Human Gene KCNQ3 (uc003ytj.3) Description and Page Index
  Description: Homo sapiens potassium voltage-gated channel, KQT-like subfamily, member 3 (KCNQ3), transcript variant 1, mRNA.
RefSeq Summary (NM_004519): This gene encodes a protein that functions in the regulation of neuronal excitability. The encoded protein forms an M-channel by associating with the products of the related KCNQ2 or KCNQ5 genes, which both encode integral membrane proteins. M-channel currents are inhibited by M1 muscarinic acetylcholine receptors and are activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 2 (BFNC2), also known as epilepsy, benign neonatal type 2 (EBN2). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014].
Transcript (Including UTRs)
   Position: hg19 chr8:133,133,105-133,493,004 Size: 359,900 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr8:133,141,509-133,492,779 Size: 351,271 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr8:133,133,105-133,493,004)mRNA (may differ from genome)Protein (872 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDHuman Cortex Gene ExpressionLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Potassium voltage-gated channel subfamily KQT member 3; AltName: Full=KQT-like 3; AltName: Full=Potassium channel subunit alpha KvLQT3; AltName: Full=Voltage-gated potassium channel subunit Kv7.3;
FUNCTION: Probably important in the regulation of neuronal excitability. Associates with KCNQ2 or KCNQ5 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs.
SUBUNIT: Heteromultimer with KCNQ2 or KCNQ5. May associate with KCNE2.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Predominantly expressed in brain.
DOMAIN: The segment S4 is probably the voltage-sensor and is characterized by a series of positively charged amino acids at every third position (By similarity).
DISEASE: Defects in KCNQ3 are the cause of benign familial neonatal seizures type 2 (BFNS2) [MIM:121201]. A disorder characterized by clusters of seizures occurring in the first days of life. Most patients have spontaneous remission by 12 months of age and show normal psychomotor development. The disorder is distinguished from benign familial infantile seizures by an earlier age at onset.
MISCELLANEOUS: Mutagenesis experiments were carried out in Xenopus oocytes by coexpression of either KCNQ3(mut) and KCNQ2 at the ratio of 1:1, or of KCNQ3(mut), KCNQ3(wt) and KCNQ2 at the ratio of 1:1:2, to mimic the situation in a heterozygous patient with BFNC2 disease.
SIMILARITY: Belongs to the potassium channel family. KQT (TC 1.A.1.15) subfamily. Kv7.3/KCNQ3 sub-subfamily.
WEB RESOURCE: Name=GeneReviews; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KCNQ3
CDC HuGE Published Literature: KCNQ3
Positive Disease Associations: Body Height , C-Reactive Protein , Erythrocyte Count , Heart Failure , Hemoglobins , Stroke
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. C-Reactive Protein
    , , . [PubMed 0]
  3. Erythrocyte Count
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: KCNQ3
Diseases sorted by gene-association score: seizures, benign neonatal, type 2* (1200), benign familial neonatal epilepsy* (260), benign familial infantile epilepsy* (183), kcnq3-related benign familial neonatal epilepsy* (100), benign neonatal seizures (27), idiopathic generalized epilepsy (16), epilepsy, generalized, with febrile seizures plus, type 5* (12), neonatal period electroclinical syndrome (11), epilepsy, nocturnal frontal lobe, 1 (10), benign epilepsy with centrotemporal spikes (6), unverricht-lundborg syndrome (5), adolescence-adult electroclinical syndrome (4), generalized epilepsy with febrile seizures plus (4), long qt syndrome (3), epileptic encephalopathy, early infantile, 6 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.79 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 93.30 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -116.10225-0.516 Picture PostScript Text
3' UTR -2359.328404-0.281 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR020969 - Ankyrin-G_BS
IPR005821 - Ion_trans_dom
IPR003091 - K_chnl
IPR003937 - K_chnl_volt-dep_KCNQ
IPR003948 - K_chnl_volt-dep_KCNQ3
IPR013821 - K_chnl_volt-dep_KCNQ_C

Pfam Domains:
PF00520 - Ion transport protein
PF03520 - KCNQ voltage-gated potassium channel
PF07885 - Ion channel
PF11956 - Ankyrin-G binding motif of KCNQ2-3

SCOP Domains:
81324 - Voltage-gated potassium channels

ModBase Predicted Comparative 3D Structure on O43525
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005216 ion channel activity
GO:0005244 voltage-gated ion channel activity
GO:0005249 voltage-gated potassium channel activity
GO:0005267 potassium channel activity
GO:0005515 protein binding
GO:0005516 calmodulin binding

Biological Process:
GO:0006811 ion transport
GO:0006813 potassium ion transport
GO:0007268 chemical synaptic transmission
GO:0034765 regulation of ion transmembrane transport
GO:0055085 transmembrane transport
GO:0060081 membrane hyperpolarization
GO:0071805 potassium ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0008076 voltage-gated potassium channel complex
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0033268 node of Ranvier
GO:0043194 axon initial segment

-  Descriptions from all associated GenBank mRNAs
  AK296293 - Homo sapiens cDNA FLJ51693 complete cds, highly similar to Potassium voltage-gated channel subfamily KQT member 3.
AF033347 - Homo sapiens potassium channel homolog (KCNQ3) mRNA, partial cds.
BC128576 - Homo sapiens potassium voltage-gated channel, KQT-like subfamily, member 3, mRNA (cDNA clone IMAGE:40128535), partial cds.
AB208890 - Homo sapiens mRNA for potassium voltage-gated channel KQT-like protein 3 variant protein.
BC152755 - Synthetic construct Homo sapiens clone IMAGE:100016013, MGC:184150 potassium voltage-gated channel, KQT-like subfamily, member 3 (KCNQ3) mRNA, encodes complete protein.
AB527350 - Synthetic construct DNA, clone: pF1KE0084, Homo sapiens KCNQ3 gene for potassium voltage-gated channel, KQT-like subfamily, member 3, without stop codon, in Flexi system.
BX538233 - Homo sapiens mRNA; cDNA DKFZp686C0248 (from clone DKFZp686C0248).
AK095711 - Homo sapiens cDNA FLJ38392 fis, clone FEBRA2006255.
AK094705 - Homo sapiens cDNA FLJ37386 fis, clone BRAMY2026538.
JD455158 - Sequence 436182 from Patent EP1572962.
JD060575 - Sequence 41599 from Patent EP1572962.
JD159459 - Sequence 140483 from Patent EP1572962.
JD537160 - Sequence 518184 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_raccPathway - Ion Channels and Their Functional Role in Vascular Endothelium

Reactome (by CSHL, EBI, and GO)

Protein O43525 (Reactome details) participates in the following event(s):

R-HSA-373739 Ankyrins link voltage-gated sodium and potassium channels to spectrin and L1
R-HSA-1296127 Activation of voltage gated Potassium channels
R-HSA-445095 Interaction between L1 and Ankyrins
R-HSA-373760 L1CAM interactions
R-HSA-422475 Axon guidance
R-HSA-1296072 Voltage gated Potassium channels
R-HSA-1266738 Developmental Biology
R-HSA-1296071 Potassium Channels
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: KCNQ3_HUMAN, NM_004519, NP_004510, O43525
UCSC ID: uc003ytj.3
RefSeq Accession: NM_004519
Protein: O43525 (aka KCNQ3_HUMAN or CIQ3_HUMAN)
CCDS: CCDS34943.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene KCNQ3:
kcnq3-dis (KCNQ3-Related Disorders)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_004519.3
exon count: 15CDS single in 3' UTR: no RNA size: 11266
ORF size: 2619CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4717.00frame shift in genome: no % Coverage: 99.84
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.