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Aliases for SLC9A9 Gene

Aliases for SLC9A9 Gene

  • Solute Carrier Family 9 Member A9 2 3 5
  • Solute Carrier Family 9, Subfamily A (NHE9, Cation Proton Antiporter 9), Member 9 2 3
  • Na(+)/H(+) Exchanger 9 3 4
  • NHE9 3 4
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Isoform 9 2
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger), Member 9 2
  • Solute Carrier Family 9 (Sodium/Hydrogen Exchanger) 3
  • Putative Protein Product Of Nbla00118 3
  • Solute Carrier Family 9 Member 9 4
  • Sodium/Proton Exchanger NHE9 3
  • Sodium/Hydrogen Exchanger 9 3
  • AUTS16 3
  • NHE-9 4

External Ids for SLC9A9 Gene

Previous GeneCards Identifiers for SLC9A9 Gene

  • GC00U907058
  • GC03M144304
  • GC03M144466
  • GC03M142984
  • GC03M140356

Summaries for SLC9A9 Gene

Entrez Gene Summary for SLC9A9 Gene

  • This gene encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein family. The encoded protein localizes the to the late recycling endosomes and may play an important role in maintaining cation homeostasis. Mutations in this gene are associated with autism susceptibility 16 and attention-deficit/hyperactivity disorder. [provided by RefSeq, Mar 2012]

GeneCards Summary for SLC9A9 Gene

SLC9A9 (Solute Carrier Family 9 Member A9) is a Protein Coding gene. Diseases associated with SLC9A9 include Autism 16 and Attention Deficit-Hyperactivity Disorder. Among its related pathways are Sweet Taste Signaling and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. 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 SLC9A9 Gene

  • May act in electroneutral exchange of protons for Na(+) across membranes. Involved in the effusion of Golgi luminal H(+) in exchange for cytosolic cations. Involved in organelle ion homeostasis by contributing to the maintenance of the unique acidic pH values of the Golgi and post-Golgi compartments in the cell.

Additional gene information for SLC9A9 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC9A9 Gene

Genomics for SLC9A9 Gene

GeneHancer (GH) Regulatory Elements for SLC9A9 Gene

Promoters and enhancers for SLC9A9 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
GH03I143846 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.9 -949 5 PKNOX1 SIN3A BATF ZNF335 SCRT2 RUNX3 JUNB ELF1 ZNF217 ZFP69B SLC9A9 RPS17P10
GH03I143814 Enhancer 0.7 FANTOM5 Ensembl 19.3 +33.6 33632 1 JUNB BATF RUNX3 SPI1 SLC9A9 C3orf58 GC03M143748
GH03I143806 Enhancer 0.5 Ensembl ENCODE 15.3 +41.4 41434 2.2 JUNB SLC9A9 GC03M143748
GH03I143786 Enhancer 0.6 Ensembl ENCODE 11.7 +61.6 61628 0.6 PKNOX1 POLR2A SLC9A9 GC03M143748 GC03M143614
GH03I143775 Enhancer 0.6 Ensembl 11.3 +72.8 72806 0.6 CTCF ZNF654 ZBTB11 ZNF10 FEZF1 ZNF843 RAD21 YY1 OSR2 CTBP1 SLC9A9 GC03M143748 GC03M143614
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC9A9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC9A9 gene promoter:

Genomic Locations for SLC9A9 Gene

Genomic Locations for SLC9A9 Gene
583,311 bases
Minus strand

Genomic View for SLC9A9 Gene

Genes around SLC9A9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC9A9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC9A9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC9A9 Gene

Proteins for SLC9A9 Gene

  • Protein details for SLC9A9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium/hydrogen exchanger 9
    Protein Accession:
    Secondary Accessions:
    • A6NMQ9
    • Q3LIC2
    • Q5JPI6
    • Q5WA58
    • Q8NAB9

    Protein attributes for SLC9A9 Gene

    645 amino acids
    Molecular mass:
    72565 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC04005.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for SLC9A9 Gene

Post-translational modifications for SLC9A9 Gene

  • Glycosylation at isoforms=96
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC9A9 Gene

No data available for DME Specific Peptides for SLC9A9 Gene

Domains & Families for SLC9A9 Gene

Gene Families for SLC9A9 Gene

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

Suggested Antigen Peptide Sequences for SLC9A9 Gene

GenScript: Design optimal peptide antigens:

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 SLC9A9: view

Function for SLC9A9 Gene

Molecular function for SLC9A9 Gene

UniProtKB/Swiss-Prot Function:
May act in electroneutral exchange of protons for Na(+) across membranes. Involved in the effusion of Golgi luminal H(+) in exchange for cytosolic cations. Involved in organelle ion homeostasis by contributing to the maintenance of the unique acidic pH values of the Golgi and post-Golgi compartments in the cell.

