Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1181
Gene name Gene Name - the full gene name approved by the HGNC.	Chloride voltage-gated channel 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CLCN2
Synonyms (NCBI Gene) Gene synonyms aliases	CIC-2, CLC2, ECA2, ECA3, EGI11, EGI3, EGMA, EJM6, EJM8, FHA2, FHII, HALD2, LKPAT, clC-2
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q27.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a voltage-gated chloride channel. The encoded protein is a transmembrane protein that maintains chloride ion homeostasis in various cells. Defects in this gene may be a cause of certain epilepsies. Four transcript variants encoding diffe

Show/Hide all(27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs71318369	C>T	Risk-factor, uncertain-significance	Intron variant, coding sequence variant, missense variant, non coding transcript variant
rs137852682	C>G,T	Risk-factor, uncertain-significance	Non coding transcript variant, missense variant, coding sequence variant
rs141242566	C>A,T	Pathogenic, uncertain-significance	Missense variant, non coding transcript variant, coding sequence variant
rs201330912	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs376823689	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, stop gained, intron variant
rs515726131	->C	Likely-pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, frameshift variant, 5 prime UTR variant
rs532632165	C>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs587777110	TGAGGA>-	Pathogenic	Upstream transcript variant, coding sequence variant, non coding transcript variant, inframe deletion, genic upstream transcript variant
rs587777111	G>A,T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs587777112	->C	Pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, frameshift variant
rs758379595	A>G,T	Pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant, upstream transcript variant
rs771507094	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, intron variant, missense variant
rs777105668	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs863225249	C>G	Pathogenic	Intron variant, upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs863225250	G>A,C	Pathogenic	Stop gained, non coding transcript variant, 5 prime UTR variant, missense variant, coding sequence variant
rs863225251	G>ATGAGCAGT	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs863225252	A>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs863225253	A>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs863225254	C>T	Pathogenic	Missense variant, intron variant, non coding transcript variant, coding sequence variant
rs863225255	AC>-	Pathogenic	Frameshift variant, intron variant, non coding transcript variant, coding sequence variant
rs863225256	T>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1085307938	C>T	Pathogenic, likely-pathogenic	Missense variant, upstream transcript variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant
rs1293789661	C>T	Pathogenic	Upstream transcript variant, non coding transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs1478304584	C>T	Pathogenic	Intron variant, splice acceptor variant, non coding transcript variant
rs1553855606	CACC>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, intron variant, coding sequence variant
rs1553856214	T>A	Pathogenic	5 prime UTR variant, non coding transcript variant, stop gained, coding sequence variant
rs1553857113	A>T	Pathogenic	Upstream transcript variant, non coding transcript variant, genic upstream transcript variant, missense variant, coding sequence variant

Show/Hide all(2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017077	hsa-miR-335-5p	Microarray	18185580
MIRT052784	hsa-miR-1260b	CLASH	23622248

Show/Hide all(50)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005247	Function	Voltage-gated chloride channel activity	IBA
GO:0005247	Function	Voltage-gated chloride channel activity	IDA	16155254, 29403011, 36964785
GO:0005247	Function	Voltage-gated chloride channel activity	IEA
GO:0005247	Function	Voltage-gated chloride channel activity	TAS	7795595
GO:0005254	Function	Chloride channel activity	IEA
GO:0005515	Function	Protein binding	IPI	26871637
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	29403011
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006821	Process	Chloride transport	IBA
GO:0006821	Process	Chloride transport	IEA
GO:0006911	Process	Phagocytosis, engulfment	IMP	36964785
GO:0008308	Function	Voltage-gated monoatomic anion channel activity	IEA
GO:0015108	Function	Chloride transmembrane transporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IDA	16155254
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0017081	Function	Chloride channel regulator activity	IMP	38345841
GO:0030322	Process	Stabilization of membrane potential	IEA
GO:0030324	Process	Lung development	IEA
GO:0030424	Component	Axon	IEA
GO:0030425	Component	Dendrite	IEA
GO:0032347	Process	Regulation of aldosterone biosynthetic process	IMP	29403011
GO:0032591	Component	Dendritic spine membrane	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034702	Component	Monoatomic ion channel complex	IEA
GO:0034707	Component	Chloride channel complex	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043194	Component	Axon initial segment	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0043209	Component	Myelin sheath	IDA	22405205
GO:0043209	Component	Myelin sheath	IEA
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0048714	Process	Positive regulation of oligodendrocyte differentiation	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0060075	Process	Regulation of resting membrane potential	IEA
GO:0060689	Process	Cell differentiation involved in salivary gland development	IEA
GO:0065008	Process	Regulation of biological quality	IEA
GO:0071476	Process	Cellular hypotonic response	IEA
GO:0072320	Function	Volume-sensitive chloride channel activity	IEA
GO:0090425	Process	Acinar cell differentiation	IEA
GO:0097450	Component	Astrocyte end-foot	IDA	22405205
GO:0097450	Component	Astrocyte end-foot	IEA
GO:0098656	Process	Monoatomic anion transmembrane transport	IEA
GO:0098902	Process	Regulation of membrane depolarization during action potential	IEA
GO:1902476	Process	Chloride transmembrane transport	IEA

MIM	HGNC	e!Ensembl
600570	2020	ENSG00000114859

Protein

UniProt ID

P51788

Protein name

Chloride channel protein 2 (ClC-2)

