SLC24A3

gene
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Summary

SLC24A3 (solute carrier family 24 member 3, HGNC:10977) is a protein-coding gene on chromosome 20p11.23, encoding Sodium/potassium/calcium exchanger 3 (Q9HC58). Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).

Source: NCBI Gene 57419 — RefSeq curated summary.

At a glance

  • GWAS associations: 56
  • Clinical variants (ClinVar): 98 total
  • MANE Select transcript: NM_020689

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10977
Approved symbolSLC24A3
Namesolute carrier family 24 member 3
Location20p11.23
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000185052
Ensembl biotypeprotein_coding
OMIM609839
Entrez57419

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000328041, ENST00000962751

RefSeq mRNA: 1 — MANE Select: NM_020689 NM_020689

CCDS: CCDS13140

Canonical transcript exons

ENST00000328041 — 17 exons

ExonStartEnd
ENSE000012949951971752819717593
ENSE000012999181969325919693425
ENSE000013002551928095919281087
ENSE000013048401968185819681991
ENSE000013052311968510019685361
ENSE000013067741951548819515564
ENSE000013086011966586419665889
ENSE000013111931965406219654136
ENSE000013116181969856819698680
ENSE000013145411967360119673654
ENSE000013199931972099119722926
ENSE000013205571968417619684336
ENSE000013287031958497119585055
ENSE000015942151958544119585544
ENSE000016690291969679719696911
ENSE000017040171921264219212984
ENSE000017474141958000019580074

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 97.87.

FANTOM5 (CAGE): breadth broad, TPM avg 4.1154 / max 339.1804, expressed in 624 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1837062.0174412
1837031.1265421
1837050.5792255
1837040.3923198

Top tissues by expression

284 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lateral nuclear group of thalamusUBERON:000273697.87gold quality
tongue squamous epitheliumUBERON:000691995.06gold quality
saphenous veinUBERON:000731893.51gold quality
cervix squamous epitheliumUBERON:000692293.27gold quality
epithelium of esophagusUBERON:000197693.20gold quality
esophagus squamous epitheliumUBERON:000692093.11gold quality
squamous epitheliumUBERON:000691492.89gold quality
triceps brachiiUBERON:000150992.45gold quality
gingivaUBERON:000182892.32gold quality
quadriceps femorisUBERON:000137792.25gold quality
vastus lateralisUBERON:000137992.24gold quality
gingival epitheliumUBERON:000194992.16gold quality
myometriumUBERON:000129691.44gold quality
deciduaUBERON:000245091.24gold quality
CA1 field of hippocampusUBERON:000388190.95gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451190.91gold quality
left uterine tubeUBERON:000130390.87gold quality
body of uterusUBERON:000985390.71gold quality
gluteal muscleUBERON:000200090.67gold quality
urethraUBERON:000005790.66gold quality
cervix epitheliumUBERON:000480189.95gold quality
Ammon’s hornUBERON:000195489.91gold quality
right coronary arteryUBERON:000162589.36gold quality
lower esophagus mucosaUBERON:003583489.24gold quality
skeletal muscle tissueUBERON:000113489.12gold quality
cerebellar vermisUBERON:000472088.34gold quality
uterusUBERON:000099588.17gold quality
deltoidUBERON:000147688.04gold quality
popliteal arteryUBERON:000225087.94gold quality
tibial arteryUBERON:000761087.93gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-ANND-2yes4909.78
E-HCAD-30yes356.11
E-HCAD-35yes63.39
E-ANND-3yes16.48
E-GEOD-81383no15.18

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

6 targets.

TargetRegulation
CALB1Repression
NR3C1Repression
PTH1RActivation
S100GActivation
TRPV5Repression
TRPV6Activation

Upstream regulators (CollecTRI, top): GATA3

miRNA regulators (miRDB)

142 targeting SLC24A3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-12118100.0065.881270
HSA-MIR-4262100.0073.263931
HSA-MIR-607799.9968.042299
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502

Literature-anchored findings (GeneRIF, showing 2)

  • Plasma membrane ion transporter.Displayed K(+)-dependent Na(+)/Ca(2+) exchanger activity when assayed in heterologous expression systems, using digital imaging of fura-2 fluorescence, electrophysiology, or radioactive (45)Ca(2+) uptake. (PMID:11294880)
  • NCKX3 is abundantly expressed within the human endometrium at the transcriptional and translational levels, and its level is regulated by steroid hormones (particularly estradiol) during the human menstrual cycle. (PMID:21321244)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioslc24a3ENSDARG00000006760
mus_musculusSlc24a3ENSMUSG00000063873
rattus_norvegicusSlc24a3ENSRNOG00000060687
drosophila_melanogasterCG17167FBGN0039941
drosophila_melanogasterCG12061FBGN0040031
drosophila_melanogasterzydFBGN0265767

Paralogs (4): SLC24A1 (ENSG00000074621), SLC24A4 (ENSG00000140090), SLC24A2 (ENSG00000155886), SLC24A5 (ENSG00000188467)

Protein

Protein identifiers

Sodium/potassium/calcium exchanger 3Q9HC58 (reviewed: Q9HC58)

Alternative names: Na(+)/K(+)/Ca(2+)-exchange protein 3, Solute carrier family 24 member 3

All UniProt accessions (1): Q9HC58

UniProt curated annotations — full annotation on UniProt →

Function. Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Subcellular location. Cell membrane.

