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

Gene ID: 10479, updated on 21-Apr-2019

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
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
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

Genomic context

See SLC9A6 in Genome Data Viewer
Location:
Xq26.3
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (135974596..136047269)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (135067583..135129428)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene cancer/testis antigen family 45 member A11, pseudogene Neighboring gene membrane magnesium transporter 1 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 67 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 FunctionsWhat'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 (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0267

Gene Ontology Provided by GOA

Process Evidence Code Pubs
axon extension IDA
Inferred from Direct Assay
more info
PubMed 
brain-derived neurotrophic factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
dendrite extension IDA
Inferred from Direct Assay
more info
PubMed 
dendritic spine development IEA
Inferred from Electronic Annotation
more info
 
ion transport TAS
Traceable Author Statement
more info
 
neuron projection morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
regulation of neurotrophin TRK receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
synapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axon terminus IEA
Inferred from Electronic Annotation
more info
 
axonal spine IEA
Inferred from Electronic Annotation
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome IEA
Inferred from Electronic Annotation
more info
 
NOT mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
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)

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_017160.1 RefSeqGene

    Range
    5001..66843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042537.1NP_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
    Q92581
    Related
    ENSP00000359729.4, ENST00000370695.7
    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_001177651.1NP_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, DC308430, R15803
    Consensus CDS
    CCDS55504.1
    UniProtKB/Swiss-Prot
    Q92581
    Related
    ENSP00000359735.1, ENST00000370701.6
    Conserved Domains (1) summary
    pfam00999
    Location:124481
    Na_H_Exchanger; Sodium/hydrogen exchanger family
  3. NM_001330652.1NP_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
    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_006359.2NP_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/Swiss-Prot
    Q92581
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    135974596..136047269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029223.2XP_016884712.1  sodium/hydrogen exchanger 6 isoform X1

    UniProtKB/Swiss-Prot
    Q92581
    Related
    ENSP00000490406.1, ENST00000636092.1
    Conserved Domains (1) summary
    pfam00999
    Location:124481
    Na_H_Exchanger; Sodium/hydrogen exchanger family
  2. XM_017029224.1XP_016884713.1  sodium/hydrogen exchanger 6 isoform X1

    UniProtKB/Swiss-Prot
    Q92581
    Related
    ENSP00000490731.1, ENST00000637581.1
    Conserved Domains (1) summary
    pfam00999
    Location:124481
    Na_H_Exchanger; Sodium/hydrogen exchanger family
  3. XM_006724726.3XP_006724789.1  sodium/hydrogen exchanger 6 isoform X1

    See identical proteins and their annotated locations for XP_006724789.1

    UniProtKB/Swiss-Prot
    Q92581
    Conserved Domains (1) summary
    pfam00999
    Location:124481
    Na_H_Exchanger; Sodium/hydrogen exchanger family
  4. XM_017029225.1XP_016884714.1  sodium/hydrogen exchanger 6 isoform X2

    UniProtKB/TrEMBL
    A0A1B0GV11
    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]
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