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Aliases for SLC9A6 Gene

Aliases for SLC9A6 Gene

  • Solute Carrier Family 9 Member A6 2 3 5
  • Solute Carrier Family 9, Subfamily A (NHE6, Cation Proton Antiporter 6), Member 6 2 3
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Member 6 2 3
  • Na(+)/H(+) Exchanger 6 3 4
  • NHE6 3 4
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Isoform 6 2
  • Solute Carrier Family 9 Member 6 4
  • Sodium/Hydrogen Exchanger 6 3
  • KIAA0267 4
  • NHE-6 4
  • MRSA 3

External Ids for SLC9A6 Gene

Previous GeneCards Identifiers for SLC9A6 Gene

  • GC0XM129708
  • GC0XP131913
  • GC0XP133012
  • GC0XP133773
  • GC0XP134793
  • GC0XP134895
  • GC0XP135068
  • GC0XP124341

Summaries for SLC9A6 Gene

Entrez Gene Summary for SLC9A6 Gene

  • 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]

GeneCards Summary for SLC9A6 Gene

SLC9A6 (Solute Carrier Family 9 Member A6) is a Protein Coding gene. Diseases associated with SLC9A6 include Mental Retardation, X-Linked, Syndromic, Christianson Type and Christianson Syndrome. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and ADP signalling through P2Y purinoceptor 12. Gene Ontology (GO) annotations related to this gene include solute:proton antiporter activity and sodium:proton antiporter activity. An important paralog of this gene is SLC9A7.

UniProtKB/Swiss-Prot for SLC9A6 Gene

  • Electroneutral exchange of protons for Na(+) and K(+) across the early and recycling endosome membranes. Contributes to calcium homeostasis.

Gene Wiki entry for SLC9A6 Gene

Additional gene information for SLC9A6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC9A6 Gene

Genomics for SLC9A6 Gene

GeneHancer (GH) Regulatory Elements for SLC9A6 Gene

Promoters and enhancers for SLC9A6 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ135972 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 0.0 -9 2.6 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B E2F8 ZNF143 SP3 NFYC MMGT1 SLC9A6 CT45A1 GC0XM135957
GH0XJ135984 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.4 +11.8 11795 2.7 PKNOX1 RB1 ARID4B SIN3A FEZF1 ZNF2 ZNF335 SCRT2 ZNF143 ZFP91 SLC9A6 LOC100420958 MAP7D3 MMGT1 GAPDHP67
GH0XJ136012 Promoter 0.5 EPDnew 662.4 +38.8 38810 0.1 SLC9A6 MMGT1 GAPDHP67
GH0XJ136210 Enhancer 0.8 Ensembl ENCODE dbSUPER 11.8 +236.8 236785 0.9 ZFP69B ZNF692 GLIS1 PIR34436 MAP7D3 SLC9A6 PIR45658 FHL1
GH0XJ136046 Enhancer 0.9 ENCODE 0.2 +73.7 73708 1.9 PKNOX1 ARNT ZSCAN4 INSM2 KLF17 MZF1 FEZF1 ZNF2 ZNF213 ZNF366 MMGT1 FHL1 MAP7D3 GAPDHP67 SLC9A6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC9A6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC9A6 gene promoter:
  • POU6F1 (c2)
  • AREB6
  • c-Ets-1
  • HNF-3beta
  • Gfi-1
  • STAT3
  • aMEF-2
  • MEF-2A
  • LCR-F1
  • MZF-1

Genomic Locations for SLC9A6 Gene

Genomic Locations for SLC9A6 Gene
73,429 bases
Plus strand
61,846 bases
Plus strand

Genomic View for SLC9A6 Gene

Genes around SLC9A6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC9A6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC9A6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC9A6 Gene

Proteins for SLC9A6 Gene

  • Protein details for SLC9A6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium/hydrogen exchanger 6
    Protein Accession:
    Secondary Accessions:
    • A6NIQ9
    • A8K160
    • B4DU30
    • B7ZAE0
    • Q3ZCW7
    • Q5JPP8
    • Q5JPP9
    • Q86VS0

