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    KCNT2 potassium sodium-activated channel subfamily T member 2 [ Homo sapiens (human) ]

    Gene ID: 343450, updated on 2-May-2024

    Summary

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    Official Symbol
    KCNT2provided by HGNC
    Official Full Name
    potassium sodium-activated channel subfamily T member 2provided by HGNC
    Primary source
    HGNC:HGNC:18866
    See related
    Ensembl:ENSG00000162687 MIM:610044; AllianceGenome:HGNC:18866
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DEE57; SLICK; EIEE57; KCa4.2; SLO2.1
    Summary
    Enables chloride-activated potassium channel activity. Involved in potassium ion export across plasma membrane. Located in plasma membrane. Implicated in developmental and epileptic encephalopathy 57. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in ovary (RPKM 1.6), lung (RPKM 0.9) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q31.3
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (196225779..196608440, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (195571842..195954779, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (196194909..196577570, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1724 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:196078321-196078852 Neighboring gene uncharacterized LOC105371674 Neighboring gene LINE-1 retrotransposable element ORF2 protein-like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:196342862-196343398 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:196577905-196578421 Neighboring gene microRNA 4735 Neighboring gene MPRA-validated peak637 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2274 Neighboring gene MPRA-validated peak638 silencer Neighboring gene complement factor H Neighboring gene complement factor H related 3

    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. Recurrent KCNT2 missense variants affecting p.Arg190 result in a recognizable phenotype. Jackson A, et al. Am J Med Genet A, 2021 Oct. PMID 34061450
    2. New mutations in KCNT2 gene causing early infantile epileptic encephalopathy type 57: Case study and literature review. Alagoz M, et al. Acta Biochim Pol, 2020 Sep 15. PMID 32931186
    3. In silico and in vitro analysis of cation-activated potassium channels in human corneal endothelial cells. Amador-Muñoz D, et al. Exp Eye Res, 2020 Aug. PMID 32561484
    4. Hydrophobic interactions between the S5 segment and the pore helix stabilizes the closed state of Slo2.1 potassium channels. Suzuki T, et al. Biochim Biophys Acta, 2016 Apr. PMID 26724206, Free PMC Article
    5. Identification of the Intracellular Na+ Sensor in Slo2.1 Potassium Channels. Thomson SJ, et al. J Biol Chem, 2015 Jun 5. PMID 25903137, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. KCNT2-Related Disorders: Phenotypes, Functional, and Pharmacological Properties.
      Title: KCNT2-Related Disorders: Phenotypes, Functional, and Pharmacological Properties.
    2. Recurrent KCNT2 missense variants affecting p.Arg190 result in a recognizable phenotype.
      Title: Recurrent KCNT2 missense variants affecting p.Arg190 result in a recognizable phenotype.
    3. New mutations in KCNT2 gene causing early infantile epileptic encephalopathy type 57: Case study and literature review.
      Title: New mutations in KCNT2 gene causing early infantile epileptic encephalopathy type 57: Case study and literature review.
    4. In silico and in vitro analysis of cation-activated potassium channels in human corneal endothelial cells.
      Title: In silico and in vitro analysis of cation-activated potassium channels in human corneal endothelial cells.
    5. An inducible circular RNA circKcnt2 inhibits ILC3 activation to facilitate colitis resolution.
      Title: An inducible circular RNA circKcnt2 inhibits ILC3 activation to facilitate colitis resolution.
    6. The expression of three genes (STK26, KCNT2, CASP12) was correlated with the prognosis of skin cutaneous melanoma (SCM). STK26 and KCNT2 were significantly different between normal skin and SCM. These three hub genes have potential value as predictors for accurate diagnosis and prognosis of SCM in the future.
      Title: Common Nevus and Skin Cutaneous Melanoma: Prognostic Genes Identified by Gene Co-Expression Network Analysis.
    7. Pathogenic Phe240Leu mutation in KCNT2 channel changes ion selectivity.
      Title: A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy.
    8. In the present study, we evaluated two other potential mechanisms for stabilization of Slo2 channels in a closed state: (1) dewetting and collapse of the inner pore (hydrophobic gating) and (2) constriction of the inner pore by tight criss-crossing of the cytoplasmic ends of the S6 alpha-helical segments.
      Title: Molecular mechanisms of Slo2 K(+) channel closure.
    9. mRNA of aquaporin 1 was co-expressed in Xenopus oocytes with homomeric or heteromeric Slick and Slack alpha-subunits. Hypotonic or hypertonic buffers caused changes in current. The heteromeric channel had a characteristic graded sensitivity to small and fast changes in cell volume. This the cell volume sensitivity is dependent on the number of volume sensitive Slick alpha-subunits in the tetrameric channels.
      Title: Heteromeric Slick/Slack K+ channels show graded sensitivity to cell volume changes.
    10. KCNT2 SNPs were associated with lifetime cannabis use, but the association did not reach genome-wide significance. [Meta-Analysis]
      Title: Genome-wide association study of lifetime cannabis use based on a large meta-analytic sample of 32 330 subjects from the International Cannabis Consortium.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    Associated conditions

