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

    Gene ID: 389015, updated on 10-Dec-2024

    Summary

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    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, Dec 2024]
    Expression
    Biased expression in stomach (RPKM 24.9) and kidney (RPKM 5.2) See more
    Orthologs
    mouse all
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    Genomic context

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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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    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

    Phenotypes

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    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp313B031

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables sodium:proton antiporter activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in gastric acid secretion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glandular epithelial cell development 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 sodium ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transepithelial ammonium transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in apical plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in zymogen granule membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    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

    NCBI Reference Sequences (RefSeq)

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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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