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KCNT1 potassium sodium-activated channel subfamily T member 1 [ Homo sapiens (human) ]

Gene ID: 57582, updated on 3-Apr-2024

Summary

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Official Symbol
KCNT1provided by HGNC
Official Full Name
potassium sodium-activated channel subfamily T member 1provided by HGNC
Primary source
HGNC:HGNC:18865
See related
Ensembl:ENSG00000107147 MIM:608167; AllianceGenome:HGNC:18865
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEE14; ENFL5; SLACK; EIEE14; KCa4.1; Slo2.2; bA100C15.2
Summary
Potassium 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. This gene encodes a sodium-activated potassium channel subunit which is thought to function in ion conductance and developmental signaling pathways. Mutations in this gene cause the early-onset epileptic disorders, malignant migrating partial seizures of infancy and autosomal dominant nocturnal frontal lobe epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
Expression
Biased expression in brain (RPKM 4.3), spleen (RPKM 2.1) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
9q34.3
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (135702185..135795502)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (147929033..148022602)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (138594031..138687348)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376317 Neighboring gene uncharacterized LOC105376318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138586423-138586937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20488 Neighboring gene spermatogenesis and oogenesis specific basic helix-loop-helix 1 Neighboring gene Sharpr-MPRA regulatory region 14740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138615694-138616271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138619907-138620844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138639213-138639970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138675789-138676289 Neighboring gene uncharacterized LOC107987140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138695080-138695746 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138712950-138713111 Neighboring gene calmodulin regulated spectrin associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 6734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138770145-138770777 Neighboring gene Sharpr-MPRA regulatory region 8889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138780903-138781606 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:138796685-138797884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20492 Neighboring gene CAMSAP1 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Functional Effects of Epilepsy Associated KCNT1 Mutations Suggest Pathogenesis via Aberrant Inhibitory Neuronal Activity. Rychkov GY, et al. Int J Mol Sci, 2022 Dec 1. PMID 36499459, Free PMC Article
  2. The phenotypic spectrum of KCNT1: a new family with variable epilepsy syndromes including mild focal epilepsy. Cherian C, et al. J Neurol, 2022 Apr. PMID 34537872
  3. KCNT1-related epilepsies and epileptic encephalopathies: phenotypic and mutational spectrum. Bonardi CM, et al. Brain, 2021 Dec 31. PMID 34114611
  4. Recurrent pulmonary hemorrhage in juvenile patients with KCNT1 mutation. Ikeda A, et al. Pediatr Int, 2021 Mar. PMID 33650128
  5. [Early infantile epileptic encephalopathy type 14: three cases of epilepsy in infancy with migrating focal seizures due to KCNT1 mutations]. Kholin AA, et al. Zh Nevrol Psikhiatr Im S S Korsakova, 2019. PMID 31532594

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Coupling of Slack and NaV1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development.
    Title: Coupling of Slack and Na(V)1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development.
  2. Functional evaluation of epilepsy-associated KCNT1 variants in multiple cellular systems reveals a predominant gain of function impact on channel properties.
    Title: Functional evaluation of epilepsy-associated KCNT1 variants in multiple cellular systems reveals a predominant gain of function impact on channel properties.
  3. Functional Effects of Epilepsy Associated KCNT1 Mutations Suggest Pathogenesis via Aberrant Inhibitory Neuronal Activity.
    Title: Functional Effects of Epilepsy Associated KCNT1 Mutations Suggest Pathogenesis via Aberrant Inhibitory Neuronal Activity.
  4. The phenotypic spectrum of KCNT1: a new family with variable epilepsy syndromes including mild focal epilepsy.
    Title: The phenotypic spectrum of KCNT1: a new family with variable epilepsy syndromes including mild focal epilepsy.
  5. KCNT1-related epilepsies and epileptic encephalopathies: phenotypic and mutational spectrum.
    Title: KCNT1-related epilepsies and epileptic encephalopathies: phenotypic and mutational spectrum.
  6. Recurrent pulmonary hemorrhage in juvenile patients with KCNT1 mutation.
    Title: Recurrent pulmonary hemorrhage in juvenile patients with KCNT1 mutation.
  7. KCNT1 mutations lead to a severe form of epilepsy; this KCNT1 mutation was found to increase the Slack current in neurons.
    Title: An Epilepsy-Associated KCNT1 Mutation Enhances Excitability of Human iPSC-Derived Neurons by Increasing Slack K(Na) Currents.
  8. Extracerebral symptoms probably linked with KCNT1 mutation were present, including arteriovenous fistula, dilated cardiomyopathy and precocious puberty. Eight patients (47%) had died at 3 (1.5-15.4) years including three from suspected sudden unexpected death in epilepsy.
    Title: KCNT1 epilepsy with migrating focal seizures shows a temporal sequence with poor outcome, high mortality and SUDEP.
  9. that KCNT1 epileptogenicity may result not only from dysregulated excitability by controlling Na+K+ transport
    Title: Mild malformations of cortical development in sleep-related hypermotor epilepsy due to KCNT1 mutations.
  10. KCNT1 is likely to be a major gene causing early infantile epileptic encephalopathy type 14
    Title: [Early infantile epileptic encephalopathy type 14: three cases of epilepsy in infancy with migrating focal seizures due to KCNT1 mutations].
Submit: New GeneRIF Correction See all GeneRIFs (31)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Homology

Clone Names

  • FLJ41282

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables intracellular sodium-activated potassium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables outward rectifier potassium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
potassium channel subfamily T member 1
Names
Sequence like a calcium-activated K+ channel
potassium channel, sodium activated subfamily T, member 1
potassium channel, subfamily T, member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033070.2 RefSeqGene

