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Protein

Chloride channel protein 2

Gene

CLCN2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.2 Publications

Miscellaneous

The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The absence of conserved gating glutamate residues is typical for family members that function as channels (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei162ChlorideBy similarity1
Binding sitei459Chloride; via amide nitrogenBy similarity1
Binding sitei553ChlorideBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChloride channel, Ion channel, Voltage-gated channel
Biological processIon transport, Transport
LigandChloride

Enzyme and pathway databases

ReactomeiR-HSA-2672351 Stimuli-sensing channels

Protein family/group databases

TCDBi2.A.49.2.12 the chloride carrier/channel (clc) family

Names & Taxonomyi

Protein namesi
Recommended name:
Chloride channel protein 2
Short name:
ClC-2
Gene namesi
Name:CLCN2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000114859.14
HGNCiHGNC:2020 CLCN2
MIMi600570 gene
neXtProtiNX_P51788

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini2 – 87CytoplasmicBy similarityAdd BLAST86
Transmembranei88 – 121HelicalBy similarityAdd BLAST34
Transmembranei130 – 155HelicalBy similarityAdd BLAST26
Intramembranei164 – 171HelicalSequence analysis8
Transmembranei180 – 198HelicalBy similarityAdd BLAST19
Transmembranei205 – 223HelicalBy similarityAdd BLAST19
Intramembranei239 – 251HelicalBy similarityAdd BLAST13
Intramembranei255 – 263HelicalBy similarity9
Transmembranei275 – 295HelicalBy similarityAdd BLAST21
Transmembranei321 – 349HelicalBy similarityAdd BLAST29
Transmembranei358 – 377HelicalBy similarityAdd BLAST20
Transmembranei429 – 449HelicalBy similarityAdd BLAST21
Transmembranei457 – 480HelicalBy similarityAdd BLAST24
Intramembranei497 – 511HelicalBy similarityAdd BLAST15
Intramembranei512 – 513Note=Loop between two helicesBy similarity2
Intramembranei514 – 525HelicalBy similarityAdd BLAST12
Intramembranei526 – 530Note=Loop between two helicesBy similarity5
Transmembranei531 – 548HelicalBy similarityAdd BLAST18
Topological domaini549 – 898CytoplasmicBy similarityAdd BLAST350

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Epilepsy, idiopathic generalized 11 (EIG11)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by recurring generalized seizures in the absence of detectable brain lesions and/or metabolic abnormalities. Generalized seizures arise diffusely and simultaneously from both hemispheres of the brain.
See also OMIM:607628
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_057890577R → Q in EIG11; associated with disease susceptibility; the mutant channel has accelerated deactivation rates compared to wild-type, but normal activation and peak current. 1 PublicationCorresponds to variant dbSNP:rs137852682EnsemblClinVar.1
Juvenile absence epilepsy 2 (JAE2)1 Publication
Disease susceptibility may be associated with variations affecting the gene represented in this entry.
Disease descriptionA subtype of idiopathic generalized epilepsy characterized by onset occurring around puberty, absence seizures, generalized tonic-clonic seizures (GTCS), GTCS on awakening, and myoclonic seizures.
See also OMIM:607628
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015989715G → E in JAE2; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs137852681EnsemblClinVar.1
Juvenile myoclonic epilepsy 8 (EJM8)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA subtype of idiopathic generalized epilepsy. Patients have afebrile seizures only, with onset in adolescence (rather than in childhood) and myoclonic jerks which usually occur after awakening and are triggered by sleep deprivation and fatigue.
See also OMIM:607628
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_057889235R → Q in EJM8; associated with disease susceptibility; the mutant channel has accelerated deactivation rates compared to wild-type, but normal activation and peak current. 1 PublicationCorresponds to variant dbSNP:rs71318369EnsemblClinVar.1
Leukoencephalopathy with ataxia (LKPAT)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive neurologic disorder with a characteristic pattern of white matter abnormalities on brain MRI. Affected individuals have prominent signal abnormalities and decreased apparent diffusion coefficient values in the posterior limbs of the internal capsules, middle cerebral peduncles, pyramidal tracts in the pons, and middle cerebellar peduncles, suggesting myelin microvacuolation. Clinical features include ataxia and unstable gait. More variable abnormalities may include visual field defects, headaches, and learning disabilities.
See also OMIM:615651
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070976144 – 145Missing in LKPAT; loss of function mutation; the mutant protein is restricted to the endoplasmic reticulum and hardly reached the plasma membrane; lower amounts of the mutant protein compared to wild-type. 1 Publication2
Natural variantiVAR_070977500A → V in LKPAT; loss of function mutation; the mutant protein is restricted to the endoplasmic reticulum and hardly reaches the plasma membrane; lower amounts of the mutant protein compared to wild-type. 1 PublicationCorresponds to variant dbSNP:rs587777111EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi1181
MalaCardsiCLCN2
MIMi607628 phenotype
615651 phenotype
OpenTargetsiENSG00000114859
Orphaneti307 Juvenile myoclonic epilepsy
363540 Leukoencephalopathy with mild cerebellar ataxia and white matter edema
PharmGKBiPA26547

