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SLC9A4 solute carrier family 9 member A4 [ Homo sapiens (human) ]

Gene ID: 389015, updated on 3-May-2025
Official Symbol
SLC9A4provided by HGNC
Official Full Name
solute carrier family 9 member A4provided by HGNC
Primary source
HGNC:HGNC:11077
See related
Ensembl:ENSG00000180251 MIM:600531; AllianceGenome:HGNC:11077
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NHE4
Summary
Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in monoatomic cation transmembrane transport; regulation of intracellular pH; and transepithelial ammonium transport. Predicted to act upstream of or within gastric acid secretion and glandular epithelial cell development. Predicted to be located in basolateral plasma membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, May 2025]
Expression
Biased expression in stomach (RPKM 24.9) and kidney (RPKM 5.2) See more
Orthologs
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See SLC9A4 in Genome Data Viewer
Location:
2q12.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (102473226..102533972)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (102932202..102992943)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (103089685..103150431)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene short chain dehydrogenase/reductase family 42E, member 1 pseudogene 5 Neighboring gene interleukin 18 receptor accessory protein Neighboring gene microRNA 4772 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11832 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:103257402-103257630 Neighboring gene solute carrier family 9 member A2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:103280688-103281887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11833 Neighboring gene uncharacterized LOC124905954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:103324753-103325253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11834 Neighboring gene major facilitator superfamily domain containing 9

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Functional role of NHE4 as a pH regulator in rat and human colonic crypts. Arena EA, et al. Am J Physiol Cell Physiol, 2012 Jan 15. PMID 22049213
  2. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4. Grosche S, et al. Nat Commun, 2021 Nov 16. PMID 34785669, Free PMC Article
  3. Integrating disease and drug-related phenotypes for improved identification of pharmacogenomic variants. Ouellette TW, et al. Pharmacogenomics, 2021 Apr. PMID 33769074
  4. NHE1, NHE2, and NHE4 contribute to regulation of cell pH in T84 colon cancer cells. Beltrán AR, et al. Pflugers Arch, 2008 Feb. PMID 17943310
  5. Chromosomal assignment of four genes encoding Na/H exchanger isoforms in human and rat. Szpirer C, et al. Mamm Genome, 1994 Mar. PMID 8199403

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Integrating disease and drug-related phenotypes for improved identification of pharmacogenomic variants.
    Title: Integrating disease and drug-related phenotypes for improved identification of pharmacogenomic variants.
  2. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
    Title: Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
  3. Data demonstrate functional NHE4 activity in the rat and human colon and suggest that this exchanger is capable of modulating intracellular pH over a wide pH spectrum and may play an important role in maintaining cellular pH homeostasis.
    Title: Functional role of NHE4 as a pH regulator in rat and human colonic crypts.
  4. T84 human colon cells contain three isoforms of the Na+/H+ exchanger, NHE1, NHE2, and NHE4, but not the Cl-dependent NHE
    Title: NHE1, NHE2, and NHE4 contribute to regulation of cell pH in T84 colon cancer cells.
Submit: New GeneRIF Correction

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling.
EBI GWAS Catalog
Identification of nine novel loci associated with white blood cell subtypes in a Japanese population.
EBI GWAS Catalog
Newly identified genetic risk variants for celiac disease related to the immune response.
EBI GWAS Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Protein interactions

Protein Gene Interaction Pubs
Nef nef EIPA, a potent and specific inhibitor of Na+/H+ exchanger activity, significantly inhibits the Nef internalization into M2-macrophages, indicating that Nef is imported by Na+/H+ exchanger (solute carrier family 9, subfamily A) PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • DKFZp313B031

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables potassium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sodium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sodium:proton antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables sodium:proton antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sodium:proton antiporter activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within gastric acid secretion IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within glandular epithelial cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in monoatomic cation transport IEA
Inferred from Electronic Annotation
more info
  
involved_in monoatomic ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in monoatomic ion transport TAS
Traceable Author Statement
more info
  
involved_in potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of pH IEA
Inferred from Electronic Annotation
more info
  
involved_in sodium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sodium ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in transepithelial ammonium transport IEA
Inferred from Electronic Annotation
more info
  
involved_in transepithelial ammonium transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in basolateral plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in zymogen granule membrane IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
sodium/hydrogen exchanger 4
Names
NHE-4
Na(+)/H(+) exchanger 4
solute carrier family 9 (sodium/hydrogen exchanger), member 4
solute carrier family 9 member 4
solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001011552.4 → NP_001011552.2  sodium/hydrogen exchanger 4 precursor

    See identical proteins and their annotated locations for NP_001011552.2

    Status: VALIDATED

    Source sequence(s)
    AC007278, AL833048, CR627411, DA442134
    Consensus CDS
    CCDS33264.1
    UniProtKB/Swiss-Prot
    Q69YK0, Q6AI14
    Related
    ENSP00000295269.4, ENST00000295269.5
    Conserved Domains (3) summary
    TIGR00840
    Location:63 → 621
    b_cpa1; sodium/hydrogen exchanger 3
    pfam00999
    Location:73 → 476
    Na_H_Exchanger; Sodium/hydrogen exchanger family
    pfam16644
    Location:569 → 675
    NEXCaM_BD; Regulatory region of Na+/H+ exchanger NHE binds to calmodulin

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    102473226..102533972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511158.2 → XP_011509460.1  sodium/hydrogen exchanger 4 isoform X1

    Conserved Domains (3) summary
    TIGR00840
    Location:63 → 592
    b_cpa1; sodium/hydrogen exchanger 3
    pfam00999
    Location:73 → 447
    Na_H_Exchanger; Sodium/hydrogen exchanger family
    pfam16644
    Location:540 → 646
    NEXCaM_BD; Regulatory region of Na+/H+ exchanger NHE binds to calmodulin

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    102932202..102992943
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341963.1 → XP_054197938.1  sodium/hydrogen exchanger 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6AI14.2 GenPept UniProtKB/Swiss-Prot:Q6AI14

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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