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

Gene ID: 56996, updated on 14-Nov-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, Nov 2024]
Expression
Ubiquitous expression in placenta (RPKM 13.3), spleen (RPKM 11.5) and 25 other tissues See more
Orthologs
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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)

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 lysosomal membrane IEA
Inferred from Electronic Annotation
more info
  
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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