Chemistry databases

ChEMBLiCHEMBL1628478
DrugBankiDB01046 Lubiprostone
GuidetoPHARMACOLOGYi699

Polymorphism and mutation databases

BioMutaiCLCN2
DMDMi288558807

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000944332 – 898Chloride channel protein 2Add BLAST897

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei20PhosphothreonineBy similarity1
Modified residuei712PhosphoserineCombined sources1
Modified residuei758PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated. Activated by dephosphorylation.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP51788
MaxQBiP51788
PaxDbiP51788
PeptideAtlasiP51788
PRIDEiP51788
ProteomicsDBi56385
56386 [P51788-2]
56387 [P51788-3]

PTM databases

iPTMnetiP51788
PhosphoSitePlusiP51788

Expressioni

Tissue specificityi

Ubiquitously expressed. Moderately expressed in aortic and coronary vascular smooth muscle cells and expressed at a low level in aortic endothelial cells.1 Publication

Gene expression databases

BgeeiENSG00000114859
CleanExiHS_CLCN2
ExpressionAtlasiP51788 baseline and differential
GenevisibleiP51788 HS

Organism-specific databases

HPAiCAB009397
HPA014545
HPA024108

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
UBQLN1Q9UMX0-23EBI-16431116,EBI-10173939

Protein-protein interaction databases

BioGridi107595, 19 interactors
IntActiP51788, 32 interactors
STRINGi9606.ENSP00000265593

Structurei

3D structure databases

ProteinModelPortaliP51788
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini584 – 642CBS 1PROSITE-ProRule annotationAdd BLAST59
Domaini790 – 850CBS 2PROSITE-ProRule annotationAdd BLAST61

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi161 – 165Selectivity filter part_1By similarity5
Motifi203 – 207Selectivity filter part_2By similarity5
Motifi457 – 461Selectivity filter part_3By similarity5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi2 – 6Poly-Ala5

Sequence similaritiesi

Keywords - Domaini

CBS domain, Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0476 Eukaryota
COG0038 LUCA
GeneTreeiENSGT00760000119109
HOGENOMiHOG000231297
HOVERGENiHBG005332
InParanoidiP51788
KOiK05011
OMAiWAMDYAI
OrthoDBiEOG091G01RJ
PhylomeDBiP51788
TreeFamiTF300522

Family and domain databases

Gene3Di1.10.3080.10, 1 hit
InterProiView protein in InterPro
IPR000644 CBS_dom
IPR002244 Cl-channel-2
IPR014743 Cl-channel_core
IPR001807 Cl-channel_volt-gated
PfamiView protein in Pfam
PF00654 Voltage_CLC, 1 hit
PRINTSiPR00762 CLCHANNEL
PR01113 CLCHANNEL2
SUPFAMiSSF81340 SSF81340, 1 hit
PROSITEiView protein in PROSITE
PS51371 CBS, 2 hits

