Seroatlas · Human Serome Atlas

CLCNKA

Chloride channel protein ClC-Ka

Also known as: CLCKA_HUMAN, hClC-Ka

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

Protein identityUniProt · HPA

UniProt accession
P51800
Gene
CLCNKA
Ensembl
ENSG00000186510
Chromosome
1
Canonical length
687 aa
Protein class
Disease related genes, Human disease related genes, Predicted membrane proteins
Quaternary structure
Homodimer

OverviewNCBI Gene

This gene is a member of the CLC family of voltage-gated chloride channels. The encoded protein is predicted to have 12 transmembrane domains, and requires a beta subunit called barttin to form a functional channel. It is thought to function in salt reabsorption in the kidney and potassium recycling in the inner ear. The gene is highly similar to CLCNKB, which is located 10 kb downstream from this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

687 residues, UniProt reviewed canonical sequence.

>P51800|CLCNKA
     1  MEELVGLREG FSGDPVTLQE LWGPCPHIRR AIQGGLEWLK QKVFRLGEDW YFLMTLGVLM
    61  ALVSYAMNFA IGCVVRAHQW LYREIGDSHL LRYLSWTVYP VALVSFSSGF SQSITPSSGG
   121  SGIPELKTML AGVILEDYLD IKNFGAKVVG LSCTLATGST LFLGKVGPFV HLSVMIAAYL
   181  GRVRTTTIGE PENKSKQNEM LVAAAAVGVA TVFAAPFSGV LFSIEVMSSH FSVRDYWRGF
   241  FAATCGAFIF RLLAVFNSEQ ETITSLYKTS FRVDVPFDLP EIFFFVALGG ICGVLSCAYL
   301  FCQRTFLSFI KTNRYSSKLL ATSKPVYSAL ATLLLASITY PPGVGHFLAS RLSMKQHLDS
   361  LFDNHSWALM TQNSSPPWPE ELDPQHLWWE WYHPRFTIFG TLAFFLVMKF WMLILATTIP
   421  MPAGYFMPIF ILGAAIGRLL GEALAVAFPE GIVTGGVTNP IMPGGYALAG AAAFSGAVTH
   481  TISTALLAFE LTGQIVHALP VLMAVLAANA IAQSCQPSFY DGTIIVKKLP YLPRILGRNI
   541  GSHHVRVEHF MNHSITTLAK DTPLEEVVKV VTSTDVTEYP LVESTESQIL VGIVQRAQLV
   601  QALQAEPPSR APGHQQCLQD ILARGCPTEP VTLTLFSETT LHQAQNLFKL LNLQSLFVTS
   661  RGRAVGCVSW VEMKKAISNL TNPPAPK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLCNKA 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
9
Mean surface accessibility (rSASA)
0.26
Highest tissue expression
332 nTPM

Expression across tissuesHPA

Tissue

  • kidney: 332 nTPM
  • parathyroid gland: 45 nTPM
  • thyroid gland: 21 nTPM
  • pituitary gland: 18 nTPM
  • choroid plexus: 12 nTPM
  • cerebellum: 7.6 nTPM

Single-cell type

  • late spermatids: 395 nCPM
  • loop of henle epithelial cells: 188 nCPM
  • distal convoluted tubule cells: 161 nCPM
  • renal collecting duct intercalated cells: 124 nCPM
  • renal connecting tubule cells: 100 nCPM
  • gonadotrophs: 86 nCPM

Immune cell

  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM
  • MAIT T-cell: 0 nTPM

Brain region

  • choroid plexus: 9.3 nTPM
  • cerebellum: 3.9 nTPM
  • hippocampal formation: 0.9 nTPM
  • pons: 0.8 nTPM
  • cerebral cortex: 0.3 nTPM
  • medulla oblongata: 0.3 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLCNKA.

Disease | AllUniProt

Conditions CLCNKA is implicated in, by any mechanism.

  • Bartter syndrome 4B, neonatal, with sensorineural deafness (BARTS4B) MIM:613090

Disease | GeneticClinVar

5 pathogenic / likely-pathogenic of 273 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)
1.12
gnomAD pLI
0
gnomAD missense Z
-0.33
DepMap mean gene effect
0.15
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

InteractionsUniProt · HPA

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

CLCNKA is annotated at the cell surface, where native CLCNKA 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 CLCNKA as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CLCNKA. 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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