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

Summary

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

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_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

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.
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.
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.
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.
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.
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.
demonstrate that the SLC9A6 mutation attenuates synapse density
Title: A Christianson syndrome-linked deletion mutation (Δ287ES288) in SLC9A6 impairs hippocampal neuronal plasticity.
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.
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.
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)

Endonuclease-mediated (5) 1 citation
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Slc9a6 (e-PCR), detects polymorphism
- UniSTS:547139

Slc9a6 (e-PCR), detects polymorphism
- UniSTS:496017

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 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
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)

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

Status: VALIDATED

Source sequence(s)

AC048362, AL672085
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

NC_000086.8 Reference GRCm39 C57BL/6J

Range

55654921..55709590

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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