KCNB1

protein-coding

potassium voltage-gated channel subfamily B member 1, 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, shab-related subfamily. This member is a delayed rectifier potassium channel and its activity is modulated by some other family members. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004975.4

Inheritance

AD

ClinVar variants

P:140U:319B:402

Top phenotype

Epileptic encephalopathy, early infantile, 26

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr20:49,293,394-49,484,297

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~190.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: ClinGen

KCNB1 encodes Kv2.1, which is responsible for a slowly deactivating delayed rectifier current thought to be responsible, in part, for repolarization following action potential. KCNB1 is genetically constrained for missense and loss of function variation. Over 25 de novo variants causing neurodevelopmental disability with epilepsy have been reported with replication since 2014, including truncating variants and missense variants demonstrated to alter channel function. Additionally, a knockout mouse shows altered seizure susceptibility. This curation was approved by the Epilepsy GCEP on 4/16/2019.

developmental and epileptic encephalopathy, 26DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014477

Submitter: G2P

developmental and epileptic encephalopathy, 26STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014477

Submitter: Labcorp Genetics (formerly Invitae)

undetermined early-onset epileptic encephalopathySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018614

Submitter: Orphanet

developmental and epileptic encephalopathy, 26STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014477

Submitter: PanelApp Australia

developmental and epileptic encephalopathy, 26STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014477

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Epileptic encephalopathy, early infantile, 26AD

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 25164438Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KCNB1 variants in ClinVar

20 Conditions Cataloged
Developmental and epileptic encephalopathy, 26Total: 707
not providedTotal: 264
not specifiedTotal: 83
Inborn genetic diseasesTotal: 72
KCNB1-related disorderTotal: 42
Epileptic encephalopathyTotal: 19
Intellectual disabilityTotal: 13
Developmental and epileptic encephalopathyTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004975.4. 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
1
clinvar
232
clinvar
6
clinvar
239
missense
29
clinvar
82
clinvar
286
clinvar
110
clinvar
49
clinvar
556
nonsense
8
clinvar
8
clinvar
9
clinvar
2
clinvar
1
clinvar
28
start loss
0
frameshift
7
clinvar
6
clinvar
22
clinvar
2
clinvar
37
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total449631934656861

Highest pathogenic variant AF is 0.00000656918

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004975.4RefSeqNP_004966.12MANE Select
ENST00000371741.6EnsemblENSP00000360806.32MANE Select
ENST00000635465.1EnsemblENSP00000489193.12Standard
ENST00000635465.2EnsemblENSP00000489193.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
kcnb1Danio rerio

Structure: tectal ventricle

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Calcium Regulation in the Cardiac Cell
  • Neuronal System
  • Voltage gated Potassium channels
  • Potassium Channels

Biological Process

  • action potential
  • vesicle docking involved in exocytosis
  • glutamate receptor signaling pathway
  • positive regulation of norepinephrine secretion
  • cellular response to nutrient levels

Molecular Function

  • voltage-gated potassium channel activity
  • delayed rectifier potassium channel activity
  • protein binding
  • ion channel binding
  • protein heterodimerization activity

Cellular Component

  • plasma membrane
  • voltage-gated potassium channel complex
  • integral component of membrane
  • lateral plasma membrane
  • cell junction

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000371741
Coding exons
2
Length
118771
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.272415130.4700.00003155666
Missense (PolyPhen)38257.150.147782827
Synonymous1.081902100.9050.00001381707
Loss of Function4.54024.00.000.00000138277

