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Aliases for KCNN3 Gene

Aliases for KCNN3 Gene

  • Potassium Calcium-Activated Channel Subfamily N Member 3 2 3 5
  • Potassium Channel, Calcium Activated Intermediate/Small Conductance Subfamily N Alpha, Member 3 2 3
  • Potassium Intermediate/Small Conductance Calcium-Activated Channel, Subfamily N, Member 3 2 3
  • Small Conductance Calcium-Activated Potassium Channel 3 2 3
  • SKCa 3 3 4
  • KCa2.3 3 4
  • SKCA3 3 4
  • SK3 3 4
  • Small Conductance Calcium-Activated Potassium Channel Protein 3 3
  • HSK3 3
  • K3 4

External Ids for KCNN3 Gene

Previous GeneCards Identifiers for KCNN3 Gene

  • GC01M152495
  • GC01M150410
  • GC01M151455
  • GC01M151896
  • GC01M151492
  • GC01M152946
  • GC01M154680
  • GC01M126042

Summaries for KCNN3 Gene

Entrez Gene Summary for KCNN3 Gene

  • Action potentials in vertebrate neurons are followed by an afterhyperpolarization (AHP) that may persist for several seconds and may have profound consequences for the firing pattern of the neuron. Each component of the AHP is kinetically distinct and is mediated by different calcium-activated potassium channels. This gene belongs to the KCNN family of potassium channels. It encodes an integral membrane protein that forms a voltage-independent calcium-activated channel, which is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene contains two CAG repeat regions in the coding sequence. It was thought that expansion of one or both of these repeats could lead to an increased susceptibility to schizophrenia or bipolar disorder, but studies indicate that this is probably not the case. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

GeneCards Summary for KCNN3 Gene

KCNN3 (Potassium Calcium-Activated Channel Subfamily N Member 3) is a Protein Coding gene. Diseases associated with KCNN3 include Retinitis Pigmentosa 19 and Spinocerebellar Ataxia 2. Among its related pathways are Transmission across Chemical Synapses and Aldosterone synthesis and secretion. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and calcium-activated potassium channel activity. An important paralog of this gene is KCNN2.

UniProtKB/Swiss-Prot for KCNN3 Gene

  • Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin.

Tocris Summary for KCNN3 Gene

  • Calcium (Ca2+) -activated potassium channels (KCa) are a group of 6/7-TM ion channels that selectively transport K+ ions across biological membranes. They are broadly classified into three subtypes: SK, IK and BK channels (small, intermediate and big conductance).

Gene Wiki entry for KCNN3 Gene

Additional gene information for KCNN3 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KCNN3 Gene

Genomics for KCNN3 Gene

GeneHancer (GH) Regulatory Elements for KCNN3 Gene

Promoters and enhancers for KCNN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I154857 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 563.6 +9.5 9494 5.7 HDGF PKNOX1 IRF4 ZNF766 GLIS2 ZNF207 ZNF143 ATF7 RUNX3 JUNB KCNN3 ADAR PBXIP1 RUSC1 MUC1 FDPS PMVK RUSC1-AS1 CLK2 PIR50309
GH01I154865 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 559.6 +1.9 1862 4.9 HDGF PKNOX1 SIN3A ETS1 TCF12 GLIS2 ZNF143 ATF7 RUNX3 SP3 KCNN3 PIR50309
GH01I154940 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.8 -72.7 -72733 6 HDGF FOXA2 SMAD1 MLX ARID4B DMAP1 YBX1 ZNF207 ZNF143 SP5 KCNN3 EFNA3 MSTO2P RUSC1 PMVK ADAR CLK2 RUSC1-AS1 GC01M154946 ENSG00000270361
GH01I154935 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.4 -67.4 -67371 3.8 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 ENSG00000270361 PMVK GON4L CLK2 KHDC4 ENSG00000271267 UBAP2L THBS3 RUSC1-AS1 CRTC2
GH01I154746 Enhancer 1.2 Ensembl ENCODE dbSUPER 11 +121.9 121872 3.5 MEIS2 CTCF PKNOX1 EBF1 ZIC2 RAD21 RFX5 ZFHX2 ZNF316 POLR2A CHRNB2 UBE2Q1 KCNN3 ADAR ADAM15 DCST1-AS1 PIR49202 PIR50309
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KCNN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KCNN3 gene promoter:

Genomic Locations for KCNN3 Gene

Genomic Locations for KCNN3 Gene
172,826 bases
Minus strand

Genomic View for KCNN3 Gene

Genes around KCNN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KCNN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KCNN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KCNN3 Gene

Proteins for KCNN3 Gene

  • Protein details for KCNN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Small conductance calcium-activated potassium channel protein 3
    Protein Accession:
    Secondary Accessions:
    • B1ANX0
    • O43517
    • Q86VF9
    • Q8WXG7

    Protein attributes for KCNN3 Gene

    736 amino acids
    Molecular mass:
    82026 Da
    Quaternary structure:
    • Heterooligomer. The complex is composed of 4 channel subunits each of which binds to a calmodulin subunit which regulates the channel activity through calcium-binding (By similarity).

    Alternative splice isoforms for KCNN3 Gene


neXtProt entry for KCNN3 Gene

Post-translational modifications for KCNN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KCNN3 Gene

No data available for DME Specific Peptides for KCNN3 Gene

Domains & Families for KCNN3 Gene

Gene Families for KCNN3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Voltage-gated ion channels

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the potassium channel KCNN family. KCa2.3/KCNN3 subfamily.
  • Belongs to the potassium channel KCNN family. KCa2.3/KCNN3 subfamily.
genes like me logo Genes that share domains with KCNN3: view

Function for KCNN3 Gene

Molecular function for KCNN3 Gene

GENATLAS Biochemistry:
potassium intermediate/small conductance calcium-activated channel,subfamily N,member 3
UniProtKB/Swiss-Prot Function:
Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin.

Phenotypes From GWAS Catalog for KCNN3 Gene

Gene Ontology (GO) - Molecular Function for KCNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005516 calmodulin binding IBA --
GO:0015269 calcium-activated potassium channel activity IEA --
GO:0016286 small conductance calcium-activated potassium channel activity IEA,IBA --
genes like me logo Genes that share ontologies with KCNN3: view
genes like me logo Genes that share phenotypes with KCNN3: view

Animal Models for KCNN3 Gene

MGI Knock Outs for KCNN3:

miRNA for KCNN3 Gene

miRTarBase miRNAs that target KCNN3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KCNN3 Gene

Localization for KCNN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KCNN3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KCNN3 gene
Compartment Confidence
plasma membrane 5
nucleus 4
endoplasmic reticulum 2
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KCNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0043025 neuronal cell body IBA --
genes like me logo Genes that share ontologies with KCNN3: view

Pathways & Interactions for KCNN3 Gene

genes like me logo Genes that share pathways with KCNN3: view

Pathways by source for KCNN3 Gene

1 KEGG pathway for KCNN3 Gene

Gene Ontology (GO) - Biological Process for KCNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006813 potassium ion transport IEA --
GO:0071805 potassium ion transmembrane transport IEA --
GO:1903955 positive regulation of protein targeting to mitochondrion IMP 24270810
genes like me logo Genes that share ontologies with KCNN3: view

No data available for SIGNOR curated interactions for KCNN3 Gene

Drugs & Compounds for KCNN3 Gene

(23) Drugs for KCNN3 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Miconazole Approved, Investigational, Vet_approved Pharma Antagonist, Pore Blocker, Target, inhibitor 3838
calcium Approved Nutra 0
Procaine Approved, Investigational, Vet_approved Pharma Channel blocker, Target, binder 60
Trimebutine Approved Pharma Target, inhibitor Antimuscarinic 7
Dequalinium Approved, Investigational Pharma 2

(6) Additional Compounds for KCNN3 Gene - From: IUPHAR and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Antagonist, Pore Blocker

(4) Tocris Compounds for KCNN3 Gene

Compound Action Cas Number
1-EBIO Activator of epithelial KCa channels 10045-45-1
BMS 191011 Potent BKCa (KCa1.1) channel opener 202821-81-6
CyPPA Activator of KCa2.2 and KCa2.3 channels 73029-73-9
SKA 31 Activator of KCa3.1 and KCa2 channels 40172-65-4
genes like me logo Genes that share compounds with KCNN3: view

Transcripts for KCNN3 Gene

Unigene Clusters for KCNN3 Gene

Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for KCNN3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c · 10d ^ 11a · 11b
SP2: - -
SP3: -
SP4: - -

Relevant External Links for KCNN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for KCNN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KCNN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KCNN3 Gene

This gene is overexpressed in Heart (32.9), Plasma (23.8), and Frontal cortex (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for KCNN3 Gene

Protein tissue co-expression partners for KCNN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of KCNN3 Gene:


SOURCE GeneReport for Unigene cluster for KCNN3 Gene:


Evidence on tissue expression from TISSUES for KCNN3 Gene

  • Nervous system(2.9)
  • Muscle(2.2)
genes like me logo Genes that share expression patterns with KCNN3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for KCNN3 Gene

Orthologs for KCNN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for KCNN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia KCNN3 33 34
  • 98.9 (n)
(Bos Taurus)
Mammalia KCNN3 33 34
  • 93.53 (n)
(Canis familiaris)
Mammalia KCNN3 33 34
  • 90.4 (n)
(Rattus norvegicus)
Mammalia Kcnn3 33
  • 90.06 (n)
(Mus musculus)
Mammalia Kcnn3 33 16 34
  • 89.88 (n)
(Monodelphis domestica)
Mammalia KCNN3 34
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia KCNN3 34
  • 61 (a)
(Gallus gallus)
Aves KCNN3 34
  • 94 (a)
(Anolis carolinensis)
Reptilia KCNN3 34
  • 93 (a)
(Danio rerio)
Actinopterygii kcnn3 33 34
  • 70.7 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.113 33
fruit fly
(Drosophila melanogaster)
Insecta SK 35 34
  • 54 (a)
(Caenorhabditis elegans)
Secernentea C03F11.1 35
  • 37 (a)
kcnl-2 34
  • 31 (a)
C53A5.5 35
  • 30 (a)
kcnl-4 34
  • 27 (a)
kcnl-1 34
  • 26 (a)
kcnl-3 34
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 62 (a)
Species where no ortholog for KCNN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for KCNN3 Gene

Gene Tree for KCNN3 (if available)
Gene Tree for KCNN3 (if available)

Paralogs for KCNN3 Gene

Paralogs for KCNN3 Gene

(5) SIMAP similar genes for KCNN3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with KCNN3: view

Variants for KCNN3 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for KCNN3 Gene

The second poly-Gln region of KCNN3 is highly polymorphic and the number of Gln varies from 12 to 28 in the population.

Sequence variations from dbSNP and Humsavar for KCNN3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs193920929 uncertain-significance, Malignant tumor of prostate 154,771,974(-) C/A splice_donor_variant
rs1051614 benign, not specified 154,772,331(-) C/G/T coding_sequence_variant, synonymous_variant
rs1131820 benign, not specified 154,772,376(-) A/G coding_sequence_variant, synonymous_variant
rs1000000159 -- 154,725,462(-) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KCNN3 Gene

Variant ID Type Subtype PubMed ID
esv1554680 CNV insertion 17803354
esv2574257 CNV insertion 19546169
esv2673228 CNV deletion 23128226
esv2718350 CNV deletion 23290073
esv2718363 CNV deletion 23290073
esv275470 CNV gain+loss 21479260
esv29982 CNV gain 17803354
esv3354801 CNV duplication 20981092
esv3362664 CNV duplication 20981092
esv3435288 CNV duplication 20981092
esv3540978 CNV deletion 23714750
esv3574452 CNV gain 25503493
nsv2966 CNV insertion 18451855
nsv464050 CNV gain 19166990
nsv464073 CNV loss 19166990
nsv470740 CNV gain 18288195
nsv472399 CNV novel sequence insertion 20440878
nsv509491 CNV insertion 20534489
nsv521887 CNV gain 19592680
nsv547958 CNV gain 21841781
nsv547960 CNV loss 21841781

Variation tolerance for KCNN3 Gene

Residual Variation Intolerance Score: 8.41% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.28; 62.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KCNN3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

Disorders for KCNN3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for KCNN3 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 19
  • rp19
spinocerebellar ataxia 2
  • sca2
bipolar disorder
  • major affective disorder 1
retinitis pigmentosa 14
  • rp14
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
- elite association - COSMIC cancer census association via MalaCards
Search KCNN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for KCNN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with KCNN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KCNN3 Gene

Publications for KCNN3 Gene

  1. Analysis of Single Nucleotide Polymorphisms (SNPs) of the small-conductance calcium activated potassium channel (SK3) gene as genetic modifier of the cardiac phenotype in myotonic dystrophy type 1 patients. (PMID: 19472917) Rinaldi F … Novelli G (Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology 2008) 3 22 44 58
  2. Schizophrenia and polymorphic CAG repeats array of calcium-activated potassium channel (KCNN3) gene in Serbian population. (PMID: 16393881) Ivković M … Romac S (The International journal of neuroscience 2006) 3 22 44 58
  3. Association analysis of a highly polymorphic CAG Repeat in the human potassium channel gene KCNN3 and migraine susceptibility. (PMID: 16162291) Curtain R … Griffiths L (BMC medical genetics 2005) 3 22 44 58
  4. [Transmission disequilibrium analysis of 1137-1140 Del GTGA frameshift mutation within the KCNN3 gene and schizophrenia based on family trios]. (PMID: 16086287) Hong XH … Wu CR (Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2005) 3 22 44 58
  5. CAG repeat polymorphism within the KCNN3 gene is a significant contributor to susceptibility to anorexia nervosa: a case-control study of female patients and several ethnic groups in the Israeli Jewish population. (PMID: 15389773) Koronyo-Hamaoui M … Weizman A (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2004) 3 22 44 58

Products for KCNN3 Gene

Sources for KCNN3 Gene

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