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

    Gene ID: 57582, updated on 3-Dec-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
    mouse all
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    Genomic context

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    See KCNT1 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (135702185..135795502)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (147929033..148022602)
    RS_2024_09 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. KCNT1-Related Epilepsy. Adam MP, et al. , 1993. PMID 30234941
    2. Gene-wide tagging study of the association between KCNT1 polymorphisms and the susceptibility and efficacy of genetic generalized epilepsy in Chinese population. Qu J, et al. CNS Neurosci Ther, 2014 Feb. PMID 24279416, Free PMC Article
    3. A recurrent KCNT1 mutation in two sporadic cases with malignant migrating partial seizures in infancy. Ishii A, et al. Gene, 2013 Dec 1. PMID 24029078
    4. Human slack potassium channel mutations increase positive cooperativity between individual channels. Kim GE, et al. Cell Rep, 2014 Dec 11. PMID 25482562, Free PMC Article
    5. Mutations in KCNT1 cause a spectrum of focal epilepsies. Møller RS, et al. Epilepsia, 2015 Sep. PMID 26122718, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A molecular switch in RCK2 triggers sodium-dependent activation of KNa1.1 (KCNT1) potassium channels.
      Title: A molecular switch in RCK2 triggers sodium-dependent activation of K(Na)1.1 (KCNT1) potassium channels.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. KCNT1-related epilepsies and epileptic encephalopathies: phenotypic and mutational spectrum.
      Title: KCNT1-related epilepsies and epileptic encephalopathies: phenotypic and mutational spectrum.
    7. Recurrent pulmonary hemorrhage in juvenile patients with KCNT1 mutation.
      Title: Recurrent pulmonary hemorrhage in juvenile patients with KCNT1 mutation.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    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)

    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 intracellular sodium-activated potassium channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables outward rectifier potassium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables outward rectifier potassium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in potassium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in potassium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein homotetramerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    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_2024_08

    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

      UniProtKB/TrEMBL
      A0A0K2GMW5

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

      UniProtKB/TrEMBL
      A0A0K2GMW5

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

      UniProtKB/TrEMBL
      A0A0D9SEY3, A0A0R4J2E0

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3, A0A6Q8PGM3

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3

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

      UniProtKB/TrEMBL
      A0A6Q8PFS3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5JUK3.2 GenPept UniProtKB/Swiss-Prot:Q5JUK3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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