    Protein attributes for SLC9A6 Gene

    669 amino acids
    Molecular mass:
    74162 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC9A6 Gene


neXtProt entry for SLC9A6 Gene

Post-translational modifications for SLC9A6 Gene

  • Glycosylation at posLast=128128
  • Ubiquitination at posLast=443443
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC9A6 Gene

Domains & Families for SLC9A6 Gene

Gene Families for SLC9A6 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family.
  • Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family.
genes like me logo Genes that share domains with SLC9A6: view

Function for SLC9A6 Gene

Molecular function for SLC9A6 Gene

UniProtKB/Swiss-Prot Function:
Electroneutral exchange of protons for Na(+) and K(+) across the early and recycling endosome membranes. Contributes to calcium homeostasis.
GENATLAS Biochemistry:
solute carrier protein family 9 (sodium/hydrogen exchange),member 6,ubiquitously expressed but most abundant in brain,skeletal muscle,heart,located in the mitochondrial inner membrane

Phenotypes From GWAS Catalog for SLC9A6 Gene

Gene Ontology (GO) - Molecular Function for SLC9A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015297 antiporter activity IEA --
GO:0015299 solute:proton antiporter activity IEA --
GO:0015385 sodium:proton antiporter activity TAS,IBA --
GO:0015386 potassium:proton antiporter activity IBA --
genes like me logo Genes that share ontologies with SLC9A6: view
genes like me logo Genes that share phenotypes with SLC9A6: view

Human Phenotype Ontology for SLC9A6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC9A6 Gene

MGI Knock Outs for SLC9A6:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC9A6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC9A6 Gene

Localization for SLC9A6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC9A6 Gene

Endosome membrane; Multi-pass membrane protein. Note=Is present in the recycling compartments including early and recycling endosomes, and only appears transiently on the plasma membrane.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC9A6 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
endosome 5
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC9A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 NOT mitochondrion IDA 11940519
GO:0005769 early endosome IEA --
GO:0005770 late endosome IEA --
GO:0005789 endoplasmic reticulum membrane IDA 11641397
GO:0005886 plasma membrane IDA,IEA 11940519
genes like me logo Genes that share ontologies with SLC9A6: view

Pathways & Interactions for SLC9A6 Gene

genes like me logo Genes that share pathways with SLC9A6: view

Gene Ontology (GO) - Biological Process for SLC9A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport TAS --
GO:0006812 cation transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006885 regulation of pH IEA --
GO:0031547 brain-derived neurotrophic factor receptor signaling pathway IEA --
genes like me logo Genes that share ontologies with SLC9A6: view

No data available for SIGNOR curated interactions for SLC9A6 Gene

Drugs & Compounds for SLC9A6 Gene

(4) Drugs for SLC9A6 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
2,3-Didehydroalanine Experimental Pharma Target 0
2-Thioethenamine Experimental Pharma Target 0
alpha-aminobutyric acid Experimental Pharma Target 0
genes like me logo Genes that share compounds with SLC9A6: view

Transcripts for SLC9A6 Gene

mRNA/cDNA for SLC9A6 Gene

Unigene Clusters for SLC9A6 Gene

Solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC9A6 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11
SP1: -
SP2: -
SP3: -
SP4: -

Relevant External Links for SLC9A6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC9A6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC9A6 Gene

mRNA differential expression in normal tissues according to GTEx for SLC9A6 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.3) and Brain - Anterior cingulate cortex (BA24) (x4.0).

Protein differential expression in normal tissues from HIPED for SLC9A6 Gene

This gene is overexpressed in Frontal cortex (25.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC9A6 Gene

Protein tissue co-expression partners for SLC9A6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC9A6 Gene:


SOURCE GeneReport for Unigene cluster for SLC9A6 Gene:


mRNA Expression by UniProt/SwissProt for SLC9A6 Gene:

Tissue specificity: Ubiquitous; but is most abundant in mitochondrion-rich tissues such as brain, skeletal muscle and heart.