Phenotypes From GWAS Catalog for SLC9A9 Gene

Gene Ontology (GO) - Molecular Function for SLC9A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24705354
GO:0015297 antiporter activity IEA --
GO:0015299 solute:proton antiporter activity IEA --
GO:0015385 sodium:proton antiporter activity TAS,IEA --
GO:0015386 potassium:proton antiporter activity IBA --
genes like me logo Genes that share ontologies with SLC9A9: view
genes like me logo Genes that share phenotypes with SLC9A9: view

Animal Model Products

CRISPR Products

miRNA for SLC9A9 Gene

miRTarBase miRNAs that target SLC9A9

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC9A9 Gene

Localization for SLC9A9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC9A9 Gene

Late endosome membrane; Multi-pass membrane protein.

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 SLC9A9 gene
Compartment Confidence
plasma membrane 5
endosome 5
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SLC9A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005886 plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031902 late endosome membrane TAS --
genes like me logo Genes that share ontologies with SLC9A9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC9A9 Gene

Pathways & Interactions for SLC9A9 Gene

genes like me logo Genes that share pathways with SLC9A9: view

Gene Ontology (GO) - Biological Process for SLC9A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport TAS --
GO:0006812 cation transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006885 regulation of pH IEA --
genes like me logo Genes that share ontologies with SLC9A9: view

No data available for SIGNOR curated interactions for SLC9A9 Gene

Drugs & Compounds for SLC9A9 Gene

No Compound Related Data Available

Transcripts for SLC9A9 Gene

Unigene Clusters for SLC9A9 Gene

Solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC9A9 Gene

No ASD Table

Relevant External Links for SLC9A9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC9A9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC9A9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SLC9A9 Gene

This gene is overexpressed in Platelet (27.7) and Peripheral blood mononuclear cells (13.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLC9A9 Gene

Protein tissue co-expression partners for SLC9A9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC9A9 Gene:


SOURCE GeneReport for Unigene cluster for SLC9A9 Gene:


mRNA Expression by UniProt/SwissProt for SLC9A9 Gene:

Tissue specificity: Ubiquitously expressed in all tissues tested. Expressed at highest levels in heart and skeletal muscle, followed by placenta, kidney, and liver. Expressed in the brain, in the medulla and spinal cord.

Evidence on tissue expression from TISSUES for SLC9A9 Gene

  • Lymph node(4.2)
  • Spleen(4.2)
  • Liver(4.1)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with SLC9A9: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC9A9 Gene

Orthologs for SLC9A9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SLC9A9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC9A9 33 34
  • 99.43 (n)
(Canis familiaris)
Mammalia SLC9A9 33 34
  • 91.67 (n)
(Bos Taurus)
Mammalia SLC9A9 33 34
  • 91.56 (n)
(Monodelphis domestica)
Mammalia SLC9A9 34
  • 87 (a)
(Rattus norvegicus)
Mammalia Slc9a9 33
  • 86.49 (n)
(Mus musculus)
Mammalia Slc9a9 33 16 34
  • 86.39 (n)
(Ornithorhynchus anatinus)
Mammalia SLC9A9 34
  • 74 (a)
(Gallus gallus)
Aves SLC9A9 33 34
  • 77.2 (n)
(Anolis carolinensis)
Reptilia SLC9A9 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc9a9 33
  • 73.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nhe3 34
  • 41 (a)
(Caenorhabditis elegans)
Secernentea nhx-5 34
  • 38 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER308C 33
  • 49.24 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NHX1 33 34
  • 48.33 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B01738g 33
  • 47 (n)
(Oryza sativa)
Liliopsida Os.5237 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 54 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00453 33
  • 49.15 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC15A10.06 33
  • 48.96 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11991 33
Species where no ortholog for SLC9A9 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)
  • zebrafish (Danio rerio)

Evolution for SLC9A9 Gene

Gene Tree for SLC9A9 (if available)
Gene Tree for SLC9A9 (if available)

Paralogs for SLC9A9 Gene

Paralogs for SLC9A9 Gene

(3) SIMAP similar genes for SLC9A9 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SLC9A9: view

