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Slc9a6 solute carrier family 9 (sodium/hydrogen exchanger), member 6 [ Mus musculus (house mouse) ]

Gene ID: 236794, updated on 2-Nov-2024

Summary

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Official Symbol
Slc9a6provided by MGI
Official Full Name
solute carrier family 9 (sodium/hydrogen exchanger), member 6provided by MGI
Primary source
MGI:MGI:2443511
See related
Ensembl:ENSMUSG00000060681 AllianceGenome:MGI:2443511
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
NHE6; NHE-6; mKIAA0267; 3732426M05; 6430520C02Rik
Summary
Enables potassium:proton antiporter activity and sodium:proton antiporter activity. Involved in regulation of intracellular pH and regulation of postsynaptic membrane neurotransmitter receptor levels. Acts upstream of or within several processes, including brain-derived neurotrophic factor receptor signaling pathway; dendritic spine development; and regulation of neurotrophin TRK receptor signaling pathway. Located in several cellular components, including axon; dendrite; and endosome. Is active in Schaffer collateral - CA1 synapse and glutamatergic synapse. Is expressed in several structures, including central nervous system; eye; genitourinary system; gut; and immune system. Used to study Christianson syndrome. Human ortholog(s) of this gene implicated in Christianson syndrome. Orthologous to human SLC9A6 (solute carrier family 9 member A6). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in CNS E18 (RPKM 21.8), placenta adult (RPKM 16.0) and 26 other tissues See more
Orthologs
human all
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Genomic context

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See Slc9a6 in Genome Data Viewer
Location:
X A5- A6; X 30.06 cM
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (55654921..55709590)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (56609556..56664230)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene microRNA 5116 Neighboring gene membrane magnesium transporter 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chrX:53851179-53851288 Neighboring gene predicted gene, 36239 Neighboring gene predicted gene, 39515 Neighboring gene 39S ribosomal protein L30, mitochondrial pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GGA1 interacts with the endosomal Na+/H+ exchanger NHE6 governing localization to the endosome compartment.
    Title: GGA1 interacts with the endosomal Na+/H+ exchanger NHE6 governing localization to the endosome compartment.
  2. A novel peptide encoded by circ-SLC9A6 promotes lipid dyshomeostasis through the regulation of H4K16ac-mediated CD36 transcription in NAFLD.
    Title: A novel peptide encoded by circ-SLC9A6 promotes lipid dyshomeostasis through the regulation of H4K16ac-mediated CD36 transcription in NAFLD.
  3. Loss of Christianson Syndrome Na(+)/H(+) Exchanger 6 (NHE6) Causes Abnormal Endosome Maturation and Trafficking Underlying Lysosome Dysfunction in Neurons.
    Title: Loss of Christianson Syndrome Na(+)/H(+) Exchanger 6 (NHE6) Causes Abnormal Endosome Maturation and Trafficking Underlying Lysosome Dysfunction in Neurons.
  4. NHE6 depletion corrects ApoE4-mediated synaptic impairments and reduces amyloid plaque load.
    Title: NHE6 depletion corrects ApoE4-mediated synaptic impairments and reduces amyloid plaque load.
  5. Deletion of the sodium/hydrogen exchanger 6 causes low bone volume in adult mice.
    Title: Deletion of the sodium/hydrogen exchanger 6 causes low bone volume in adult mice.
  6. Sodium-hydrogen exchanger 6 (NHE6) deficiency leads to hearing loss, via reduced endosomal signalling through the BDNF/Trk pathway.
    Title: Sodium-hydrogen exchanger 6 (NHE6) deficiency leads to hearing loss, via reduced endosomal signalling through the BDNF/Trk pathway.
  7. demonstrate that the SLC9A6 mutation attenuates synapse density
    Title: A Christianson syndrome-linked deletion mutation (Δ287ES288) in SLC9A6 impairs hippocampal neuronal plasticity.
  8. NHE6 and ClC-7 are both expressed in the choroid plexus epithelial cells, and are potentially involved in pH regulation of the CSF.
    Title: The murine choroid plexus epithelium expresses the 2Cl(-)/H(+) exchanger ClC-7 and Na(+)/H(+) exchanger NHE6 in the luminal membrane domain.
  9. analysis of the heterozygous Slc9a6 KO female mice model of X-linked Christianson syndrome
    Title: X-linked Christianson syndrome: heterozygous female Slc9a6 knockout mice develop mosaic neuropathological changes and related behavioral abnormalities.
  10. deletion of (370)Trp-Ser-Thr(372) leads to endoplasmic reticulum retention and loss of NHE6 function
    Title: Impaired posttranslational processing and trafficking of an endosomal Na+/H+ exchanger NHE6 mutant (Δ(370)WST(372)) associated with X-linked intellectual disability and autism.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables potassium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables potassium:proton antiporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables sodium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sodium:proton antiporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within axon extension ISO
Inferred from Sequence Orthology
more info
 PubMed 
acts_upstream_of_or_within brain-derived neurotrophic factor receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within dendrite extension ISO
Inferred from Sequence Orthology
more info
 PubMed 
acts_upstream_of_or_within dendritic spine development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment of cell polarity ISO
Inferred from Sequence Orthology
more info
  
