U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    SLC9A6 solute carrier family 9 member A6 [ Homo sapiens (human) ]

    Gene ID: 10479, updated on 4-Dec-2023

    Summary

    Official Symbol
    SLC9A6provided by HGNC
    Official Full Name
    solute carrier family 9 member A6provided by HGNC
    Primary source
    HGNC:HGNC:11079
    See related
    Ensembl:ENSG00000198689 MIM:300231; AllianceGenome:HGNC:11079
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MRSA; NHE6; MRXSCH
    Summary
    This gene encodes a sodium-hydrogen exchanger that is amember of the solute carrier family 9. The encoded protein localizes to early and recycling endosomes and may be involved in regulating endosomal pH and volume. Defects in this gene are associated with X-linked syndromic cognitive disability, Christianson type. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
    Expression
    Ubiquitous expression in brain (RPKM 26.2), adrenal (RPKM 4.9) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC9A6 in Genome Data Viewer
    Location:
    Xq26.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (135973837..136047269)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (134282570..134355980)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (135055996..135129428)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:134987035-134988234 Neighboring gene sarcoma antigen 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:135014477-135014713 Neighboring gene cancer/testis antigen family 45 member A11, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21024 Neighboring gene membrane magnesium transporter 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29988 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 67 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:135179522-135180721 Neighboring gene E2F transcription factor 6 pseudogene 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Christianson syndrome
    MedGen: C2678194 OMIM: 300243 GeneReviews: Christianson Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-12-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-12-08)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of solute carrier family 9 (sodium/hydrogen exchanger), member 6 (SLC9A6) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0267

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables potassium:proton antiporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sodium:proton antiporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables sodium:proton antiporter activity TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    NOT located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in recycling endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sodium/hydrogen exchanger 6
    Names
    Na(+)/H(+) exchanger 6
    solute carrier family 9 (sodium/hydrogen exchanger), member 6
    solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_017160.2 RefSeqGene

      Range
      16600..78434
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001042537.2NP_001036002.1  sodium/hydrogen exchanger 6 isoform a precursor

      See identical proteins and their annotated locations for NP_001036002.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AF030409, BC035029, DB483081, R15803
      Consensus CDS
      CCDS44003.1
      UniProtKB/Swiss-Prot
      A6NIQ9, A8K160, B4DU30, B7ZAE0, Q3ZCW7, Q5JPP8, Q5JPP9, Q86VS0, Q8WYK8, Q92581
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000359729.4, ENST00000370695.8
      Conserved Domains (1) summary
      cl25615
      Location:93583
      NhaP2; NhaP-type Na+/H+ and K+/H+ antiporter with C-terminal TrkAC and CorC domains [Energy production and conversion, Inorganic ion transport and metabolism]
    2. NM_001177651.2NP_001171122.1  sodium/hydrogen exchanger 6 isoform c

      See identical proteins and their annotated locations for NP_001171122.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AK300475, AL732579, R15803
      Consensus CDS
      CCDS55504.1
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000359735.1, ENST00000370701.6
      Conserved Domains (1) summary
      pfam00999
      Location:124481
      Na_H_Exchanger; Sodium/hydrogen exchanger family
    3. NM_001330652.2NP_001317581.1  sodium/hydrogen exchanger 6 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS83492.1
      UniProtKB/TrEMBL
      A0A1B0GV11, B4DK83
      Related
      ENSP00000490330.1, ENST00000637195.1
      Conserved Domains (1) summary
      cl25615
      Location:41499
      NhaP2; NhaP-type Na+/H+ and K+/H+ antiporter with C-terminal TrkAC and CorC domains [Energy production and conversion, Inorganic ion transport and metabolism]
    4. NM_001379110.1NP_001366039.1  sodium/hydrogen exchanger 6 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS94676.1
      UniProtKB/TrEMBL
      A0A0D9SGH0, B4DK83
      Related
      ENSP00000487486.2, ENST00000630721.3
      Conserved Domains (1) summary
      TIGR00840
      Location:41487
      b_cpa1; sodium/hydrogen exchanger 3
    5. NM_001400909.1NP_001387838.1  sodium/hydrogen exchanger 6 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS55504.1
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000490648.1, ENST00000636347.1
    6. NM_001400910.1NP_001387839.1  sodium/hydrogen exchanger 6 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS55504.1
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000490406.1, ENST00000636092.1
    7. NM_001400911.1NP_001387840.1  sodium/hydrogen exchanger 6 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS55504.1
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000490731.1, ENST00000637581.1
    8. NM_001400912.1NP_001387841.1  sodium/hydrogen exchanger 6 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS55504.1
      UniProtKB/TrEMBL
      B4DK83
    9. NM_001400913.1NP_001387842.1  sodium/hydrogen exchanger 6 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL732579
      Consensus CDS
      CCDS83492.1
      UniProtKB/TrEMBL
      A0A1B0GV11, B4DK83
    10. NM_006359.3NP_006350.1  sodium/hydrogen exchanger 6 isoform b precursor

      See identical proteins and their annotated locations for NP_006350.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AF030409, BC035029, BC049169, DB483081, R15803
      Consensus CDS
      CCDS14654.1
      UniProtKB/TrEMBL
      B4DK83
      Related
      ENSP00000359732.3, ENST00000370698.7
      Conserved Domains (1) summary
      cl25615
      Location:93551
      NhaP2; NhaP-type Na+/H+ and K+/H+ antiporter with C-terminal TrkAC and CorC domains [Energy production and conversion, Inorganic ion transport and metabolism]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      135973837..136047269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441765.1XP_047297721.1  sodium/hydrogen exchanger 6 isoform X1

      UniProtKB/TrEMBL
      A0A7I2V2B0, B4DK83
      Related
      ENSP00000502845.1, ENST00000678163.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      134282570..134355980
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326369.1XP_054182344.1  sodium/hydrogen exchanger 6 isoform X1

      UniProtKB/TrEMBL
      A0A7I2V2B0, B4DK83