CLCN3 - chloride voltage-gated channel 3 Gene

Homo sapiens

Also known as CLC3; ClC-3; NEDSBA; NEDHYBA

Gene ID: 1182 | Gene type: protein coding

About CLCN3

Cytogenetic location: 4q33 Genomic coordinates (GRCh38): 4:169,620,578-169,723,673 (from NCBI)

This gene has 9 transcripts (splice variants), 209 orthologues, 8 paralogues and is associated with 5 phenotypes. Ubiquitous expression in brain (RPKM 27.7), colon (RPKM 19.9) and 25 other tissues.

Summary

This gene encodes a member of the voltage-gated Chloride Channel (ClC) family. The encoded protein is present in all cell types and localized in plasma membranes and in intracellular vesicles. It is a multi-pass membrane protein which contains a ClC domain and two additional C-terminal CBS (cystathionine beta-synthase) domains. The ClC domain catalyzes the selective flow of Cl- ions across cell membranes, and the CBS domain may have a regulatory function. This protein plays a role in both acidification and transmitter loading of GABAergic synaptic vesicles, and in smooth muscle cell activation and neointima formation. This protein is required for lysophosphatidic acid (LPA)-activated Cl- current activity and fibroblast-to-myofibroblast differentiation. The protein activity is regulated by CA(2+)/calmodulin-dependent protein kinase II (CaMKII) in glioma cells. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

CLCN3 Products(4)

mRNA	Protein	Name
NM_001243372.2	NP_001230301.1	H(+)/Cl(-) exchange transporter 3 isoform a
NM_001243374.2	NP_001230303.2	H(+)/Cl(-) exchange transporter 3 isoform c
NM_001829.4	NP_001820.2	H(+)/Cl(-) exchange transporter 3 isoform b
NM_173872.4	NP_776297.2	H(+)/Cl(-) exchange transporter 3 isoform e

Gene Ontology

Molecular Function
Biological Process
Cellular Component

Molecular Function GO Annotation	Evidence	Reference	Source
enables PDZ domain binding	IDA IDA: Inferred from direct assay	12471024	GOA
enables chloride channel activity	IDA IDA: Inferred from direct assay	11274166	GOA
enables protein binding	IPI IPI: Inferred from physical interaction	12471024	GOA
enables volume-sensitive chloride channel activity	IMP IMP: Inferred from mutant phenotype	12183454	GOA

Biological Process GO Annotation	Evidence	Reference	Source
involved in chloride transmembrane transport	IDA IDA: Inferred from direct assay	11274166	GOA
involved in negative regulation of cell volume	IMP IMP: Inferred from mutant phenotype	12183454	GOA

Cellular Component GO Annotation	Evidence	Reference	Source
is active in GABA-ergic synapse	IDA IDA: Inferred from direct assay	11182090	GOA
is active in GABA-ergic synapse	IMP IMP: Inferred from mutant phenotype	11182090	GOA
located in Golgi apparatus	IDA IDA: Inferred from direct assay	12471024	GOA
located in cytoplasmic vesicle	IDA IDA: Inferred from direct assay	11274166	GOA
located in early endosome	IDA IDA: Inferred from direct assay	12471024	GOA
located in external side of plasma membrane	IDA IDA: Inferred from direct assay	11274166	GOA
is active in glutamatergic synapse	IDA IDA: Inferred from direct assay	11182090	GOA
is active in glutamatergic synapse	IMP IMP: Inferred from mutant phenotype	11182090	GOA
located in late endosome	IDA IDA: Inferred from direct assay	12471024	GOA
located in phagocytic vesicle	IDA IDA: Inferred from direct assay	16522634	GOA
located in plasma membrane	IDA IDA: Inferred from direct assay	11274166	GOA
located in secretory granule	IDA IDA: Inferred from direct assay	16522634	GOA
located in specific granule	IDA IDA: Inferred from direct assay	16522634	GOA
located in synaptic vesicle	IDA IDA: Inferred from direct assay	11182090	GOA
is active in synaptic vesicle membrane	IDA IDA: Inferred from direct assay	11182090	GOA
is active in synaptic vesicle membrane	IMP IMP: Inferred from mutant phenotype	11182090	GOA
located in vesicle membrane	IDA IDA: Inferred from direct assay	12471024	GOA

EXP: Inferred from Experiment IDA: Inferred from direct assay IPI: Inferred from physical interaction IMP: Inferred from mutant phenotype IGI: Inferred from genetic interaction IEP: Inferred from expression pattern

CLCN3 Protein Structure

Voltage_CLC

CBS

0
200
400
600
818 a.a.