    Range
    5001..98318
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001272003.2 → NP_001258932.1  potassium channel subfamily T member 1 isoform 2

    See identical proteins and their annotated locations for NP_001258932.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, uses an alternate splice site in the 5' region and contains an additional exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL158822
    Consensus CDS
    CCDS65188.1
    UniProtKB/TrEMBL
    A0A6Q8PFS3
    Related
    ENSP00000486374.1, ENST00000628528.2
    Conserved Domains (2) summary
    pfam03493
    Location:458 → 553
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:252 → 305
    Ion_trans_2; Ion channel

  2. NM_020822.3 → NP_065873.2  potassium channel subfamily T member 1 isoform 1

    See identical proteins and their annotated locations for NP_065873.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK127272, AL158822, BC171770, BX110871, DA095802
    Consensus CDS
    CCDS35175.2
    UniProtKB/TrEMBL
    A0A0K2GMW5
    Related
    ENSP00000360822.2, ENST00000371757.7
    Conserved Domains (3) summary
    pfam00520
    Location:162 → 342
    Ion_trans; Ion transport protein
    pfam03493
    Location:504 → 598
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:297 → 350
    Ion_trans_2; Ion channel

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    135702185..135795502
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518878.4 → XP_011517180.1  potassium channel subfamily T member 1 isoform X1

    UniProtKB/TrEMBL
    A0A0K2GMW5
    Conserved Domains (2) summary
    pfam03493
    Location:551 → 646
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:345 → 398
    Ion_trans_2; Ion channel

  2. XM_011518879.4 → XP_011517181.1  potassium channel subfamily T member 1 isoform X2

    UniProtKB/TrEMBL
    A0A0K2GMW5
    Conserved Domains (2) summary
    pfam03493
    Location:548 → 643
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:322 → 395
    Ion_trans_2; Ion channel

  3. XM_011518880.2 → XP_011517182.1  potassium channel subfamily T member 1 isoform X4

    UniProtKB/TrEMBL
    A0A0D9SEY3, A0A0R4J2E0
    Related
    ENSP00000263604.4, ENST00000263604.5
    Conserved Domains (2) summary
    pfam03493
    Location:470 → 565
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:244 → 317
    Ion_trans_2; Ion channel

  4. XM_024447618.2 → XP_024303386.1  potassium channel subfamily T member 1 isoform X6

    UniProtKB/TrEMBL
    A0A6Q8PFS3
    Conserved Domains (3) summary
    pfam00520
    Location:3 → 172
    Ion_trans; Ion transport protein
    pfam03493
    Location:326 → 428
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:127 → 180
    Ion_trans_2; Ion channel

  5. XM_017014933.2 → XP_016870422.1  potassium channel subfamily T member 1 isoform X6

    UniProtKB/TrEMBL
    A0A6Q8PFS3
    Conserved Domains (3) summary
    pfam00520
    Location:3 → 172
    Ion_trans; Ion transport protein
    pfam03493
    Location:326 → 428
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:127 → 180
    Ion_trans_2; Ion channel

  6. XM_017014931.2 → XP_016870420.1  potassium channel subfamily T member 1 isoform X3

    UniProtKB/TrEMBL
    A0A6Q8PFS3

  7. XM_017014932.2 → XP_016870421.1  potassium channel subfamily T member 1 isoform X5

    UniProtKB/TrEMBL
    A0A6Q8PFS3, A0A6Q8PGM3
    Related
    ENSP00000502322.1, ENST00000676421.1

  8. XM_024447617.2 → XP_024303385.1  potassium channel subfamily T member 1 isoform X6

    UniProtKB/TrEMBL
    A0A6Q8PFS3
    Conserved Domains (3) summary
    pfam00520
    Location:3 → 172
    Ion_trans; Ion transport protein
    pfam03493
    Location:326 → 428
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:127 → 180
    Ion_trans_2; Ion channel

  9. XM_011518881.4 → XP_011517183.1  potassium channel subfamily T member 1 isoform X6

    UniProtKB/TrEMBL
    A0A6Q8PFS3
    Conserved Domains (3) summary
    pfam00520
    Location:3 → 172
    Ion_trans; Ion transport protein
    pfam03493
    Location:326 → 428
    BK_channel_a; Calcium-activated BK potassium channel alpha subunit
    pfam07885
    Location:127 → 180
    Ion_trans_2; Ion channel

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    147929033..148022602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363320.1 → XP_054219295.1  potassium channel subfamily T member 1 isoform X1

  2. XM_054363321.1 → XP_054219296.1  potassium channel subfamily T member 1 isoform X2

  3. XM_054363323.1 → XP_054219298.1  potassium channel subfamily T member 1 isoform X4

    UniProtKB/TrEMBL
    A0A0R4J2E0

  4. XM_054363326.1 → XP_054219301.1  potassium channel subfamily T member 1 isoform X6

  5. XM_054363328.1 → XP_054219303.1  potassium channel subfamily T member 1 isoform X6

  6. XM_054363322.1 → XP_054219297.1  potassium channel subfamily T member 1 isoform X3

  7. XM_054363324.1 → XP_054219299.1  potassium channel subfamily T member 1 isoform X5

    UniProtKB/TrEMBL
    A0A6Q8PGM3

  8. XM_054363325.1 → XP_054219300.1  potassium channel subfamily T member 1 isoform X6

  9. XM_054363327.1 → XP_054219302.1  potassium channel subfamily T member 1 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JUK3.2 GenPept UniProtKB/Swiss-Prot:Q5JUK3

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