Seroatlas · Human Serome Atlas

CLCN1

Chloride channel protein 1

Also known as: ClC-1, CLC1, CLCN1_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: P35523
Gene: CLCN1
Ensembl: ENSG00000188037
Chromosome: 7
Canonical length: 988 aa
Protein class: Disease related genes, Human disease related genes, Potential drug targets, Predicted membrane proteins, Transporters
Quaternary structure: Homodimer

OverviewNCBI Gene

The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. The protein encoded by this gene regulates the electric excitability of the skeletal muscle membrane. Mutations in this gene cause two forms of inherited human muscle disorders: recessive generalized myotonia congenita (Becker) and dominant myotonia (Thomsen). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

Canonical amino-acid sequenceUniProt

988 residues, UniProt reviewed canonical sequence.

>P35523|CLCN1
     1  MEQSRSQQRG GEQSWWGSDP QYQYMPFEHC TSYGLPSENG GLQHRLRKDA GPRHNVHPTQ
    61  IYGHHKEQFS DREQDIGMPK KTGSSSTVDS KDEDHYSKCQ DCIHRLGQVV RRKLGEDGIF
   121  LVLLGLLMAL VSWSMDYVSA KSLQAYKWSY AQMQPSLPLQ FLVWVTFPLV LILFSALFCH
   181  LISPQAVGSG IPEMKTILRG VVLKEYLTMK AFVAKVVALT AGLGSGIPVG KEGPFVHIAS
   241  ICAAVLSKFM SVFCGVYEQP YYYSDILTVG CAVGVGCCFG TPLGGVLFSI EVTSTYFAVR
   301  NYWRGFFAAT FSAFVFRVLA VWNKDAVTIT ALFRTNFRMD FPFDLKELPA FAAIGICCGL
   361  LGAVFVYLHR QVMLGVRKHK ALSQFLAKHR LLYPGIVTFV IASFTFPPGM GQFMAGELMP
   421  REAISTLFDN NTWVKHAGDP ESLGQSAVWI HPRVNVVIII FLFFVMKFWM SIVATTMPIP
   481  CGGFMPVFVL GAAFGRLVGE IMAMLFPDGI LFDDIIYKIL PGGYAVIGAA ALTGAVSHTV
   541  STAVICFELT GQIAHILPMM VAVILANMVA QSLQPSLYDS IIQVKKLPYL PDLGWNQLSK
   601  YTIFVEDIMV RDVKFVSASY TYGELRTLLQ TTTVKTLPLV DSKDSMILLG SVERSELQAL
   661  LQRHLCPERR LRAAQEMARK LSELPYDGKA RLAGEGLPGA PPGRPESFAF VDEDEDEDLS
   721  GKSELPPSLA LHPSTTAPLS PEEPNGPLPG HKQQPEAPEP AGQRPSIFQS LLHCLLGRAR
   781  PTKKKTTQDS TDLVDNMSPE EIEAWEQEQL SQPVCFDSCC IDQSPFQLVE QTTLHKTHTL
   841  FSLLGLHLAY VTSMGKLRGV LALEELQKAI EGHTKSGVQL RPPLASFRNT TSTRKSTGAP
   901  PSSAENWNLP EDRPGATGTG DVIAASPETP VPSPSPEPPL SLAPGKVEGE LEELELVESP
   961  GLEEELADIL QGPSLRSTDE EDEDELIL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLCN1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 5
Mean surface accessibility (rSASA): 0.4
Highest tissue expression: 60 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 60 nTPM
tongue: 15 nTPM
esophagus: 0.9 nTPM
small intestine: 0.9 nTPM
testis: 0.9 nTPM
salivary gland: 0.4 nTPM

Single-cell type

myonuclei: 280 nCPM
late spermatids: 203 nCPM
early spermatids: 45 nCPM
medullary thymic epithelial cells: 12 nCPM
enterocytes: 9.1 nCPM
esophageal apical cells: 6.1 nCPM

Immune cell

non-classical monocyte: 1.4 nTPM
intermediate monocyte: 0.9 nTPM
classical monocyte: 0.8 nTPM
myeloid DC: 0.6 nTPM
total PBMC: 0.3 nTPM
neutrophil: 0.2 nTPM

Brain region

cerebellum: 1.5 nTPM
white matter: 0.6 nTPM
cerebral cortex: 0.5 nTPM
basal ganglia: 0.4 nTPM
hypothalamus: 0.4 nTPM
medulla oblongata: 0.4 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLCN1.

Disease | AllUniProt

Conditions CLCN1 is implicated in, by any mechanism.

Myotonia congenita, autosomal dominant (MCAD) MIM:160800
Myotonia congenita, autosomal recessive (MCAR) MIM:255700

Disease | GeneticClinVar

346 pathogenic / likely-pathogenic of 1,744 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Congenital myotonia, autosomal recessive form
Congenital myotonia, autosomal dominant form
CLCN1-related disorder
Skeletal muscle channelopathy
Batten-Turner congenital myopathy

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.99
gnomAD pLI: 0
gnomAD missense Z: 0.21
DepMap mean gene effect: -0.05
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLCN1 as an antibody target. Whether an autoantibody or antibody against CLCN1 could matter depends on whether native CLCN1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLCN1 is annotated at the cell surface, where native CLCN1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label CLCN1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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