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Aliases for SLC12A9 Gene

Aliases for SLC12A9 Gene

  • Solute Carrier Family 12 Member 9 2 3 3 5
  • Cation-Chloride Cotransporter-Interacting Protein 1 3 4
  • Potassium-Chloride Transporter 9 3 4
  • Cation-Chloride Cotransporter 6 3 4
  • CCC-Interacting Protein 1 3 4
  • WO3.3 3 4
  • HCCC6 3 4
  • CCC6 3 4
  • CIP1 3 4
  • Solute Carrier Family 12 (Potassium/Chloride Transporters), Member 9 3
  • Cation-Chloride Cotransporter-Interacting Protein 2
  • HCIP1 4

External Ids for SLC12A9 Gene

Previous GeneCards Identifiers for SLC12A9 Gene

  • GC07P100047
  • GC07P100061
  • GC07P100095
  • GC07P100290
  • GC07P100424
  • GC07P095080

Summaries for SLC12A9 Gene

GeneCards Summary for SLC12A9 Gene

SLC12A9 (Solute Carrier Family 12 Member 9) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include cation:chloride symporter activity. An important paralog of this gene is SLC12A1.

UniProtKB/Swiss-Prot for SLC12A9 Gene

  • May be an inhibitor of SLC12A1. Seems to correspond to a subunit of a multimeric transport system and thus, additional subunits may be required for its function.

Gene Wiki entry for SLC12A9 Gene

Additional gene information for SLC12A9 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC12A9 Gene

Genomics for SLC12A9 Gene

GeneHancer (GH) Regulatory Elements for SLC12A9 Gene

Promoters and enhancers for SLC12A9 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
GH07J100823 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 655 +0.3 296 6.7 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 EPHB4 SLC12A9 ZNF3 TRIM4 GIGYF1 SRRT STAG3L5P ENSG00000242798 PPP1R35 PILRB
GH07J100851 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 655.1 +25.9 25948 1.9 HDGF CLOCK ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 ZNF213 SLC12A9 SLC12A9-AS1 GIGYF1 TRIM4 SRRT PPP1R35 ZNF3 AP4M1 ENSG00000242798 MEPCE
GH07J100873 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 15.4 +48.5 48486 2.9 CLOCK MLX DMAP1 YY1 E2F8 ZNF143 SP3 NFYC ZC3H11A MEF2D SRRT PIR40651 TRIM4 ZNF3 GIGYF1 PPP1R35 STAG3L5P PCOLCE PILRB ENSG00000242798
GH07J100894 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 14.1 +69.6 69587 4.6 HDGF PKNOX1 ARID4B SIN3A ZNF2 ZBTB7B ZNF143 SP3 REST ZNF592 ACHE MOSPD3 ENSG00000242798 PPP1R35 SRRT MEPCE SLC12A9 MUC3A TRIP6 ZNF3
GH07J100886 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 14.8 +62.5 62508 5.2 CLOCK DMAP1 E2F8 ZNF143 ZNF263 SP3 MEF2D GLIS1 NBN NR2C1 GC07M100887 UFSP1 TRIM4 SRRT GIGYF1 PPP1R35 ZNF3 ENSG00000242798 AP4M1 STAG3L5P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC12A9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC12A9 gene promoter:
  • AP-1
  • STAT1
  • p53
  • c-Jun
  • c-Fos
  • NF-kappaB
  • NF-kappaB1

Genomic Locations for SLC12A9 Gene

Genomic Locations for SLC12A9 Gene
40,193 bases
Plus strand
40,193 bases
Plus strand

Genomic View for SLC12A9 Gene

Genes around SLC12A9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC12A9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC12A9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC12A9 Gene

Proteins for SLC12A9 Gene

  • Protein details for SLC12A9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Solute carrier family 12 member 9
    Protein Accession:
    Secondary Accessions:
    • B7Z740
    • D6W5X0
    • D6W5X2
    • F5H8C2
    • Q9BWL2
    • Q9BXP1
    • Q9BYI0
    • Q9NQR5

    Protein attributes for SLC12A9 Gene

    914 amino acids
    Molecular mass:
    96110 Da
    Quaternary structure:
    • Interacts with SLC12A1.

    Alternative splice isoforms for SLC12A9 Gene


neXtProt entry for SLC12A9 Gene

Post-translational modifications for SLC12A9 Gene

  • Glycosylation at posLast=243243 and posLast=228228
  • Ubiquitination at posLast=386386
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC12A9 Gene

Domains & Families for SLC12A9 Gene

Gene Families for SLC12A9 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC12A9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SLC12A transporter family.
  • Belongs to the SLC12A transporter family.
genes like me logo Genes that share domains with SLC12A9: view

Function for SLC12A9 Gene

Molecular function for SLC12A9 Gene

UniProtKB/Swiss-Prot Function:
May be an inhibitor of SLC12A1. Seems to correspond to a subunit of a multimeric transport system and thus, additional subunits may be required for its function.

