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    SLC12A9 solute carrier family 12 member 9 [ Homo sapiens (human) ]

    Gene ID: 56996, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SLC12A9provided by HGNC
    Official Full Name
    solute carrier family 12 member 9provided by HGNC
    Primary source
    HGNC:HGNC:17435
    See related
    Ensembl:ENSG00000146828 MIM:616861; AllianceGenome:HGNC:17435
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CCC6; CIP1; WO3.3; hCCC6
    Summary
    Predicted to enable potassium:chloride symporter activity. Predicted to be involved in several processes, including chloride ion homeostasis; chloride transmembrane transport; and potassium ion homeostasis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in placenta (RPKM 13.3), spleen (RPKM 11.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC12A9 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100826869..100867012)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102066955..102107112)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100424491..100464634)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26384 Neighboring gene zonadhesin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100382347-100382846 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:100391649-100392196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26385 Neighboring gene Sharpr-MPRA regulatory region 9506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100399088-100399791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100399792-100400494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100402349-100403064 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:100403701-100404900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100412721-100413220 Neighboring gene EPH receptor B4 Neighboring gene RNA, 7SL, cytoplasmic 750, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100425149-100425944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100426741-100427536 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100432899-100433818 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100433819-100434738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100434739-100435658 Neighboring gene SLC12A9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456152-100456652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456653-100457153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100457811-100458310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100458529-100459030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26390 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100471610-100472274 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100472275-100472939 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18466 Neighboring gene microRNA 6875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100478564-100479401 Neighboring gene thyroid hormone receptor interactor 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100483425-100484158 Neighboring gene serrate, RNA effector molecule

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Clinical value of SLC12A9 for diagnosis and prognosis in colorectal cancer. Du W, et al. Aging (Albany NY), 2023 Dec 28. PMID 38157260, Free PMC Article
    2. Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder. Accogli A, et al. Genet Med, 2024 May. PMID 38334070
    3. Cloning and functional characterization of a cation-Cl- cotransporter-interacting protein. Caron L, et al. J Biol Chem, 2000 Oct 13. PMID 10871601
    4. Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma. Yan C, et al. Lab Invest, 2023 Mar. PMID 36925204
    5. Physiology of SLC12 transporters: lessons from inherited human genetic mutations and genetically engineered mouse knockouts. Gagnon KB, et al. Am J Physiol Cell Physiol, 2013 Apr 15. PMID 23325410, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder.
      Title: Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder.
    2. Clinical value of SLC12A9 for diagnosis and prognosis in colorectal cancer.
      Title: Clinical value of SLC12A9 for diagnosis and prognosis in colorectal cancer.
    3. Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma.
      Title: Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma.
    4. Review summarizes three human disorders that have been linked to the mutation/dysfunction of Na-Cl, Na-K-2Cl, and K-Cl cotransporters (Bartter's, Gitleman's, and Andermann's syndromes).
      Title: Physiology of SLC12 transporters: lessons from inherited human genetic mutations and genetically engineered mouse knockouts.
    5. Observational study, meta-analysis, and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association analysis identifies multiple loci related to resting heart rate.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies multiple loci related to resting heart rate.
    EBI GWAS Catalog
    Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.
    EBI GWAS Catalog
    Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ46905

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chloride:monoatomic cation symporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell volume homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chloride ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in potassium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in potassium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    solute carrier family 12 member 9
    Names
    CCC-interacting protein 1
    cation-chloride cotransporter 6
    cation-chloride cotransporter-interacting protein 1
    potassium-chloride transporter 9
    solute carrier family 12 (potassium/chloride transporters), member 9

    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)

    1. NM_001267812.2 → NP_001254741.1  solute carrier family 12 member 9 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011895
      Consensus CDS
      CCDS59068.1
      UniProtKB/Swiss-Prot
      Q9BXP2
      Related
      ENSP00000443702.1, ENST00000540482.5
      Conserved Domains (2) summary
      pfam00324
      Location:42 → 535
      AA_permease; Amino acid permease
      pfam03522
      Location:546 → 619
      SLC12; Solute carrier family 12

    2. NM_001267814.2 → NP_001254743.1  solute carrier family 12 member 9 isoform 3

      See identical proteins and their annotated locations for NP_001254743.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site and lacks two consecutive exons in the 5' coding region and differs in the 3' UTR, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011895
      Consensus CDS
      CCDS59069.1
      UniProtKB/Swiss-Prot
      Q9BXP2
      Related
      ENSP00000413796.1, ENST00000415287.5
      Conserved Domains (1) summary
      cl27256
      Location:140 → 530
      SLC12; Solute carrier family 12

    3. NM_001363493.2 → NP_001350422.1  solute carrier family 12 member 9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AA825567, AB033284, AF284422, AK024494, HY053006
      Consensus CDS
      CCDS5707.1
      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5
      UniProtKB/TrEMBL
      Q9H7Q7
      Conserved Domains (1) summary
      cl27256
      Location:36 → 905
      SLC12; Solute carrier family 12

    4. NM_001363494.1 → NP_001350423.1  solute carrier family 12 member 9 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC011895
      UniProtKB/TrEMBL
      Q9H7Q7
      Conserved Domains (1) summary
      cl27256
      Location:86 → 762
      SLC12; Solute carrier family 12

    5. NM_020246.4 → NP_064631.2  solute carrier family 12 member 9 isoform 1

      See identical proteins and their annotated locations for NP_064631.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011895
      Consensus CDS
      CCDS5707.1
      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5
      UniProtKB/TrEMBL
      Q9H7Q7
      Related
      ENSP00000275730.4, ENST00000354161.8
      Conserved Domains (1) summary
      cl27256
      Location:36 → 905
      SLC12; Solute carrier family 12

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100826869..100867012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420627.1 → XP_047276583.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    2. XM_047420628.1 → XP_047276584.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    3. XM_047420632.1 → XP_047276588.1  solute carrier family 12 member 9 isoform X4

    4. XM_047420629.1 → XP_047276585.1  solute carrier family 12 member 9 isoform X2

    5. XM_047420631.1 → XP_047276587.1  solute carrier family 12 member 9 isoform X3

    6. XM_047420626.1 → XP_047276582.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    7. XM_047420630.1 → XP_047276586.1  solute carrier family 12 member 9 isoform X2

    8. XM_047420633.1 → XP_047276589.1  solute carrier family 12 member 9 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      102066955..102107112
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358674.1 → XP_054214649.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    2. XM_054358676.1 → XP_054214651.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    3. XM_054358680.1 → XP_054214655.1  solute carrier family 12 member 9 isoform X4

    4. XM_054358677.1 → XP_054214652.1  solute carrier family 12 member 9 isoform X2

    5. XM_054358679.1 → XP_054214654.1  solute carrier family 12 member 9 isoform X3

    6. XM_054358675.1 → XP_054214650.1  solute carrier family 12 member 9 isoform X1

      UniProtKB/Swiss-Prot
      B7Z740, D6W5X0, D6W5X2, F5H8C2, Q9BWL2, Q9BXP1, Q9BXP2, Q9BYI0, Q9NQR5

    7. XM_054358678.1 → XP_054214653.1  solute carrier family 12 member 9 isoform X2

    8. XM_054358681.1 → XP_054214656.1  solute carrier family 12 member 9 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BXP2.1 GenPept UniProtKB/Swiss-Prot:Q9BXP2

    Gene LinkOut

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