Seroatlas · Human Serome Atlas

SLC24A1

Sodium/potassium/calcium exchanger 1

Also known as: CSNB1D, HsT17412, KIAA0702, NCKX, NCKX1, NCKX1_HUMAN, RODX

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

Protein identityUniProt · HPA

UniProt accession: O60721
Gene: SLC24A1
Ensembl: ENSG00000074621
Chromosome: 15
Canonical length: 1099 aa
Protein class: Disease related genes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins, Transporters

OverviewNCBI Gene

This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night blindness. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

Canonical amino-acid sequenceUniProt

1099 residues, UniProt reviewed canonical sequence.

>O60721|SLC24A1
     1  MGKLIRMGPQ ERWLLRTKRL HWSRLLFLLG MLIIGSTYQH LRRPRGLSSL WAAVSSHQPI
    61  KLASRDLSSE EMMMMSSSPS KPSSEMGGKM LVPQASVGSD EATLSMTVEN IPSMPKRTAK
   121  MIPTTTKNNY SPTAAGTERR KEDTPTSSRT LTYYTSTSSR QIVKKYTPTP RGEMKSYSPT
   181  QVREKVKYTP SPRGRRVGTY VPSTFMTMET SHAITPRTTV KDSDITATYK ILETNSLKRI
   241  MEETTPTTLK GMFDSTPTFL THEVEANVLT SPRSVMEKNN LFPPRRVESN SSAHPWGLVG
   301  KSNPKTPQGT VLLHTPATSE GQVTISTMTG SSPAETKAFT AAWSLRNPSP RTSVSAIKTA
   361  PAIVWRLAKK PSTAPSTSTT PTVRAKLTMQ VHHCVVVKPT PAMLTTPSPS LTTALLPEEL
   421  SPSPSVLPPS LPDLHPKGEY PPDLFSVEER RQGWVVLHVF GMMYVFVALA IVCDEYFVPA
   481  LGVITDKLQI SEDVAGATFM AAGGSAPELF TSLIGVFISH SNVGIGTIVG SAVFNILFVI
   541  GTCSLFSREI LNLTWWPLFR DVSFYILDLI MLILFFLDSL IAWWESLLLL LAYAFYVFTM
   601  KWNKHIEVWV KEQLSRRPVA KVMALEDLSK PGDGAIAVDE LQDNKKLKLP SLLTRGSSST
   661  SLHNSTIRST IYQLMLHSLD PLREVRLAKE KEEESLNQGA RAQPQAKAES KPEEEEPAKL
   721  PAVTVTPAPV PDIKGDQKEN PGGQEDVAEA ESTGEMPGEE GETAGEGETE EKSGGETQPE
   781  GEGETETQGK GEECEDENEA EGKGDNEGED EGEIHAEDGE MKGNEGETES QELSAENHGE
   841  AKNDEKGVED GGGSDGGDSE EEEEEEEEQE EEEEEEEQEE EEEEEEEEEE KGNEEPLSLD
   901  WPETRQKQAI YLFLLPIVFP LWLTVPDVRR QESRKFFVFT FLGSIMWIAM FSYLMVWWAH
   961  QVGETIGISE EIMGLTILAA GTSIPDLITS VIVARKGLGD MAVSSSVGSN IFDITVGLPV
  1021  PWLLFSLING LQPVPVSSNG LFCAIVLLFL MLLFVISSIA SCKWRMNKIL GFTMFLLYFV
  1081  FLIISVMLED RIISCPVSV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SLC24A1 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: 11
Mean surface accessibility (rSASA): 0.52
Highest tissue expression: 179 nTPM

Expression across tissuesHPA

Tissue

retina: 179 nTPM
kidney: 5.2 nTPM
ovary: 5.2 nTPM
thyroid gland: 4.9 nTPM
fallopian tube: 4.8 nTPM
skin: 4.8 nTPM

Single-cell type

rod photoreceptor cells: 440 nCPM
epicardial cells: 134 nCPM
epididymal basal cells: 110 nCPM
retinal bipolar cells: 90 nCPM
lymphatic endothelial cells: 77 nCPM
retinal horizontal cells: 68 nCPM

Immune cell

basophil: 1.6 nTPM
naive B-cell: 1 nTPM
NK-cell: 0.8 nTPM
plasmacytoid DC: 0.8 nTPM
eosinophil: 0.7 nTPM
classical monocyte: 0.5 nTPM

Brain region

cerebellum: 14 nTPM
cerebral cortex: 8.2 nTPM
choroid plexus: 8.1 nTPM
medulla oblongata: 7.7 nTPM
spinal cord: 7.6 nTPM
white matter: 7.6 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SLC24A1.

Disease | AllUniProt

Conditions SLC24A1 is implicated in, by any mechanism.

Night blindness, congenital stationary, 1D (CSNB1D) MIM:613830

Disease | GeneticClinVar

44 pathogenic / likely-pathogenic of 774 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Congenital stationary night blindness 1D
Retinal dystrophy
Retinitis pigmentosa
SLC24A1-related disorder
Congenital stationary night blindness autosomal dominant 2

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): 0.57
gnomAD pLI: 0
gnomAD missense Z: 1.8
DepMap mean gene effect: 0.02
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% 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

Sodium/potassium/calcium exchanger
Sodium/calcium exchanger membrane region
NCX, central ion-binding domain superfamily
Sodium/calcium exchanger protein
Sodium/potassium/calcium exchanger 1

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SLC24A1 as an antibody target. Whether an autoantibody or antibody against SLC24A1 could matter depends on whether native SLC24A1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SLC24A1 is annotated at the cell surface, where native SLC24A1 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 SLC24A1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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