Protein Preferred Names

Protein Names

H(+)/Cl(-) exchange transporter 3

chloride channel 3

Related Diseases

Diseases

Alias

Neurodevelopmental Disorder With Seizures And Brain Abnormalities

NEDSBA

Neurodevelopmental Disorder With Hypotonia And Brain Abnormalities

NEDHYBA

Non-Specific Syndromic Intellectual Disability

Complex Neurodevelopmental Disorder

Juxtacortical Chondrosarcoma

Cystic Fibrosis

Mucoviscidosis	CF
Pseudomonas Aeruginosa, Susceptibility To Chronic Infection By, In Cystic Fibrosis	Pseudomonas Aeruginosa Chronic Infection By, In Cystic Fibrosis
Cystic Fibrosis Lung Disease, Modifier Of	Cystic Fibrosis Of Pancreas
Fibrocystic Disease Of Pancreas	Cf - [Cystic Fibrosis]
Cystic Fibrosis Nos	Fibrocystic Disease
Fibrocystic Disease Of The Pancreas	Mucoviscidosis Of Pancreas
Nonproliferative Fibrocystic Disease	Pancreatic Cystic Fibrosis

Dent Disease 1

Dent Disease	Dent'S Disease
Dent Disease 2	Dent Disease Type 1
DENT1	Urolithiasis, Hypercalciuric, X-Linked
Nephrolithiasis 2	Nphl2
Dent Syndrome	Dents Disease
Low-Molecular-Weight Proteinuria With Hypercalciuria And Nephrocalcinosis	Renal Fanconi Syndrome With Nephrocalcinosis And Renal Stones
X-Linked Recessive Hypercalciuric Hypophosphatemic Rickets	X-Linked Recessive Nephrolithiasis
Fanconi Syndrome, Renal, With Nephrocalcinosis And Renal Stones	Nephrolithiasis, Hypercalciuric, X-Linked
Nephrolithiasis-Hypercalciuria X-Linked Recessive	Nephrolithiasis, X-Linked Recessive
Dent Disease, Type 1

Glioma

Myotonia Congenita

Congenital Myotonia, Autosomal Dominant Form	Congenital Myotonia
Thomsen And Becker Disease	Thomsen Disease
Thomsen'S Disease	Generalized Myotonia Of Thomsen
Congenital Myotonic Muscular Dystrophy	Myotonia Congenita Nos

Bartter Disease

Bartter Syndrome	Bartter'S Syndrome
Aldosteronism With Hyperplasia Of The Adrenal Cortex	Hypokalemic Alkalosis With Hypercalciuria
Potassium Wasting	Juxtaglomerular Hyperplasia With Secondary Aldosteronism
Renal Tubular Normotensive Hypokalemic Alkalosis With Hypercalciuria	Salt-Losing Tubular Disorder, Henle'S Loop Type
Salt-Wasting Tubulopathy, Henle'S Loop Type	Bartters Syndrome

Diseases	Alias
Waldenstroem'S Macroglobulinemia	Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma

Related Agents

Pre-clinical Phase

Bioactive Molecules (1)

Cat. No.	Product Name	Effect	Purity	Rare Diseases
HY-RS02755	CLCN3 Human Pre-designed siRNA Set A	Pre-designed Sets	/	Unkown

Orthologs Information

Species	Symbol	Source	ID
Rattus norvegicus	CLCN3	RGD	RGD:621219
Bos taurus	CLCN3	VGNC	VGNC:27397
Felis catus	CLCN3	VGNC	VGNC:60925
Macaca mulatta	CLCN3	VGNC	VGNC:71236
Canis familiaris	CLCN3	VGNC	VGNC:39303
Mus musculus	CLCN3	MGD	MGI:103555

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