involved_in establishment of cell polarity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in glial cell activation IEA
Inferred from Electronic Annotation
more info
  
involved_in glial cell activation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neuron projection morphogenesis ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in potassium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within proton transmembrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of intracellular pH IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of intracellular pH ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of neurotrophin TRK receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels EXP
Inferred from Experiment
more info
 PubMed 
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of synaptic vesicle lumen acidification 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 transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within synapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Schaffer collateral - CA1 synapse EXP
Inferred from Experiment
more info
 PubMed 
is_active_in Schaffer collateral - CA1 synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in Schaffer collateral - CA1 synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in axon terminus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in axonal spine IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendrite IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in early endosome membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse EXP
Inferred from Experiment
more info
 PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion HDA 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 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in recycling endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in recycling endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in recycling endosome membrane ISO
Inferred from Sequence Orthology
more info
  
located_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
sodium/hydrogen exchanger 6
Names
Na(+)/H(+) exchanger 6
sodium/hydrogen exchanger
solute carrier family 9 member 6

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_001358861.1 → NP_001345790.1  sodium/hydrogen exchanger 6 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC048362, AL672085
    UniProtKB/TrEMBL
    Q80U52
    Conserved Domains (1) summary
    TIGR00840
    Location:41 → 531
    b_cpa1; sodium/hydrogen exchanger 3

  2. NM_001419589.1 → NP_001406518.1  sodium/hydrogen exchanger 6 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC048362, AL672085

  3. NM_172780.5 → NP_766368.2  sodium/hydrogen exchanger 6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_766368.2

    Status: VALIDATED

    Source sequence(s)
    AC048362, AL672085
    Consensus CDS
    CCDS40979.1
    UniProtKB/Swiss-Prot
    A1L3P4, Q8BTG0
    UniProtKB/TrEMBL
    Q80U52
    Related
    ENSMUSP00000076922.6, ENSMUST00000077741.12
    Conserved Domains (1) summary
    TIGR00840
    Location:94 → 584
    b_cpa1; sodium/hydrogen exchanger 3

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000086.8 Reference GRCm39 C57BL/6J

    Range
    55654921..55709590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006527980.4 → XP_006528043.1  sodium/hydrogen exchanger 6 isoform X1

    See identical proteins and their annotated locations for XP_006528043.1

    UniProtKB/TrEMBL
    Q80U52
    Conserved Domains (1) summary
    TIGR00840
    Location:41 → 531
    b_cpa1; sodium/hydrogen exchanger 3

  2. XM_036161923.1 → XP_036017816.1  sodium/hydrogen exchanger 6 isoform X2

    UniProtKB/TrEMBL
    Q80U52
    Conserved Domains (1) summary
    TIGR00840
    Location:94 → 540
    b_cpa1; sodium/hydrogen exchanger 3
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A1L3P4.1 GenPept UniProtKB/Swiss-Prot:A1L3P4

Gene LinkOut

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