Protein function

Voltage-gated and osmosensitive chloride channel. Forms a homodimeric channel where each subunit has its own ion conduction pathway. Conducts double-barreled currents controlled by two types of gates, two fast glutamate gates that control each s

PDB

7XF5 , 7XJA , 8GQU , 8TA2 , 8TA3 , 8TA4 , 8TA5 , 8TA6

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00654	Voltage_CLC	143 → 547	Voltage gated chloride channel	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. Moderately expressed in aortic and coronary vascular smooth muscle cells and expressed at a low level in aortic endothelial cells. Expressed in the adrenal gland, predominantly in the zona glomerulosa (PubMed:29

Sequence

MAAAAAEEGMEPRALQYEQTLMYGRYTQDLGAFAKEEAARIRLGGPEPWKGPPSSRAAPE
LLEYGRSRCARCRVCSVRCHKFLVSRVGEDWIFLVLLGLLMALVSWVMDYAIAACLQAQQ
WMSRGLNTSILLQYLAWVTYPVVLITFSAGFTQILAPQAVGSGIPEMKTILRGVVLKEYL
TLKTFIAKVIGLTCALGSGMPLGKEGPFVHIASMCAALLSKFLSLFGGIYENESRNTEML
AAACAVGVGCCFAAPIGGVLFSIEVTSTFFAVRNYWRGFFAATFSAFIFRVLAVWNRDEE
TITALFKTRFRLDFPFDLQELPAFAVIGIASGFGGALFVYLNRKIVQVMRKQKTINRFLM
RKRLLFPALVTLLISTLTFPPGFGQFMAGQLSQKETLVTLFDNRTWVRQGLVEELEPPST
SQAWNPPRANVFLTLVIFILMKFWMSALATTIPVPCGAFMPVFVIGAAFGRLVGESMAAW
FPDGIHTDSSTYRIVPGGYAVVGAAALAGAVTHTVSTAVIVFELTGQIAHILPVMIAVIL
ANAVAQSLQPSLYDSIIRIKKLPYLPELGWGRHQQYRVRVEDIMVRDVPHVALSCTFRDL
RLALHRTKGRMLALVESPESMILLGSIERSQVVALLGAQLSPARRRQHMQERRATQTSPL
SDQEGPPTPEASVCFQVNTEDSAFPAARGETHKPLKPALKRGPSVTRNLGESPTGSAESA
GIALRSLFCGSPPPEAASEKLESCEKRKLKRVRISLASDADLEGEMSPEEILEWEEQQLD
EPVNFSDCKIDPAPFQLVERTSLHKTHTIFSLLGVDHAYVTSIGRLIGIVTLKELRKAIE
GSVTAQGVKVRPPLASFRDSATSSSDTETTEVHALWGPHSRHGLPREGSPSDSDDKCQ

Sequence length

898

Interactions

View interactions

	KEGG		Reactome
	Mineral absorption		Stimuli-sensing channels

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hyperaldosteronism	Familial hyperaldosteronism type II	rs1085307938, rs1553853557, rs1553856214, rs1293789661, rs1553857113, rs758379595, rs771507094	N/A
Leukoencephalopathy With Mild Cerebellar Ataxia And White Matter Edema	leukoencephalopathy with mild cerebellar ataxia and white matter edema	rs201330912, rs587777110, rs587777111, rs587777112, rs376823689, rs771507094, rs1478304584, rs863225252, rs863225251, rs863225250	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Cerebral palsy	cerebral palsy	N/A	N/A	ClinVar
Epilepsy	Epilepsy, idiopathic generalized, susceptibility to, 11, epilepsy, epilepsy, idiopathic generalized, susceptibility to, 11	N/A	N/A	ClinVar, GenCC
Mental retardation	intellectual disability	N/A	N/A	ClinVar
seizure	Seizure	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Atrial Fibrillation	Associate	31996765
Carcinoma Hepatocellular	Associate	33340691
Cerebellar Ataxia	Associate	23707145
Cognition Disorders	Associate	23707145
Cystic Fibrosis	Associate	9520461
Demyelinating Diseases	Associate	23707145
Encephalitis Herpes Simplex	Inhibit	23707145
Epilepsy	Associate	17156979, 31056551
Epilepsy Absence	Associate	17580110, 40147727
Epilepsy Idiopathic Generalized	Associate	17580110, 23632988
Epileptic Syndromes	Associate	17156979
Eye Diseases	Associate	23707145
Glioma	Associate	12843258
Headache	Associate	23707145
Hyperaldosteronism Familial Type II	Associate	29403011, 36384999
Leukodystrophy Metachromatic	Associate	23707145, 26033718
Leukoencephalopathies	Associate	23707145, 32278302, 40199115
Lymphoma	Associate	32439996
Microcephaly with Chorioretinopathy Autosomal Dominant	Associate	23707145
Muscle Spasticity	Associate	23707145
Neoplasms	Associate	26491211, 35527349
Optic Nerve Diseases	Associate	23707145
Prostatic Neoplasms	Associate	26491211, 36246902
Prostatitis	Associate	26491211
Stroke	Associate	23707145
Sudden Unexpected Death in Epilepsy	Associate	34816733
Tang Hsi Ryu syndrome	Associate	23707145

CLCN2 (chloride voltage-gated channel 2)