    Description Tests
    Developmental and epileptic encephalopathy, 57
    MedGen: C4540411 OMIM: 617771 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.
    EBI GWAS Catalog
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC119610, MGC119611, MGC119612, MGC119613, RP11-58O13.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chloride-activated potassium channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chloride-activated potassium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    Process Evidence Code Pubs
    involved_in potassium ion export across plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in potassium ion export across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    potassium channel subfamily T member 2
    Names
    potassium channel, subfamily T, member 2
    sequence like an intermediate conductance potassium channel subunit
    sodium and chloride-activated ATP-sensitive potassium channel Slo2.1
    sodium-and chloride-activated ATP-sensitive potassium channel (SLICK)

    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.

    mRNA and Protein(s)

    1. NM_001287819.3 → NP_001274748.1  potassium channel subfamily T member 2 isoform 2

      See identical proteins and their annotated locations for NP_001274748.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AL139137, BC103948, DA799907, DB071968
      Consensus CDS
      CCDS72995.1
      UniProtKB/Swiss-Prot
      Q6UVM3
      Related
      ENSP00000356403.5, ENST00000367433.9
      Conserved Domains (3) summary
      pfam00520
      Location:63 → 270
      Ion_trans; Ion transport protein
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    2. NM_001287820.3 → NP_001274749.1  potassium channel subfamily T member 2 isoform 3

      See identical proteins and their annotated locations for NP_001274749.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two in-frame exons and contains one alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AK131498, AL139137, BC103949, DB071968
      Consensus CDS
      CCDS72994.1
      UniProtKB/Swiss-Prot
      Q6UVM3
      Related
      ENSP00000476657.1, ENST00000609185.5
      Conserved Domains (3) summary
      pfam00520
      Location:63 → 270
      Ion_trans; Ion transport protein
      pfam03493
      Location:431 → 468
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    3. NM_198503.5 → NP_940905.2  potassium channel subfamily T member 2 isoform 1

      See identical proteins and their annotated locations for NP_940905.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL139137, AY359444, DB071968
      Consensus CDS
      CCDS1384.1
      UniProtKB/Swiss-Prot
      Q3SY59, Q5VTN1, Q6UVM3, Q6ZMT3
      UniProtKB/TrEMBL
      A9LNM6
      Related
      ENSP00000294725.8, ENST00000294725.14
      Conserved Domains (3) summary
      pfam00520
      Location:63 → 270
      Ion_trans; Ion transport protein
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    RNA

    1. NR_146057.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL138931, AL139137, AL358853, AL591604

    2. NR_146058.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL138931, AL139137, AL358853, AL591604

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      196225779..196608440 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006711295.4 → XP_006711358.1  potassium channel subfamily T member 2 isoform X2