Evidence on tissue expression from TISSUES for SLC9A6 Gene

  • Nervous system(4.9)
  • Bone marrow(4.1)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC9A6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • pharynx
  • salivary gland
  • skull
  • tooth
  • chest wall
  • esophagus
  • heart
  • rib
  • rib cage
  • sternum
  • intestine
  • large intestine
  • small intestine
  • stomach
  • prostate
  • urinary bladder
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with SLC9A6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for SLC9A6 Gene

Orthologs for SLC9A6 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC9A6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC9A6 34 33
  • 99.87 (n)
(Bos Taurus)
Mammalia SLC9A6 34 33
  • 93.2 (n)
(Canis familiaris)
Mammalia SLC9A6 34 33
  • 92.34 (n)
(Mus musculus)
Mammalia Slc9a6 16 34 33
  • 90.94 (n)
(Rattus norvegicus)
Mammalia Slc9a6 33
  • 89.57 (n)
(Monodelphis domestica)
Mammalia SLC9A6 34
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia SLC9A6 34
  • 83 (a)
(Gallus gallus)
Aves SLC9A6 34 33
  • 79.76 (n)
(Anolis carolinensis)
Reptilia SLC9A6 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc9a6 33
  • 77.22 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.31047 33
(Danio rerio)
Actinopterygii slc9a6a 34 33
  • 71.29 (n)
slc9a6b 34
  • 71 (a)
fruit fly
(Drosophila melanogaster)
Insecta Nhe3 34 35 33
  • 56.85 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008718 33
  • 55.15 (n)
(Caenorhabditis elegans)
Secernentea nhx-5 34 33
  • 51.06 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHX1 36 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 57 (a)
Species where no ortholog for SLC9A6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC9A6 Gene

Gene Tree for SLC9A6 (if available)
Gene Tree for SLC9A6 (if available)
Evolutionary constrained regions (ECRs) for SLC9A6: view image

Paralogs for SLC9A6 Gene

Paralogs for SLC9A6 Gene

(3) SIMAP similar genes for SLC9A6 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SLC9A6: view

Variants for SLC9A6 Gene

Sequence variations from dbSNP and Humsavar for SLC9A6 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057519394 pathogenic, Christianson syndrome 136,002,195(+) TT/T coding_sequence_variant, frameshift
rs1060502675 uncertain-significance, Christianson syndrome 135,994,822(+) A/G coding_sequence_variant, missense_variant
rs1060504684 likely-benign, Christianson syndrome 136,016,637(+) C/G/T intron_variant
rs1060504685 likely-benign, Christianson syndrome 135,998,934(+) A/G coding_sequence_variant, synonymous_variant
rs1060504686 likely-benign, Christianson syndrome 136,013,023(+) C/G coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC9A6 Gene

Variant ID Type Subtype PubMed ID
esv2758895 CNV gain+loss 17122850
dgv2475e212 CNV loss 25503493

Variation tolerance for SLC9A6 Gene

Residual Variation Intolerance Score: 6.66% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.41; 9.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC9A6 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC9A6 Gene

Disorders for SLC9A6 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SLC9A6 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked, syndromic, christianson type
  • mrxsch
christianson syndrome
  • mental retardation, x-linked, syndromic, christianson type
angelman syndrome
  • as
pitt-hopkins syndrome
  • phs
scapuloperoneal myopathy
- elite association - COSMIC cancer census association via MalaCards


  • Mental retardation, X-linked, syndromic, Christianson type (MRXSCH) [MIM:300243]: A syndrome characterized by profound mental retardation, epilepsy, ataxia, and microcephaly. It shows phenotypic overlap with Angelman syndrome. {ECO:0000269 PubMed:18342287, ECO:0000269 PubMed:24123876}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC9A6

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC9A6: view

No data available for Genatlas for SLC9A6 Gene

Publications for SLC9A6 Gene

  1. SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome. (PMID: 18342287) Gilfillan GD … Strømme P (American journal of human genetics 2008) 3 4 22 58
  2. Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria. (PMID: 11940519) Brett CL … Rao R (American journal of physiology. Cell physiology 2002) 3 4 22 58
  3. Identification of a mitochondrial Na+/H+ exchanger. (PMID: 9507001) Numata M … Orlowski J (The Journal of biological chemistry 1998) 2 3 4 58
  4. Mutation in the SLC9A6 gene is not a frequent cause of sporadic Angelman-like syndrome. (PMID: 19471312) Fichou Y … Bienvenu T (European journal of human genetics : EJHG 2009) 3 44 58
  5. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 3 4 58

Products for SLC9A6 Gene

Sources for SLC9A6 Gene

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