KCND2

protein-coding

potassium 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

NM_012281.3

Inheritance

AD

ClinVar variants

P:11U:262B:154

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr7:120,273,175-120,750,337

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~477.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

KCND2-related neurodevelopmental disorder with or without seizuresMODERATE

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).

KCND2-related neurodevelopmental disorder with or without seizuresMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:1040003

Submitter: G2P

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Illumina

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KCND2 variants in ClinVar

10 Conditions Cataloged
Early Myoclonic EncephalopathyTotal: 409
not providedTotal: 84
Inborn genetic diseasesTotal: 45
not specifiedTotal: 21
KCND2-related disorderTotal: 8
KCND2-related neurodevelopmental disorderTotal: 5
Neurodevelopmental disorderTotal: 3
KCND2-related neurodevelopmental disorder with or without seizuresTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
134
clinvar
5
clinvar
142
missense
4
clinvar
7
clinvar
235
clinvar
14
clinvar
1
clinvar
261
nonsense
9
clinvar
9
start loss
1
clinvar
1
frameshift
10
clinvar
10
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total472621486427

Highest pathogenic variant AF is 6.8450674e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_012281.3RefSeqNP_036413.16MANE Select
ENST00000331113.9EnsemblENSP00000333496.46MANE Select
ENST00000425288.1EnsemblENSP00000415463.15Standard
ENST00001134454.1EnsemblENSP00000807435.16Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.511893820.4940.00002444118
Missense (PolyPhen)56181.830.307991930
Synonymous0.4521471540.9540.00001111281
Loss of Function3.17825.10.3180.00000155256

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish0.0000920.000092rare
European (Non-Finnish)0.0000880.000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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