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

Gene ID: 23416, updated on 28-Oct-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 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)

Genotypes

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

  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

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