Gene
KCNT1
potassium sodium-activated channel subfamily T member 1
- HGNC 18865(opens in a new tab)
- Ensembl gene ENSG00000107147(opens in a new tab)
- NCBI Gene 57582(opens in a new tab)
Summary
- Cytogenetic location
- 9q34.3
- Coordinates
- Chromosome 9: 135,702,185–135,795,502 (GRCh38)
- Exons
- 31 exons across 93.3 kb
- Protein
- 1,235 amino acids
- Also known as
- KCa4.1, KIAA1422, SLACK, Slo2.2
- MANE Select transcript
- ENST00000371757.7NM_020822.3
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Epilepsy (Full Panel)
- Epilepsy
One of 171 genes linked to it
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
- ClinGen rates the link definitive
- 4 GenCC submitters rate it definitive or strong
How KCNT1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 7.1 kb of the gene's 93.3 kb; 3,708 of those bases code for the protein.
How a genome test reads KCNT1
55
positions in KCNT1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 93.3 kb of KCNT1, introns included, not only the 7.1 kb of exons.
Traits linked to KCNT1
The Human Phenotype Ontology lists these as features of the rare conditions KCNT1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Brain degeneration
- Epileptic encephalopathy
- Focal motor seizure
- Generalized-onset motor seizure
- Interictal epileptiform activity
- Cognitive impairment
- Inability to walk
- Loss of developmental milestones
Show 54 more traits
- Multifocal epileptiform discharges
- Neurodevelopmental delay
- Nocturnal seizures
- Behavioral abnormality
- Bilateral tonic-clonic seizure with focal onset
- Decrease in size of the outer layer of the brain due to loss of brain cells
- Degeneration of cerebrum
- Delayed CNS myelination
- Focal autonomic seizure
- Focal emotional seizure with laughing
- Focal hemiclonic seizure
- Focal impaired awareness seizure
- Focal tonic seizure
- Generalized tonic seizure
- Grand mal seizures
- Inability to walk by childhood/adolescence
- Intellectual disability
- Involuntary movements
- Myoclonic seizure
- Paroxysmal dystonia
- Profound global developmental delay
- Repetitive movements
- Thin corpus callosum
- Underdevelopment of part of brain called corpus callosum
- Abnormal corpus callosum morphology
- Absent speech development
- Aggressive behavior
- Anxiety
- Delayed myelination
- Depression
- EEG with focal spikes
- Epileptic spasm
- Focal autonomic seizure with palpitations/tachycardia/bradycardia/asystole
- Focal clonic seizure
- Focal hyperkinetic seizure
- Generalized clonic seizure
- Hypsarrhythmia
- Increased theta frequency activity in EEG
- Personality disorder
- Poor eye contact
- Psychosis
- Repeated seizures without recovery between them
- Sleep walking
- Suicidal ideation
- Attention deficit
- Intellectual disability, mild
- NREM parasomnia
- Psychotic mentation
- Clonus
- Gliosis
- Increased reflexes
- Loss of brain cells
- Paralysis of all four limbs
- Seizure affecting one half of brain
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). KCNT1 gene: potassium sodium-activated channel subfamily T member 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/kcnt1
Dante Labs. KCNT1 gene: potassium sodium-activated channel subfamily T member 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/kcnt1
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