Tissue specificity. Abundant in the brain. Expressed at low levels in the aorta, uterus and intestine.

Similarity. Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.

RefSeq proteins (1): NP_065740* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004481K/Na/Ca-exchangerFamily
IPR004837NaCa_ExmembDomain
IPR044880NCX_ion-bd_dom_sfHomologous_superfamily

Pfam: PF01699

Catalyzed reactions (Rhea), 1 shown:

  • Ca(2+)(out) + K(+)(out) + 4 Na(+)(in) = Ca(2+)(in) + K(+)(in) + 4 Na(+)(out) (RHEA:69967)

UniProt features (34 total): topological domain 11, transmembrane region 10, sequence variant 4, repeat 2, glycosylation site 2, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HC58-F170.310.29

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 308

Glycosylation sites (2): 71, 86

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-425561Sodium/Calcium exchangers
R-HSA-382551Transport of small molecules
R-HSA-425393
R-HSA-425407SLC-mediated transmembrane transport

MSigDB gene sets: 223 (showing top): GOBP_POTASSIUM_ION_TRANSPORT, RNGTGGGC_UNKNOWN, CLAUS_PGR_POSITIVE_MENINGIOMA_UP, ELVIDGE_HYPOXIA_DN, RRAGTTGT_UNKNOWN, AAGCAAT_MIR137, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GCANCTGNY_MYOD_Q6, AREB6_03, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, CAGCTG_AP4_Q5, GOBP_MONOATOMIC_CATION_TRANSPORT

GO Biological Process (13): monoatomic ion transport (GO:0006811), intracellular calcium ion homeostasis (GO:0006874), positive regulation of gene expression (GO:0010628), negative regulation of gene expression (GO:0010629), bone mineralization (GO:0030282), sodium ion transmembrane transport (GO:0035725), calcium ion transmembrane transport (GO:0070588), potassium ion transmembrane transport (GO:0071805), transport across blood-brain barrier (GO:0150104), potassium ion transport (GO:0006813), sodium ion transport (GO:0006814), calcium ion transport (GO:0006816), transmembrane transport (GO:0055085)

GO Molecular Function (4): calcium channel activity (GO:0005262), calcium, potassium:sodium antiporter activity (GO:0008273), symporter activity (GO:0015293), antiporter activity (GO:0015297)

GO Cellular Component (3): plasma membrane (GO:0005886), cell periphery (GO:0071944), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Metal ion SLC transporters1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
monoatomic cation transmembrane transport3
metal ion transport3
transport2
gene expression2
regulation of gene expression2
secondary active transmembrane transporter activity2
cellular anatomical structure2
intracellular monoatomic cation homeostasis1
calcium ion homeostasis1
positive regulation of macromolecule biosynthetic process1
negative regulation of macromolecule biosynthetic process1
ossification1
biomineral tissue development1
sodium ion transport1
calcium ion transport1
potassium ion transport1
vascular transport1
cellular process1
monoatomic cation channel activity1
calcium ion transmembrane transporter activity1
calcium:sodium antiporter activity1
solute:potassium antiporter activity1
membrane1
cell periphery1

Protein interactions and networks

STRING

1301 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC24A3OR8G5Q8NG78514
SLC24A3ZNF133P52736494
SLC24A3RBBP9O75884488
SLC24A3DENND5BQ6ZUT9443
SLC24A3ITFG1Q8TB96433
SLC24A3TMEM212A6NML5428
SLC24A3KCNK18Q7Z418421
SLC24A3KAT14Q9H8E8418
SLC24A3KCNK5O95279417
SLC24A3CDC42EP1Q00587401
SLC24A3KCNK10P57789395
SLC24A3CCDC15Q0P6D6390
SLC24A3CFAP61Q8NHU2389
SLC24A3SPATC1Q76KD6380
SLC24A3AKT3Q9Y243371

IntAct

3 interactions, top by confidence:

ABTypeScore
SLC24A3GPR89Apsi-mi:“MI:0914”(association)0.350
SLC24A3SNRPGP15psi-mi:“MI:0914”(association)0.350

