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    KCNH3 potassium voltage-gated channel subfamily H member 3 [ Homo sapiens (human) ]

    Gene ID: 23416, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KCNH3provided by HGNC
    Official Full Name
    potassium voltage-gated channel subfamily H member 3provided by HGNC
    Primary source
    HGNC:HGNC:6252
    See related
    Ensembl:ENSG00000135519 MIM:604527; AllianceGenome:HGNC:6252
    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
    BEC1; ELK2; Kv12.2
    Summary
    The protein encoded by this gene is a voltage-gated potassium channel alpha subunit predominantly expressed in the forebrain. Studies in mice have found that cognitive function increases when this gene is knocked out. In humans, the encoded protein has been shown to be capable of binding glycoprotein 120 of the human immunodeficiency virus type 1 (HIV-1) envelope. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
    Expression
    Biased expression in brain (RPKM 7.0), testis (RPKM 0.9) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KCNH3 in Genome Data Viewer
    Location:
    12q13.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (49539030..49558337)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (49501276..49520593)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49932813..49952120)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49741370-49742313 Neighboring gene DnaJ heat shock protein family (Hsp40) member C22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6315 Neighboring gene FGFR1 oncogene partner 2 pseudogene Neighboring gene spermatogenesis associated serine rich 2 Neighboring gene Sharpr-MPRA regulatory region 14813 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49846952-49847452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49873095-49873682 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:49907610-49907788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49932121-49932932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49932933-49933742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6316 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:49936243-49937442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49941330-49942138 Neighboring gene uncharacterized LOC105369761 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49961221-49962024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6319 Neighboring gene microspherule protein 1 Neighboring gene family with sequence similarity 186 member B Neighboring gene RNA, U6 small nuclear 834, pseudogene Neighboring gene RNA polymerase II subunit K pseudogene 1

    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. Interaction of human immunodeficiency virus gp120 with the voltage-gated potassium channel BEC1. Herrmann M, et al. FEBS Lett, 2010 Aug 20. PMID 20638388
    2. Disruption of the ether-a-go-go K+ channel gene BEC1/KCNH3 enhances cognitive function. Miyake A, et al. J Neurosci, 2009 Nov 18. PMID 19923296, Free PMC Article
    3. Distribution and functional properties of human KCNH8 (Elk1) potassium channels. Zou A, et al. Am J Physiol Cell Physiol, 2003 Dec. PMID 12890647
    4. New ether-à-go-go K(+) channel family members localized in human telencephalon. Miyake A, et al. J Biol Chem, 1999 Aug 27. PMID 10455180
    5. Bimodal regulation of an Elk subfamily K+ channel by phosphatidylinositol 4,5-bisphosphate. Li X, et al. J Gen Physiol, 2015 Nov. PMID 26503718, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 binds to the C-terminus (amino acids 973-1083) of BEC1 in vitro and in living cells. Overexpression of BEC1 inhibits HIV-1 particle release from 293T cells. This requires the C-terminus of BEC1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1282

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables inward rectifier potassium channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables voltage-gated potassium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables voltage-gated potassium channel activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in potassium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in potassium ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in potassium ion transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of membrane potential IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of monoatomic ion channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    voltage-gated inwardly rectifying potassium channel KCNH3; potassium voltage-gated channel subfamily H member 3
    Names
    ELK channel 2
    brain-specific eag-like channel 1
    ether-a-go-go K(+) channel family member
    ether-a-go-go-like potassium channel 2
    potassium channel, voltage gated eag related subfamily H, member 3
    potassium voltage-gated channel, subfamily H (eag-related), member 3
    voltage-gated potassium channel subunit Kv12.2

    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_001314030.2 → NP_001300959.1  voltage-gated inwardly rectifying potassium channel KCNH3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction at the end of a 5' exon and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AB033108, AC020612, AW248597, BC144254
      UniProtKB/TrEMBL
      B9EK44
      Conserved Domains (4) summary
      smart00086
      Location:36 → 75
      PAC; Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)
      cd00038
      Location:522 → 632
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      pfam00520
      Location:186 → 451
      Ion_trans; Ion transport protein
      pfam07885
      Location:392 → 446
      Ion_trans_2; Ion channel

    2. NM_012284.3 → NP_036416.1  voltage-gated inwardly rectifying potassium channel KCNH3 isoform 1

      See identical proteins and their annotated locations for NP_036416.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB033108, AC020612, AW248597
      Consensus CDS
      CCDS8786.1
      UniProtKB/Swiss-Prot
      Q9ULD8, Q9UQ06
      UniProtKB/TrEMBL
      B9EK44
      Related
      ENSP00000257981.5, ENST00000257981.7
      Conserved Domains (5) summary
      cd00038
      Location:582 → 692
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00130
      Location:42 → 133
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam00520
      Location:246 → 511
      Ion_trans; Ion transport protein
      pfam07885
      Location:452 → 506
      Ion_trans_2; Ion channel
      pfam08447
      Location:42 → 123
      PAS_3; PAS fold

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      49539030..49558337
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538085.3 → XP_011536387.1  potassium voltage-gated channel subfamily H member 3 isoform X1

      UniProtKB/TrEMBL
      B9EK44
      Conserved Domains (5) summary
      cd00038
      Location:582 → 692
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
      cd00130
      Location:42 → 133
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam00520
      Location:246 → 511
      Ion_trans; Ion transport protein
      pfam07885
      Location:452 → 506
      Ion_trans_2; Ion channel
      pfam08447
      Location:42 → 123
      PAS_3; PAS fold

    2. XM_047428613.1 → XP_047284569.1  potassium voltage-gated channel subfamily H member 3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      49501276..49520593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371580.1 → XP_054227555.1  potassium voltage-gated channel subfamily H member 3 isoform X1

      UniProtKB/TrEMBL
      B9EK44

    2. XM_054371581.1 → XP_054227556.1  potassium voltage-gated channel subfamily H member 3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ULD8.2 GenPept UniProtKB/Swiss-Prot:Q9ULD8

    Gene LinkOut

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