Seroatlas · Human Serome Atlas

CLCN4

H(+)/Cl(-) exchange transporter 4

Also known as: ClC-4, CLC4, CLCN4_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
P51793
Gene
CLCN4
Ensembl
ENSG00000073464
Chromosome
X
Canonical length
760 aa
Protein class
Disease related genes, Human disease related genes, Potential drug targets, Predicted membrane proteins, Transporters
Subcellular location
Vesicles

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. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders. Alternate splicing results in two transcript variants that encode different proteins. [provided by RefSeq, Mar 2012]

Canonical amino-acid sequenceUniProt

760 residues, UniProt reviewed canonical sequence.

>P51793|CLCN4
     1  MVNAGAMSGS GNLMDFLDEP FPDVGTYEDF HTIDWLREKS RDTDRHRKIT SKSKESIWEF
    61  IKSLLDAWSG WVVMLLIGLL AGTLAGVIDL AVDWMTDLKE GVCLSAFWYS HEQCCWTSNE
   121  TTFEDRDKCP LWQKWSELLV NQSEGASAYI LNYLMYILWA LLFAFLAVSL VRVFAPYACG
   181  SGIPEIKTIL SGFIIRGYLG KWTLLIKTVT LVLVVSSGLS LGKEGPLVHV ACCCGNFFSS
   241  LFSKYSKNEG KRREVLSAAA AAGVSVAFGA PIGGVLFSLE EVSYYFPLKT LWRSFFAALV
   301  AAFTLRSINP FGNSRLVLFY VEYHTPWYMA ELFPFILLGV FGGLWGTLFI RCNIAWCRRR
   361  KTTRLGKYPV LEVIVVTAIT AIIAYPNPYT RQSTSELISE LFNDCGALES SQLCDYINDP
   421  NMTRPVDDIP DRPAGVGVYT AMWQLALALI FKIVVTIFTF GMKIPSGLFI PSMAVGAIAG
   481  RMVGIGVEQL AYHHHDWIIF RNWCRPGADC VTPGLYAMVG AAACLGGVTR MTVSLVVIMF
   541  ELTGGLEYIV PLMAAAVTSK WVADAFGKEG IYEAHIHLNG YPFLDVKDEF THRTLATDVM
   601  RPRRGEPPLS VLTQDSMTVE DVETLIKETD YNGFPVVVSR DSERLIGFAQ RRELILAIKN
   661  ARQRQEGIVS NSIMYFTEEP PELPANSPHP LKLRRILNLS PFTVTDHTPM ETVVDIFRKL
   721  GLRQCLVTRS GRLLGIITKK DVLRHMAQMA NQDPESIMFN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLCN4 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
Other membrane
Secreted
No
Transmembrane segments
10
Mean surface accessibility (rSASA)
0.25
Highest tissue expression
42 nTPM

Expression across tissuesHPA

Tissue

  • skeletal muscle: 42 nTPM
  • retina: 35 nTPM
  • tongue: 32 nTPM
  • cerebral cortex: 27 nTPM
  • cerebellum: 22 nTPM
  • epididymis: 21 nTPM

Single-cell type

  • cone photoreceptor cells: 151 nCPM
  • epididymal principal cells: 125 nCPM
  • retinal pigment epithelial cells: 107 nCPM
  • retinal bipolar cells: 92 nCPM
  • oligodendrocytes: 86 nCPM
  • erythrocyte progenitors: 68 nCPM

Immune cell

  • naive B-cell: 2.6 nTPM
  • neutrophil: 2.2 nTPM
  • basophil: 1.7 nTPM
  • memory B-cell: 1 nTPM
  • myeloid DC: 0.4 nTPM
  • classical monocyte: 0.3 nTPM

Brain region

  • white matter: 83 nTPM
  • cerebellum: 78 nTPM
  • medulla oblongata: 74 nTPM
  • thalamus: 73 nTPM
  • basal ganglia: 73 nTPM
  • pons: 69 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLCN4.

Disease | AllUniProt

Conditions CLCN4 is implicated in, by any mechanism.

Disease | GeneticClinVar

68 pathogenic / likely-pathogenic of 847 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
0.15
gnomAD pLI
1
gnomAD missense Z
4.52
DepMap mean gene effect
0.15
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% 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

InteractionsUniProt · HPA

Protein binding partners of CLCN4 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLCN4 as an antibody target. Whether an autoantibody or antibody against CLCN4 could matter depends on whether native CLCN4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLCN4 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label CLCN4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CLCN4. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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