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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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SLC9A3
solute carrier family 9 member A3
Chromosome 5 Β· 5p15.33
NCBI Gene: 6550Ensembl: ENSG00000066230.12HGNC: HGNC:11073UniProt: P48764
122PubMed Papers
21Diseases
4Drugs
24Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sodium ion import across plasma membraneregulation of intracellular pHprotein bindingextracellular exosomecongenital sodium diarrheairritable bowel syndromehyperphosphatemianeurodegenerative disease
✦AI Summary

SLC9A3 encodes a plasma membrane Na+/H+ antiporter that exchanges intracellular H+ ions for extracellular Na+ in 1:1 stoichiometry, playing a critical role in salt and fluid absorption and pH homeostasis 1. As the major apical Na+/H+ exchanger in kidney and intestine, SLC9A3 is essential for renal and intestinal Na+ absorption and blood pressure regulation 23. The protein functions as part of neutral NaCl absorption through scaffolding complexes involving ezrin and PDZ domain-containing proteins 4. SLC9A3 is regulated by post-prandial digestion-related signals and controls intracellular pH homeostasis 4. Loss-of-function mutations cause congenital diarrhea characterized by secretory sodium loss 5, while SLC9A3 deficiency has been associated with congenital bilateral absence of the vas deferens (CBAVD) through interaction with CFTR 67. SLC9A3 variants modulate cystic fibrosis lung disease severity and susceptibility to Pseudomonas aeruginosa infection, with the T allele of rs4957061 associated with earlier infection acquisition and reduced lung function 8. SLC9A3 deficiency causes progressive lower urinary tract dysfunction through electrolyte imbalance-induced bladder inflammation and fibrosis 9. The selective NHE3 inhibitor tenapanor was approved for irritable bowel syndrome treatment and hyperphosphatemia management 510.

Sources cited
1
SLC9A3 is a plasma membrane Na+/H+ antiporter exchanging intracellular H+ for extracellular Na+
PMID: 18829453
2
SLC9A3 is the major apical Na+/H+ exchanger in kidney and intestine important for Na+ absorption and blood pressure regulation
PMID: 24622516
3
SLC9A3 is a major apical Na+/H+ exchanger in kidney and intestine for Na+ absorption
PMID: 26358773
4
NHE3 is regulated by post-prandial signals and functions through scaffolding complexes involving ezrin and PDZ proteins
PMID: 19448074
5
Tenapanor, a selective NHE3 inhibitor, was approved for IBS-C and hyperphosphatemia treatment
PMID: 31677150
6
SLC9A3 deficiency causes decreased CFTR expression and obstructive azoospermia through interaction with CFTR in reproductive tract
PMID: 28384194
7
SLC9A3 deficiency interacts with CFTR to cause congenital bilateral absence of vas deferens
PMID: 30797621
8
SLC9A3 variant rs4957061 T allele is associated with earlier Pseudomonas aeruginosa infection and reduced lung function in cystic fibrosis
PMID: 20967843
9
SLC9A3 deficiency causes progressive lower urinary tract dysfunction through electrolyte imbalance-induced bladder inflammation and fibrosis
PMID: 36916397
10
NHE3 tissue-specific knockout models and tenapanor demonstrate distinct intestinal and renal functions in sodium and phosphate handling
PMID: 38448727
Disease Associationsβ“˜21
congenital sodium diarrheaOpen Targets
0.65Moderate
irritable bowel syndromeOpen Targets
0.56Moderate
hyperphosphatemiaOpen Targets
0.51Moderate
neurodegenerative diseaseOpen Targets
0.47Moderate
chronic kidney diseaseOpen Targets
0.39Weak
ConstipationOpen Targets
0.39Weak
cystic fibrosisOpen Targets
0.38Weak
constipation disorderOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.35Weak
age-related macular degenerationOpen Targets
0.34Weak
autism spectrum disorderOpen Targets
0.33Weak
Barrett's esophagusOpen Targets
0.22Weak
esophageal adenocarcinomaOpen Targets
0.22Weak
Abnormality of the skeletal systemOpen Targets
0.21Weak
genetic disorderOpen Targets
0.19Weak
ulcerative colitisOpen Targets
0.13Weak
osteoarthritis, hipOpen Targets
0.13Weak
osteoarthritis, kneeOpen Targets