Sequences (5)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P51788-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAAAAAEEGM EPRALQYEQT LMYGRYTQDL GAFAKEEAAR IRLGGPEPWK
60 70 80 90 100
GPPSSRAAPE LLEYGRSRCA RCRVCSVRCH KFLVSRVGED WIFLVLLGLL
110 120 130 140 150
MALVSWVMDY AIAACLQAQQ WMSRGLNTSI LLQYLAWVTY PVVLITFSAG
160 170 180 190 200
FTQILAPQAV GSGIPEMKTI LRGVVLKEYL TLKTFIAKVI GLTCALGSGM
210 220 230 240 250
PLGKEGPFVH IASMCAALLS KFLSLFGGIY ENESRNTEML AAACAVGVGC
260 270 280 290 300
CFAAPIGGVL FSIEVTSTFF AVRNYWRGFF AATFSAFIFR VLAVWNRDEE
310 320 330 340 350
TITALFKTRF RLDFPFDLQE LPAFAVIGIA SGFGGALFVY LNRKIVQVMR
360 370 380 390 400
KQKTINRFLM RKRLLFPALV TLLISTLTFP PGFGQFMAGQ LSQKETLVTL
410 420 430 440 450
FDNRTWVRQG LVEELEPPST SQAWNPPRAN VFLTLVIFIL MKFWMSALAT
460 470 480 490 500
TIPVPCGAFM PVFVIGAAFG RLVGESMAAW FPDGIHTDSS TYRIVPGGYA
510 520 530 540 550
VVGAAALAGA VTHTVSTAVI VFELTGQIAH ILPVMIAVIL ANAVAQSLQP
560 570 580 590 600
SLYDSIIRIK KLPYLPELGW GRHQQYRVRV EDIMVRDVPH VALSCTFRDL
610 620 630 640 650
RLALHRTKGR MLALVESPES MILLGSIERS QVVALLGAQL SPARRRQHMQ
660 670 680 690 700
ERRATQTSPL SDQEGPPTPE ASVCFQVNTE DSAFPAARGE THKPLKPALK
710 720 730 740 750
RGPSVTRNLG ESPTGSAESA GIALRSLFCG SPPPEAASEK LESCEKRKLK
760 770 780 790 800
RVRISLASDA DLEGEMSPEE ILEWEEQQLD EPVNFSDCKI DPAPFQLVER
810 820 830 840 850
TSLHKTHTIF SLLGVDHAYV TSIGRLIGIV TLKELRKAIE GSVTAQGVKV
860 870 880 890
RPPLASFRDS ATSSSDTETT EVHALWGPHS RHGLPREGSP SDSDDKCQ
Length:898
Mass (Da):98,535
Last modified:February 9, 2010 - v2
Checksum:i5F20FA8713C0C74E
GO
Isoform 2 (identifier: P51788-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-359: Missing.
     443-485: FWMSALATTI...SMAAWFPDGI → HLGVWWVKAW...WSGQLRWQER
     486-898: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:126
Mass (Da):14,383
Checksum:i69843C961A8FC3DF
GO
Isoform 3 (identifier: P51788-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     466-482: Missing.

Show »
Length:881
Mass (Da):96,786
Checksum:iF44E1264FC92758F
GO
Isoform 4 (identifier: P51788-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     74-117: Missing.

Note: No experimental confirmation available.
Show »
Length:854
Mass (Da):93,583
Checksum:iEA949779A2E7B686
GO
Isoform 5 (identifier: P51788-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     806-834: Missing.

Note: No experimental confirmation available.
Show »
Length:869
Mass (Da):95,399
Checksum:iE0D9292146DD1AA5
GO