BioGRID (48): FADS1 (Affinity Capture-MS), SLC30A5 (Affinity Capture-MS), UBXN8 (Affinity Capture-MS), NAT14 (Affinity Capture-MS), GPR89A (Affinity Capture-MS), ELOVL4 (Affinity Capture-MS), SLC35B2 (Affinity Capture-MS), LDHC (Affinity Capture-MS), MTX3 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), LPCAT3 (Affinity Capture-MS), HMGCR (Affinity Capture-MS), SYVN1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), SLC30A6 (Affinity Capture-MS)

ESM2 similar proteins: A2WR31, A2X5B4, A2XGM7, A2YQB8, A2ZIM4, A8XI14, B8A833, B8AYH1, B8BKP4, F4IJ08, O45102, O82587, P0DI37, P0DKJ4, P0DKJ5, P93332, Q0D2K0, Q0DJY3, Q10LI8, Q10LN5, Q19VE6, Q2QR07, Q2QWX8, Q2R3P9, Q5JJY5, Q5N8J1, Q5NAZ9, Q60EC2, Q6K602, Q6L8F9, Q6NQN5, Q6YZF3, Q6Z1Y7, Q7RTP0, Q84WN3, Q8BZF2, Q8LBF7, Q8LFH5, Q8RZQ8, Q99PD7

Diamond homologs: B8K1V7, O22252, O54701, P23685, P32418, P48765, P48766, P48767, P48768, P57103, P70414, P70549, Q01728, Q2R041, Q6H641, Q8BUN9, Q8CGQ8, Q8K596, Q8NFF2, Q99PD7, Q9EPQ0, Q9HC58, Q9UI40, Q9UPR5, Q9VDG5, Q9VN12, S4R2P9, F1NXU8, O04034, O16242, P87122, Q49SH1, Q6AXS0, Q71RS6, Q925Q3, Q9FKP1, Q9FKP2, Q9U6A0, P34315, P34322

SIGNOR signaling

3 interactions.

AEffectBMechanism
SLC24A3“down-regulates quantity”calcium(2+)relocalization
SLC24A3“down-regulates quantity”potassium(1+)relocalization
SLC24A3“up-regulates quantity”sodium(1+)relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

98 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance83
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5086 predictions. Top by Δscore:

VariantEffectΔscore
20:19212980:GAAGG:Gdonor_gain1.0000
20:19212983:GG:Gdonor_gain1.0000
20:19212984:GG:Gdonor_gain1.0000
20:19212985:G:GAdonor_loss1.0000
20:19212986:T:Adonor_loss1.0000
20:19280954:CCCA:Cacceptor_loss1.0000
20:19280956:CAGA:Cacceptor_loss1.0000
20:19280957:A:AGacceptor_gain1.0000
20:19280958:G:GAacceptor_gain1.0000
20:19280958:GA:Gacceptor_gain1.0000
20:19280958:GAGC:Gacceptor_gain1.0000
20:19280958:GAGCT:Gacceptor_gain1.0000
20:19281083:ACCAG:Adonor_loss1.0000
20:19281084:CCAG:Cdonor_loss1.0000
20:19281085:CAG:Cdonor_loss1.0000
20:19281086:AG:Adonor_loss1.0000
20:19281087:GG:Gdonor_loss1.0000
20:19281088:GTAAC:Gdonor_loss1.0000
20:19281089:T:Adonor_loss1.0000
20:19515486:A:AGacceptor_gain1.0000
20:19515487:G:GGacceptor_gain1.0000
20:19579994:TTCCA:Tacceptor_loss1.0000
20:19579995:TCCAG:Tacceptor_loss1.0000
20:19579996:CCA:Cacceptor_loss1.0000
20:19579997:CAG:Cacceptor_loss1.0000
20:19579998:A:AGacceptor_gain1.0000
20:19579998:AG:Aacceptor_gain1.0000
20:19579998:AGGC:Aacceptor_loss1.0000
20:19579999:G:Aacceptor_loss1.0000
20:19579999:G:GAacceptor_gain1.0000