0.13Weak
gastroesophageal reflux diseaseOpen Targets
0.12Weak
psoriasisOpen Targets
0.12Weak
Diarrhea 8, secretory sodium, congenitalUniProt
Pathogenic Variants24
NM_004174.4(SLC9A3):c.932+1G>APathogenic
Congenital secretory sodium diarrhea 8|not provided
β˜…β˜…β˜†β˜†2025
NM_004174.4(SLC9A3):c.805G>A (p.Ala269Thr)Pathogenic
Congenital secretory sodium diarrhea 8|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 269
NM_004174.4(SLC9A3):c.164_165insT (p.Tyr56fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 56
NM_004174.4(SLC9A3):c.712G>T (p.Gly238Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 238
NM_004174.4(SLC9A3):c.1446+1G>APathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_004174.4(SLC9A3):c.1270del (p.Val424fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 424
NM_004174.4(SLC9A3):c.1357-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_004174.4(SLC9A3):c.1638C>A (p.Tyr546Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 546
NM_004174.4(SLC9A3):c.1214A>G (p.Asp405Gly)Pathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024β†’ Residue 405
NM_004174.4(SLC9A3):c.650C>T (p.Ser217Leu)Likely pathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024β†’ Residue 217
NM_004174.4(SLC9A3):c.1145G>A (p.Arg382Gln)Pathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024β†’ Residue 382
NM_004174.4(SLC9A3):c.1745del (p.Ser582fs)Pathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024β†’ Residue 582
NM_004174.4(SLC9A3):c.1446+1delinsCAPathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024
NM_004174.4(SLC9A3):c.1052dup (p.Met352fs)Pathogenic
Congenital secretory sodium diarrhea 8
β˜…β˜†β˜†β˜†2024β†’ Residue 352
NM_004174.4(SLC9A3):c.676-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_004174.4(SLC9A3):c.2376del (p.Tyr793fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 793
NM_004174.4(SLC9A3):c.933-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2022
NM_004174.4(SLC9A3):c.1007_1011dup (p.Thr338fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 338
NM_004174.4(SLC9A3):c.1443_1446+150delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2021
NM_004174.4(SLC9A3):c.796del (p.Val266fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 266
View on ClinVar β†—
Drug Targets4
SQUALAMINEPhase III
Sodium/hydrogen exchanger 3 inhibitor
SQUALAMINE LACTATEPhase III
Sodium/hydrogen exchanger 3 inhibitor
age-related macular degeneration
TENAPANORApproved
Sodium/hydrogen exchanger 3 inhibitor
Constipation
TENAPANOR HYDROCHLORIDEApproved
Sodium/hydrogen exchanger 3 inhibitor
hyperphosphatemia
Related Genes
MSNProtein interaction100%SLC34A1Protein interaction98%SLC26A6Protein interaction92%EZRProtein interaction90%SLC9A5Shared pathway89%SLC12A1Protein interaction85%
Tissue Expression6 tissues
Ovary
100%
Brain
97%
Bone Marrow
73%
Liver
44%
Heart
26%
Lung
23%
Gene Interaction Network
Click a node to explore
SLC9A3MSNSLC34A1SLC26A6EZRSLC9A5SLC12A1
PROTEIN STRUCTURE
Preparing viewer…
PDB7X2U Β· 3.20 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.60LoF Tolerant
pLIβ“˜
0.03Tolerant
Observed/Expected LoF0.44 [0.33–0.60]
RankingsWhere SLC9A3 stands among ~20K protein-coding genes
  • #3,866of 20,598
    Most Researched122 Β· top quartile
  • #584of 1,025
    FDA-Approved Drug Targets2
  • #2,010of 5,498
    Most Pathogenic Variants24
  • #4,107of 17,882
    Most Constrained (LOEUF)0.60 Β· top quartile
Genes detectedSLC9A3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Tenapanor: First Approval.
PMID: 31677150
Drugs Β· 2019
1.00
2
The role of SLC9A3 in Taiwanese patients with congenital bilateral absence of vas deferens (CBAVD).
PMID: 30797621
J Formos Med Assoc Β· 2019
0.90
3
Modulatory effect of the SLC9A3 gene on susceptibility to infections and pulmonary function in children with cystic fibrosis.
PMID: 20967843
Pediatr Pulmonol Β· 2011
0.80
4
NHE3 regulatory complexes.
PMID: 19448074
J Exp Biol Β· 2009
0.70
5
Insight into SLC9A3 deficiency-mediated micturition dysfunction caused by electrolyte imbalance.
PMID: 36916397
Biomed Pharmacother Β· 2023
0.60