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

Gene ID: 343450, updated on 5-Mar-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
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Genomic context

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See KCNT2 in Genome Data Viewer
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 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 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 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

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