AlphaMissense

4263 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:19515500:T:GF95C1.000
20:19580022:T:CL124P1.000
20:19580034:G:AC128Y1.000
20:19580035:T:GC128W1.000
20:19584996:C:AA150D1.000
20:19584998:G:AG151R1.000
20:19584998:G:CG151R1.000
20:19584998:G:TG151W1.000
20:19584999:G:AG151E1.000
20:19585005:C:AT153K1.000
20:19585012:G:AM155I1.000
20:19585012:G:CM155I1.000
20:19585012:G:TM155I1.000
20:19585019:G:AG158R1.000
20:19585019:G:CG158R1.000
20:19585020:G:AG158E1.000
20:19585022:A:CS159R1.000
20:19585024:T:AS159R1.000
20:19585024:T:GS159R1.000
20:19585029:C:AA161D1.000
20:19585032:C:AP162Q1.000
20:19585038:T:CL164P1.000
20:19585485:G:CG185R1.000
20:19585486:G:AG185D1.000
20:19585497:T:CF189L1.000
20:19585499:C:AF189L1.000
20:19585499:C:GF189L1.000
20:19585502:C:AN190K1.000
20:19585502:C:GN190K1.000
20:19585519:G:AG196D1.000

dbSNP variants (sampled 300 via entrez): RS1000005342 (20:19507318 G>C), RS1000007644 (20:19513753 C>G,T), RS1000017187 (20:19305864 C>T), RS1000023847 (20:19696596 T>C), RS1000026385 (20:19475863 T>G), RS1000028680 (20:19583449 G>A), RS1000029248 (20:19360333 C>G), RS1000033106 (20:19661661 A>G), RS1000034434 (20:19267673 C>A,G,T), RS1000037094 (20:19340218 C>T), RS1000037433 (20:19644026 A>G), RS1000037931 (20:19347699 T>C), RS1000048307 (20:19306108 C>A), RS1000049637 (20:19260435 C>G), RS1000061549 (20:19715190 G>A)

Disease associations

OMIM: gene MIM:609839 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

56 associations (top):

StudyTraitp-value
GCST000450_3Matrix metalloproteinase levels3.000000e-07
GCST001113_9Age at smoking initiation in chronic obstructive pulmonary disease3.000000e-06
GCST001444_18Pulmonary function decline3.000000e-06
GCST002211_5Psychosis (atypical)1.000000e-06
GCST003720_27Migraine2.000000e-19
GCST003811_3Response to citalopram or escitalopram and depression7.000000e-07
GCST003986_6Migraine2.000000e-15
GCST004031_7QT interval (sulfonylurea treatment interaction)1.000000e-07
GCST004141_1Body fat mass2.000000e-09
GCST004278_10Pulse pressure2.000000e-13
GCST004599_209Mean platelet volume4.000000e-11
GCST006009_11Pulse pressure1.000000e-08
GCST006035_18Breast cancer and/or colorectal cancer9.000000e-06
GCST006431_13Plasma parathyroid hormone levels7.000000e-07
GCST006631_27Nicotine dependence and major depression (severity of comorbidity)9.000000e-06
GCST007096_246Pulse pressure3.000000e-15
GCST007097_86Pulse pressure6.000000e-06
GCST007268_68Diastolic blood pressure9.000000e-11
GCST007269_140Pulse pressure9.000000e-24
GCST007637_5Diffusing capacity of carbon monoxide9.000000e-06
GCST007705_4Pulse pressure3.000000e-06
GCST007705_6Pulse pressure1.000000e-06
GCST007705_60Pulse pressure6.000000e-08
GCST008141_7HDL cholesterol4.000000e-06
GCST008512_39Multisite chronic pain4.000000e-10
GCST009391_451Metabolite levels2.000000e-06
GCST009963_20Cataracts (operation)7.000000e-40
GCST010105_204Nicotine dependence symptom count3.000000e-06
GCST010105_50Nicotine dependence symptom count3.000000e-06
GCST012013_18Cataracts2.000000e-51

EFO canonical traits (15, from GWAS)

EFO IDTrait name
EFO:0004744matrix metalloproteinase measurement
EFO:0005670smoking initiation
EFO:0004713FEV/FVC ratio
EFO:0004682QT interval
EFO:0007922response to sulfonylurea
EFO:0005763pulse pressure measurement
EFO:0007006depressive symptom measurement
EFO:0009262nicotine dependence symptom count
EFO:0006336diastolic blood pressure
EFO:0009369diffusing capacity of the lung for carbon monoxide
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0010100multisite chronic pain
EFO:0010521phosphocreatine measurement
EFO:0004309platelet count
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC24 family of sodium/potassium/calcium exchangers

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects expression, affects methylation, decreases expression3
Valproic Acidincreases expression, affects expression, affects cotreatment3
entinostatincreases expression, affects cotreatment2
Panobinostataffects cotreatment, increases expression2
Estradioldecreases expression, affects cotreatment2
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression, increases expression2
fluorene-9-bisphenolincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation1
sodium arseniteaffects methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sincreases methylation1
Decitabinedecreases expression, decreases reaction1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Allergensincreases expression1
Leadaffects expression1
Lipopolysaccharidesdecreases expression, affects cotreatment1
Smokedecreases expression, decreases reaction1
Tobacco Smoke Pollutiondecreases expression1
Tretinoinincreases expression1
Triclosanincreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsincreases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.