      See identical proteins and their annotated locations for XP_006711358.1

      Conserved Domains (3) summary
      pfam00520
      Location:63 → 270
      Ion_trans; Ion transport protein
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    2. XM_006711294.4 → XP_006711357.1  potassium channel subfamily T member 2 isoform X1

      See identical proteins and their annotated locations for XP_006711357.1

      Conserved Domains (2) summary
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    3. XM_017001181.2 → XP_016856670.1  potassium channel subfamily T member 2 isoform X6

    4. XM_017001183.2 → XP_016856672.1  potassium channel subfamily T member 2 isoform X7

      Conserved Domains (1) summary
      pfam03493
      Location:2 → 47
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit

    5. XM_017001185.3 → XP_016856674.1  potassium channel subfamily T member 2 isoform X8

      Conserved Domains (2) summary
      pfam03493
      Location:406 → 501
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:201 → 247
      Ion_trans_2; Ion channel

    6. XM_017001179.3 → XP_016856668.1  potassium channel subfamily T member 2 isoform X3

    7. XM_011509483.4 → XP_011507785.1  potassium channel subfamily T member 2 isoform X5

      Conserved Domains (2) summary
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    8. XM_017001180.3 → XP_016856669.1  potassium channel subfamily T member 2 isoform X4

      UniProtKB/TrEMBL
      A0A3B3IRL4
      Related
      ENSP00000496885.1, ENST00000647658.1
      Conserved Domains (3) summary
      pfam00520
      Location:63 → 270
      Ion_trans; Ion transport protein
      pfam03493
      Location:431 → 526
      BK_channel_a; Calcium-activated BK potassium channel alpha subunit
      pfam07885
      Location:226 → 272
      Ion_trans_2; Ion channel

    RNA

    1. XR_001737149.3 RNA Sequence

    2. XR_001737151.3 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791754.1 Reference GRCh38.p14 PATCHES

      Range
      75455..458104 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332752.1 → XP_054188727.1  potassium channel subfamily T member 2 isoform X2

    2. XM_054332751.1 → XP_054188726.1  potassium channel subfamily T member 2 isoform X1

    3. XM_054332756.1 → XP_054188731.1  potassium channel subfamily T member 2 isoform X6

    4. XM_054332757.1 → XP_054188732.1  potassium channel subfamily T member 2 isoform X7

    5. XM_054332758.1 → XP_054188733.1  potassium channel subfamily T member 2 isoform X8

    6. XM_054332753.1 → XP_054188728.1  potassium channel subfamily T member 2 isoform X3

    7. XM_054332755.1 → XP_054188730.1  potassium channel subfamily T member 2 isoform X5

    8. XM_054332754.1 → XP_054188729.1  potassium channel subfamily T member 2 isoform X4

      UniProtKB/TrEMBL
      A0A3B3IRL4

    RNA

    1. XR_008485791.1 RNA Sequence

    2. XR_008485792.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      195571842..195954779 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336360.1 → XP_054192335.1  potassium channel subfamily T member 2 isoform X2

    2. XM_054336359.1 → XP_054192334.1  potassium channel subfamily T member 2 isoform X1

    3. XM_054336364.1 → XP_054192339.1  potassium channel subfamily T member 2 isoform X6

    4. XM_054336365.1 → XP_054192340.1  potassium channel subfamily T member 2 isoform X7

    5. XM_054336366.1 → XP_054192341.1  potassium channel subfamily T member 2 isoform X8

    6. XM_054336361.1 → XP_054192336.1  potassium channel subfamily T member 2 isoform X3

    7. XM_054336363.1 → XP_054192338.1  potassium channel subfamily T member 2 isoform X5

    8. XM_054336362.1 → XP_054192337.1  potassium channel subfamily T member 2 isoform X4

      UniProtKB/TrEMBL
      A0A3B3IRL4

    RNA

    1. XR_008486022.1 RNA Sequence

    2. XR_008486023.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UVM3.1 GenPept UniProtKB/Swiss-Prot:Q6UVM3

    Gene LinkOut

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

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