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

Summary

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

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

report on the binding of HIV-1 gp120 to the cytoplasmic C-terminus of the voltage-gated potassium channel BEC1, an interaction that can result in the repression of BEC's activity and the inhibition of HIV-1 particle-release
Title: Interaction of human immunodeficiency virus gp120 with the voltage-gated potassium channel BEC1.
BEC1 is negatively involved in cognitive functions with no abnormal behaviors such as spontaneous seizures or motor dysfunction.
Title: Disruption of the ether-a-go-go K+ channel gene BEC1/KCNH3 enhances cognitive function.

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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

STS-F09935 (e-PCR)
- UniSTS:26162

MCRS1_9110 (e-PCR)
- UniSTS:468082

KCNH3_2115 (e-PCR)
- UniSTS:280799

RH41888 (e-PCR)
- UniSTS:72695

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)

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
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

49539030..49558337

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

49501276..49520593

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B9EK44
XM_054371581.1 → XP_054227556.1 potassium voltage-gated channel subfamily H member 3 isoform X2