Variants for SLC9A9 Gene

Sequence variations from dbSNP and Humsavar for SLC9A9 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs121912597 risk-factor, Autism 16 143,493,701(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs111291437 likely-benign, not specified 143,382,098(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1057518347 uncertain-significance, not specified 143,552,369(-) G/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1085307858 uncertain-significance, not specified 143,266,898(-) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs886043034 uncertain-significance, not specified 143,693,301(-) AA/A coding_sequence_variant, frameshift, genic_upstream_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC9A9 Gene

Variant ID Type Subtype PubMed ID
esv1190500 CNV deletion 17803354
esv1621744 CNV deletion 17803354
esv1701091 CNV deletion 17803354
esv2653887 CNV deletion 19546169
esv2661107 CNV deletion 23128226
esv2661666 CNV deletion 23128226
esv27203 CNV loss 19812545
esv2750736 CNV loss 17666407
esv2759184 CNV loss 17122850
esv32611 CNV gain 17666407
esv3309904 CNV mobile element insertion 20981092
esv33993 CNV loss 17666407
esv3451148 CNV insertion 20981092
esv3569031 CNV loss 25503493
esv3569033 CNV loss 25503493
esv3575616 CNV gain 25503493
esv3598018 CNV loss 21293372
esv3598020 CNV loss 21293372
esv3598021 CNV loss 21293372
esv3598022 CNV loss 21293372
esv3598024 CNV gain 21293372
esv3598027 CNV loss 21293372
nsv1011088 CNV gain 25217958
nsv1012559 CNV gain 25217958
nsv10334 CNV loss 18304495
nsv1073254 CNV deletion 25765185
nsv1139163 CNV deletion 24896259
nsv1139164 CNV deletion 24896259
nsv1139165 CNV deletion 24896259
nsv1145005 CNV deletion 24896259
nsv4041 CNV insertion 18451855
nsv473075 CNV novel sequence insertion 20440878
nsv476489 CNV novel sequence insertion 20440878
nsv477138 CNV novel sequence insertion 20440878
nsv511204 CNV loss 21212237
nsv513082 CNV loss 21212237
nsv513083 CNV loss 21212237
nsv518873 CNV loss 19592680
nsv520125 CNV loss 19592680
nsv523529 CNV loss 19592680
nsv822273 CNV loss 20364138
nsv829745 CNV gain 17160897
nsv956805 CNV deletion 24416366
nsv965219 CNV duplication 23825009
nsv979886 CNV duplication 23825009
nsv999000 CNV loss 25217958

Variation tolerance for SLC9A9 Gene

Residual Variation Intolerance Score: 26.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.37; 53.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC9A9 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 SLC9A9 Gene

Disorders for SLC9A9 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SLC9A9 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autism 16
  • autism, susceptibility to, 16
attention deficit-hyperactivity disorder
  • adhd
christianson syndrome
  • mental retardation, microcephaly, epilepsy, and ataxia syndrome
pervasive developmental disorder
  • pervasive development disorder
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards


  • Autism 16 (AUTS16) [MIM:613410]: A complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation. AUTS16 can be associated with epilepsy. {ECO:0000269 PubMed:18621663}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving SLC9A9 has been found in a family with early-onset behavioral/developmental disorder with features of attention deficit-hyperactivity disorder and intellectual disability. Inversion inv(3)(p14:q21). The inversion disrupts DOCK3 and SLC9A9.

Additional Disease Information for SLC9A9

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 SLC9A9: view

No data available for Genatlas for SLC9A9 Gene

Publications for SLC9A9 Gene

  1. Disruption of a novel member of a sodium/hydrogen exchanger family and DOCK3 is associated with an attention deficit hyperactivity disorder-like phenotype. (PMID: 14569117) de Silva MG … Forrest S (Journal of medical genetics 2003) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Genetic variants in SLC9A9 are associated with measures of attention-deficit/hyperactivity disorder symptoms in families. (PMID: 20032819) Markunas CA … Ashley-Koch AE (Psychiatric genetics 2010) 3 44 58
  4. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PMID: 20708005) Chalasani N … Nonalcoholic Steatohepatitis Clinical Research Network (Gastroenterology 2010) 3 44 58
  5. Family-based genome-wide association scan of attention-deficit/hyperactivity disorder. (PMID: 20732626) Mick E … Faraone SV (Journal of the American Academy of Child and Adolescent Psychiatry 2010) 3 44 58

Products for SLC9A9 Gene

Sources for SLC9A9 Gene

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