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
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, but also in the pancreas and cardiovascular system. Contributes to the regulation of the action potential (AP) repolarization, duration and frequency of repetitive AP firing in neurons, muscle cells and endocrine cells and plays a role in homeostatic attenuation of electrical excitability throughout the brain (PubMed:23161216). Plays also a role in the regulation of exocytosis independently of its electrical function (By similarity). Forms tetrameric potassium- selective channels through which potassium ions pass in accordance with their electrochemical gradient. The channel alternates between opened and closed conformations in response to the voltage difference across the membrane. Homotetrameric channels mediate a delayed-rectifier voltage-dependent outward potassium current that display rapid activation and slow inactivation in response to membrane depolarization (PubMed:8081723, PubMed:1283219, PubMed:10484328, PubMed:12560340, PubMed:19074135, PubMed:19717558, PubMed:24901643). Can form functional homotetrameric and heterotetrameric channels that contain variable proportions of KCNB2; channel properties depend on the type of alpha subunits that are part of the channel (By similarity). Can also form functional heterotetrameric channels with other alpha subunits that are non-conducting when expressed alone, such as KCNF1, KCNG1, KCNG3, KCNG4, KCNH1, KCNH2, KCNS1, KCNS2, KCNS3 and KCNV1, creating a functionally diverse range of channel complexes (PubMed:10484328, PubMed:11852086, PubMed:12060745, PubMed:19074135, PubMed:19717558, PubMed:24901643). Heterotetrameric channel activity formed with KCNS3 show increased current amplitude with the threshold for action potential activation shifted towards more negative values in hypoxic-treated pulmonary artery smooth muscle cells (By similarity). Channel properties are also modulated by cytoplasmic ancillary beta subunits such as AMIGO1, KCNE1, KCNE2 and KCNE3, slowing activation and inactivation rate of the delayed rectifier potassium channels (By similarity). In vivo, membranes probably contain a mixture of heteromeric potassium channel complexes, making it difficult to assign currents observed in intact tissues to any particular potassium channel family member. Major contributor to the slowly inactivating delayed-rectifier voltage- gated potassium current in neurons of the central nervous system, sympathetic ganglion neurons, neuroendocrine cells, pancreatic beta cells, cardiomyocytes and smooth muscle cells. Mediates the major part of the somatodendritic delayed-rectifier potassium current in hippocampal and cortical pyramidal neurons and sympathetic superior cervical ganglion (CGC) neurons that acts to slow down periods of firing, especially during high frequency stimulation. Plays a role in the induction of long-term potentiation (LTP) of neuron excitability in the CA3 layer of the hippocampus (By similarity). Contributes to the regulation of glucose-induced action potential amplitude and duration in pancreatic beta cells, hence limiting calcium influx and insulin secretion (PubMed:23161216). Plays a role in the regulation of resting membrane potential and contraction in hypoxia-treated pulmonary artery smooth muscle cells. May contribute to the regulation of the duration of both the action potential of cardiomyocytes and the heart ventricular repolarization QT interval. Contributes to the pronounced pro-apoptotic potassium current surge during neuronal apoptotic cell death in response to oxidative injury. May confer neuroprotection in response to hypoxia/ischemic insults by suppressing pyramidal neurons hyperexcitability in hippocampal and cortical regions (By similarity). Promotes trafficking of KCNG3, KCNH1 and KCNH2 to the cell surface membrane, presumably by forming heterotetrameric channels with these subunits (PubMed:12060745). Plays a role in the calcium-dependent recruitment and release of fusion-competent vesicles from the soma of neurons, neuroendocrine and glucose- induced pancreatic beta cells by binding key components of the fusion machinery in a pore-independent manner (By similarity). {ECO:0000250|UniProtKB:P15387, ECO:0000250|UniProtKB:Q03717, ECO:0000269|PubMed:10484328, ECO:0000269|PubMed:11852086, ECO:0000269|PubMed:12060745, ECO:0000269|PubMed:12560340, ECO:0000269|PubMed:1283219, ECO:0000269|PubMed:19074135, ECO:0000269|PubMed:19717558, ECO:0000269|PubMed:23161216, ECO:0000269|PubMed:24901643, ECO:0000269|PubMed:8081723}.;
Disease
DISEASE: Epileptic encephalopathy, early infantile, 26 (EIEE26) [MIM:616056]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE26 patients manifest multiple types of seizures, delayed psychomotor development, poor or absent speech, hypotonia, hypsarrhythmia. {ECO:0000269|PubMed:25164438, ECO:0000269|PubMed:26477325, ECO:0000269|PubMed:26503721}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.141

Intolerance Scores

LoFtool
0.00937
RVIS EVS
-0.05
RVIS percentile EVS
50.34

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.877

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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