Sequence cautioni

The sequence AAH21578 differs from that shown. Reason: Erroneous translation. Wrong choice of frame.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti17Y → H in AAB34722 (PubMed:7795595).Curated1
Sequence conflicti537A → V in AAH21578 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05788648P → R Polymorphism; reduces channel activity. 1 PublicationCorresponds to variant dbSNP:rs115661422EnsemblClinVar.1
Natural variantiVAR_05788768R → H Polymorphism; reduces channel activity. 1 PublicationCorresponds to variant dbSNP:rs61729156EnsemblClinVar.1
Natural variantiVAR_070976144 – 145Missing in LKPAT; loss of function mutation; the mutant protein is restricted to the endoplasmic reticulum and hardly reached the plasma membrane; lower amounts of the mutant protein compared to wild-type. 1 Publication2
Natural variantiVAR_057888199G → A Polymorphism; no effect. 1 PublicationCorresponds to variant dbSNP:rs863225248EnsemblClinVar.1
Natural variantiVAR_057889235R → Q in EJM8; associated with disease susceptibility; the mutant channel has accelerated deactivation rates compared to wild-type, but normal activation and peak current. 1 PublicationCorresponds to variant dbSNP:rs71318369EnsemblClinVar.1
Natural variantiVAR_070977500A → V in LKPAT; loss of function mutation; the mutant protein is restricted to the endoplasmic reticulum and hardly reaches the plasma membrane; lower amounts of the mutant protein compared to wild-type. 1 PublicationCorresponds to variant dbSNP:rs587777111EnsemblClinVar.1
Natural variantiVAR_057890577R → Q in EIG11; associated with disease susceptibility; the mutant channel has accelerated deactivation rates compared to wild-type, but normal activation and peak current. 1 PublicationCorresponds to variant dbSNP:rs137852682EnsemblClinVar.1
Natural variantiVAR_057891644R → C Polymorphism; no effect. 1 PublicationCorresponds to variant dbSNP:rs148545588EnsemblClinVar.1
Natural variantiVAR_057892646R → Q Polymorphism; reduces channel activity. 1 PublicationCorresponds to variant dbSNP:rs115961753EnsemblClinVar.1
Natural variantiVAR_054550668T → S3 PublicationsCorresponds to variant dbSNP:rs9820367EnsemblClinVar.1
Natural variantiVAR_015989715G → E in JAE2; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs137852681EnsemblClinVar.1
Natural variantiVAR_054551718E → D. Corresponds to variant dbSNP:rs2228292EnsemblClinVar.1
Natural variantiVAR_058426719S → L Found in a patient with childhood absence epilepsy; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs138573287Ensembl.1
Natural variantiVAR_057893725R → W Polymorphism; slightly faster channel activation. 1 PublicationCorresponds to variant dbSNP:rs114702742EnsemblClinVar.1
Natural variantiVAR_057894747R → H Polymorphism; slightly faster channel activation. 1 PublicationCorresponds to variant dbSNP:rs144164281EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0078311 – 359Missing in isoform 2. 1 PublicationAdd BLAST359
Alternative sequenceiVSP_04545774 – 117Missing in isoform 4. 1 PublicationAdd BLAST44
Alternative sequenceiVSP_007832443 – 485FWMSA…FPDGI → HLGVWWVKAWLPGSQMEFIR TAAPTGLCLGATLWSGQLRW QER in isoform 2. 1 PublicationAdd BLAST43
Alternative sequenceiVSP_036456466 – 482Missing in isoform 3. 1 PublicationAdd BLAST17
Alternative sequenceiVSP_036455486 – 898Missing in isoform 2. 1 PublicationAdd BLAST413
Alternative sequenceiVSP_045458806 – 834Missing in isoform 5. 1 PublicationAdd BLAST29

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S77770 mRNA Translation: AAB34722.2
AF026004 mRNA Translation: AAB88807.1
AK298952 mRNA Translation: BAG61051.1
AK302759 mRNA Translation: BAG63970.1
AC078797 Genomic DNA No translation available.
BC021578 mRNA Translation: AAH21578.1 Sequence problems.
BC072004 mRNA Translation: AAH72004.1
CCDSiCCDS3263.1 [P51788-1]
CCDS54690.1 [P51788-4]
CCDS54691.1 [P51788-3]
CCDS54692.1 [P51788-5]
RefSeqiNP_001164558.1, NM_001171087.2 [P51788-3]
NP_001164559.1, NM_001171088.2 [P51788-4]
NP_001164560.1, NM_001171089.2 [P51788-5]
NP_004357.3, NM_004366.5 [P51788-1]
UniGeneiHs.436847

Genome annotation databases

EnsembliENST00000265593; ENSP00000265593; ENSG00000114859 [P51788-1]
ENST00000344937; ENSP00000345056; ENSG00000114859 [P51788-3]
ENST00000434054; ENSP00000400425; ENSG00000114859 [P51788-4]
ENST00000457512; ENSP00000391928; ENSG00000114859 [P51788-5]
GeneIDi1181
KEGGihsa:1181
UCSCiuc003foi.4 human [P51788-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiCLCN2_HUMAN
AccessioniPrimary (citable) accession number: P51788
Secondary accession number(s): B4DQT9
, B4DZ58, E9PBD9, E9PCD2, O14864, Q6IPA9, Q8WU13
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: February 9, 2010
Last modified: July 18, 2018
This is version 172 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

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