Phenotypes From GWAS Catalog for SLC12A9 Gene

Gene Ontology (GO) - Molecular Function for SLC12A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015377 cation:chloride symporter activity TAS 10871601
GO:0015379 potassium:chloride symporter activity IBA --
genes like me logo Genes that share ontologies with SLC12A9: view
genes like me logo Genes that share phenotypes with SLC12A9: view

Animal Model Products

miRNA for SLC12A9 Gene

miRTarBase miRNAs that target SLC12A9

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC12A9 Gene

Localization for SLC12A9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC12A9 Gene

Cell 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 SLC12A9 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for SLC12A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,TAS --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with SLC12A9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC12A9 Gene

Pathways & Interactions for SLC12A9 Gene

SuperPathways for SLC12A9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SLC12A9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006884 cell volume homeostasis IBA --
GO:0010107 potassium ion import IBA --
GO:0055064 chloride ion homeostasis IBA --
GO:0055075 potassium ion homeostasis IBA --
genes like me logo Genes that share ontologies with SLC12A9: view

No data available for Pathways by source and SIGNOR curated interactions for SLC12A9 Gene

Drugs & Compounds for SLC12A9 Gene

No Compound Related Data Available

Transcripts for SLC12A9 Gene

Unigene Clusters for SLC12A9 Gene

Solute carrier family 12 (potassium/chloride transporters), member 9:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC12A9 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^
SP1: - - - - - -
SP2: - - - - - - - - -
SP3: - -
SP5: - - - - - - - - - -
SP6: - - - - - - - - - -
SP7: -
SP8: - - -
SP9: -
SP11: -
SP12: - - - - - - - - - - - -
SP13: - - - - - -

ExUns: 15 ^ 16 ^ 17
SP1: -
SP3: -
SP4: -

Relevant External Links for SLC12A9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC12A9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC12A9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC12A9 Gene

This gene is overexpressed in Whole Blood (x15.4).

Protein differential expression in normal tissues from HIPED for SLC12A9 Gene

This gene is overexpressed in Monocytes (26.5), Heart (6.5), Peripheral blood mononuclear cells (6.2), and Placenta (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC12A9 Gene

Protein tissue co-expression partners for SLC12A9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC12A9 Gene:


SOURCE GeneReport for Unigene cluster for SLC12A9 Gene:


mRNA Expression by UniProt/SwissProt for SLC12A9 Gene:

Tissue specificity: Highly expressed in placenta, brain and kidney. Lower expression in lung, liver and heart.

Evidence on tissue expression from TISSUES for SLC12A9 Gene

  • Heart(4.1)
genes like me logo Genes that share expression patterns with SLC12A9: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC12A9 Gene

Orthologs for SLC12A9 Gene

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

Orthologs for SLC12A9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC12A9 34 33
  • 99.38 (n)
(Canis familiaris)
Mammalia SLC12A9 34 33
  • 88.26 (n)
(Bos Taurus)
Mammalia SLC12A9 34 33
  • 88.15 (n)
(Monodelphis domestica)
Mammalia SLC12A9 34
  • 86 (a)
(Mus musculus)
Mammalia Slc12a9 16 34 33
  • 85.03 (n)
(Rattus norvegicus)
Mammalia Slc12a9 33
  • 83.74 (n)
(Ornithorhynchus anatinus)
Mammalia SLC12A9 34
  • 75 (a)
(Gallus gallus)
Aves SLC12A9 34 33
  • 64.26 (n)
(Anolis carolinensis)
Reptilia SLC12A9 34
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100498108 33
  • 56.44 (n)
(Danio rerio)
Actinopterygii slc12a9 34 33
  • 60.94 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1845 33
fruit fly
(Drosophila melanogaster)
Insecta CG10413 34 33
  • 50.99 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010249 33
  • 49.13 (n)
(Caenorhabditis elegans)
Secernentea T04B8.5 34 33
  • 48.7 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL025C 33
  • 46.11 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F10549g 33
  • 42.97 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VHC1 36 33
  • 42.76 (n)
-- 34
  • 25 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU03784 33
  • 48.54 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes can1 33
  • 42.01 (n)
Species where no ortholog for SLC12A9 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 SLC12A9 Gene

Gene Tree for SLC12A9 (if available)
Gene Tree for SLC12A9 (if available)
Evolutionary constrained regions (ECRs) for SLC12A9: view image

Paralogs for SLC12A9 Gene

Paralogs for SLC12A9 Gene

(10) SIMAP similar genes for SLC12A9 Gene using alignment to 7 proteins:

  • S12A9_HUMAN
  • C9J0I5_HUMAN
  • D6W5X3_HUMAN
  • D6W5X5_HUMAN
genes like me logo Genes that share paralogs with SLC12A9: view

Variants for SLC12A9 Gene

Sequence variations from dbSNP and Humsavar for SLC12A9 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000093956 -- 100,853,576(+) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000549709 -- 100,859,890(+) T/C 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000616346 -- 100,858,669(+) A/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000627721 -- 100,865,441(+) G/A 3_prime_UTR_variant, intron_variant
rs1000705298 -- 100,867,323(+) G/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC12A9 Gene

Variant ID Type Subtype PubMed ID
esv2734888 CNV deletion 23290073
esv2759547 CNV gain+loss 17122850
nsv1020837 CNV loss 25217958
nsv5870 CNV insertion 18451855
nsv607965 CNV loss 21841781
nsv607966 CNV loss 21841781
nsv831073 CNV loss 17160897

Variation tolerance for SLC12A9 Gene

Residual Variation Intolerance Score: 6.71% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.83; 34.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC12A9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC12A9 Gene

Disorders for SLC12A9 Gene

Additional Disease Information for SLC12A9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SLC12A9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SLC12A9 Gene

Publications for SLC12A9 Gene

  1. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. (PMID: 11239002) Wilson MD … Koop BF (Nucleic acids research 2001) 2 3 4 58
  2. Cloning and functional characterization of a cation-Cl- cotransporter-interacting protein. (PMID: 10871601) Caron L … Isenring P (The Journal of biological chemistry 2000) 2 3 4 58
  3. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. (PMID: 21347282) Lettre G … Boerwinkle E (PLoS genetics 2011) 3 44 58
  4. Genome-wide association analysis identifies multiple loci related to resting heart rate. (PMID: 20639392) Eijgelsheim M … O'Donnell CJ (Human molecular genetics 2010) 3 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for SLC12A9 Gene

Sources for SLC12A9 Gene

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