronal excitability and in nociception mediated by activation of GRM5 (By similarity). Mediates the transient outward current I(to) in rodent heart left ventricle apex cells, but not in human heart, where this current is mediated by another family member. Forms tetrameric potassium-selective channels through which potassium ions pass in accordance with their electrochemical gradient (PubMed:10551270, PubMed:15454437, PubMed:14695263, PubMed:14623880, PubMed:14980201, PubMed:16934482, PubMed:24811166, PubMed:24501278). The channel alternates between opened and closed conformations in response to the voltage difference across the membrane (PubMed:11507158). Can form functional homotetrameric channels and heterotetrameric channels that contain variable proportions of KCND2 and KCND3; channel properties depend on the type of pore-forming alpha subunits that are part of the channel. In vivo, membranes probably contain a mixture of heteromeric potassium channel complexes. Interaction with specific isoforms of the regulatory subunits KCNIP1, KCNIP2, KCNIP3 or KCNIP4 strongly increases expression at the cell surface and thereby increases channel activity; it modulates the kinetics of channel activation and inactivation, shifts the threshold for channel activation to more negative voltage values, shifts the threshold for inactivation to less negative voltages and accelerates recovery after inactivation (PubMed:15454437, PubMed:14623880, PubMed:14980201, PubMed:19171772, PubMed:24501278, PubMed:24811166). Likewise, interaction with DPP6 or DPP10 promotes expression at the cell membrane and regulates both channel characteristics and activity (By similarity). {ECO:0000250|UniProtKB:Q63881, ECO:0000250|UniProtKB:Q9Z0V2, ECO:0000269|PubMed:10551270, ECO:0000269|PubMed:10729221, ECO:0000269|PubMed:11507158, ECO:0000269|PubMed:14623880, ECO:0000269|PubMed:14695263, ECO:0000269|PubMed:14980201, ECO:0000269|PubMed:15454437, ECO:0000269|PubMed:16934482, ECO:0000269|PubMed:19171772, ECO:0000269|PubMed:24501278, ECO:0000269|PubMed:24811166}.;
- Disease
- DISEASE: Note=KNCD2 mutations have been found in a family with autism and epilepsy and may play a role in disease pathogenesis. Autism is a complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Epilepsy is characterized by paroxysmal transient disturbances of the electrical activity of the brain that may be manifested as episodic impairment or loss of consciousness, abnormal motor phenomena, psychic or sensory disturbances, or perturbation of the autonomic nervous system. {ECO:0000269|PubMed:24501278}.; DISEASE: Note=A KCND2 mutation leading to the production of a C- terminally truncated protein has been identified in a patient with epilepsy. Epilepsy is characterized by paroxysmal transient disturbances of the electrical activity of the brain that may be manifested as episodic impairment or loss of consciousness, abnormal motor phenomena, psychic or sensory disturbances, or perturbation of the autonomic nervous system. {ECO:0000269|PubMed:16934482}.;
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- LoFtool
- 0.0711
- RVIS EVS
- -0.65
- RVIS percentile EVS
- 16.44
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.832
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |