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CLCN3

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From Wikipedia, the free encyclopedia

Protein-coding gene in humans

CLCN3

Identifiers

Aliases

CLCN3, CLC3, ClC-3, chloride voltage-gated channel 3, NEDSBA, NEDHYBA

External IDs

OMIM:600580;MGI:103555;HomoloGene:20435;GeneCards:CLCN3;OMA:CLCN3 - orthologs

Gene location (Human)

Chr.	Chromosome 4 (human)^[1]

Band	4q33	Start	169,612,633bp^[1]
Band	4q33	End	169,723,673bp^[1]

Gene location (Mouse)

Chr.	Chromosome 8 (mouse)^[2]

Band	8 B3.1\|8 30.9 cM	Start	61,363,423bp^[2]
Band	8 B3.1\|8 30.9 cM	End	61,436,334bp^[2]

RNA expression pattern

Bgee

Human

Mouse (ortholog)

Top expressed in

mucosa of sigmoid colon

endothelial cell

Brodmann area 46

Epithelium of choroid plexus

retinal pigment epithelium

postcentral gyrus

islet of Langerhans

parotid gland

right ventricle

superior vestibular nucleus

Top expressed in

Rostral migratory stream

mammillary body

lateral septal nucleus

ventromedial nucleus

lateral geniculate nucleus

lateral hypothalamus

cingulate gyrus

anterior amygdaloid area

paraventricular nucleus of hypothalamus

subiculum

More reference expression data

BioGPS


More reference expression data

Gene ontology
Molecular function	nucleotide binding volume-sensitive chloride channel activity PDZ domain binding protein homodimerization activity ion channel activity protein binding protein heterodimerization activity antiporter activity ATP binding chloride channel activity voltage-gated chloride channel activity solute:proton antiporter activity chloride ion binding
Cellular component	integral component of membrane endosome late endosome Golgi apparatus early endosome membrane membrane late endosome membrane synaptic vesicle vesicle membrane Golgi membrane plasma membrane transport vesicle membrane secretory granule cell surface early endosome specific granule phagocytic vesicle external side of plasma membrane cytoplasmic vesicle integral component of plasma membrane
Biological process	negative regulation of cell volume endosomal lumen acidification ion transport regulation of anion transmembrane transport chloride transport regulation of pH chloride transmembrane transport regulation of anion transport transmembrane transport transport synaptic vesicle lumen acidification
Sources:Amigo /QuickGO

Orthologs

Species

Human

Mouse

Entrez


1182


12725

Ensembl


ENSG00000109572


ENSMUSG00000004319

UniProt


P51790


P51791

RefSeq (mRNA)


NM_001243372 NM_001243374 NM_001829 NM_173872


NM_007711 NM_173873 NM_173874 NM_173876

RefSeq (protein)


NP_001230301 NP_001230303 NP_001820 NP_776297


NP_031737 NP_776298 NP_776299 NP_776301

Location (UCSC)

Chr 4: 169.61 – 169.72 Mb

Chr 8: 61.36 – 61.44 Mb

PubMed search

^[3]

^[4]

Wikidata

View/Edit Human

View/Edit Mouse

2Cl^-/H⁺ exchanger 3 is aprotein that in humans is encoded by theCLCN3gene.^[5]

Interactions

[edit]

CLCN3 has been shown tointeract withPDZK1^[6] andTMEM9.^[7]

References

[edit]

^^a ^b ^cGRCh38: Ensembl release 89: ENSG00000109572 –Ensembl, May 2017
^^a ^b ^cGRCm38: Ensembl release 89: ENSMUSG00000004319 –Ensembl, May 2017
^"Human PubMed Reference:".National Center for Biotechnology Information, U.S. National Library of Medicine.
^"Mouse PubMed Reference:".National Center for Biotechnology Information, U.S. National Library of Medicine.
^"Entrez Gene: CLCN3 chloride channel 3".
^Gentzsch M, Cui L, Mengos A, Chang XB, Chen JH, Riordan JR (Feb 2003)."The PDZ-binding chloride channel ClC-3B localizes to the Golgi and associates with cystic fibrosis transmembrane conductance regulator-interacting PDZ proteins".J. Biol. Chem.278 (8):6440–9.doi:10.1074/jbc.M211050200.PMID 12471024.
^Planells-Cases R, Vorobeva V, Kar S, Schmitt F, Schulte U, Schrecker M, Hite R, Fakler B, Jentsch T (2025)."Endosomal chloride/proton exchangers need inhibitory TMEM9 β-subunits for regulation and prevention of disease-causing overactivity".Nature Communications.16:1–17.doi:10.1038/s41467-025-58546-3.PMC 11962092.PMID 40169677.

External links

[edit]

CLCN3+protein,+human at the U.S. National Library of MedicineMedical Subject Headings (MeSH)
HumanCLCN3 genome location andCLCN3 gene details page in theUCSC Genome Browser.

This article incorporates text from theUnited States National Library of Medicine, which is in thepublic domain.

Membrane transport protein:ion channels (TC 1A)

Ca²⁺:Calcium channel

Ligand-gated	Inositol trisphosphate receptor 1 2 3 Ryanodine receptor 1 2 3
Voltage-gated	L-type/Ca_vα 1.1 1.2 1.3 1.4 N-type/Ca_vα2.2 P-type/Ca_vα 2.1 Q-type/Ca_vα2.1 R-type/Ca_vα2.3 T-type/Ca_vα 3.1 3.2 3.3 α₂δ-subunits 1 2 β-subunits β1 β2 β3 β4 γ-subunits γ1 γ2 γ3 γ4 Cation channels of sperm 1 2 3 4 Two-pore channel 1 2

Na⁺:Sodium channel

Constitutively active	Epithelial sodium channel α β γ δ
Proton-gated	Amiloride-sensitive cation channel 1 2 3 4
Voltage-gated	Na_vα 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 7A Na_vβ 1 2 3 4

K⁺:Potassium channel

Calcium-activated	BK channel α1 β1 β2 β3 β4 SK channel SK1 SK2 SK3 IK channel IK1 K_Ca 1.1 2.1 2.2 2.3 3.1 4.1 4.2 5.1
Inward-rectifier	K_ATP K_ir 1.1 2.1 2.2 2.3 2.4 2.6 GIRK/K_ir 3.1 3.2 3.3 3.4 K_ir 4.1 4.2 5.1 6.1 6.2 7.1
Tandem pore domain	K2P 1 2 3 4 5 6 7 9 10 12 13 15 16 17 18
Voltage-gated	K_vα1-6 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.1 2.2 3.1 3.2 3.3 3.4 4.1 4.2 4.3 5.1 6.1 6.2 6.3 6.4 K_vα7-12 7.1 7.2 7.3 7.4 7.5 8.1 8.2 9.1 9.2 9.3 10.1 10.2 11.1/hERG 11.2 11.3 12.1 12.2 12.3 K_vβ 1 2 3 KCNIP 1 2 3 4 minK/ISK minK/ISK-like MiRP 1 2 3 Shaker (gene)

Miscellaneous

Cl⁻:Chloride channel	Calcium-activated chloride channels Anoctamin ANO1 Bestrophin 1 2 Chloride Channel Accessory 1 2 3 4 CFTR CLCN 1 2 3 4 5 6 7 KA KB CLIC 1 2 3 4 5 6 L1 CLNS 1A 1B
H⁺:Proton channel	HVCN1
M⁺:CNG cation channel	α 1 2 3 4 β 1 2 3 HCN FC 1 2 3 4
M⁺:TRP cation channel	TRPA (1) TRPC 1 2 3 4 4AP 5 6 7 TRPM 1 2 3 4 5 6 7 8 TRPML 1 2 3 TRPN TRPP 1 2 TRPV 1 2 3 4 5 6
H₂O (+solutes):Porin	Aquaporin 0 1 2 3 4 5 6 7 8 9 Voltage-dependent anion channel 1 2 3 General bacterial porin family
Cytoplasm:Gap junction	Connexin A GJA1 GJA3 GJA4 GJA5 GJA8 GJA9 GJA10 B GJB1 GJB2 GJB3 GJB4 GJB5 GJB6 GJB7 C GJC1 GJC2 GJC3 D GJD2 GJD3 GJD4 Innexin