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    SLC12A6 solute carrier family 12 member 6 [ Homo sapiens (human) ]

    Gene ID: 9990, updated on 19-Jun-2024

    Summary

    Official Symbol
    SLC12A6provided by HGNC
    Official Full Name
    solute carrier family 12 member 6provided by HGNC
    Primary source
    HGNC:HGNC:10914
    See related
    Ensembl:ENSG00000140199 MIM:604878; AllianceGenome:HGNC:10914
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KCC3; ACCPN; KCC3A; KCC3B; CMT2II
    Summary
    This gene is a member of the K-Cl cotransporter (KCC) family. K-Cl cotransporters are integral membrane proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The proteins encoded by this gene are activated by cell swelling induced by hypotonic conditions. Alternate splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are associated with agenesis of the corpus callosum with peripheral neuropathy. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 15.1), bone marrow (RPKM 10.0) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC12A6 in Genome Data Viewer
    Location:
    15q14
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (34229784..34338057, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (32028044..32136362, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (34521985..34630258, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34393207-34394064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9174 Neighboring gene piggyBac transposable element derived 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:34446570-34447769 Neighboring gene katanin regulatory subunit B1 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6277 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:34506245-34506840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9175 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:34531007-34532206 Neighboring gene uncharacterized LOC124903461 Neighboring gene ER membrane protein complex subunit 4 Neighboring gene MPRA-validated peak2292 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:34585393-34585612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6280 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:34645972-34647171 Neighboring gene NOP10 ribonucleoprotein Neighboring gene NUT midline carcinoma family member 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp434D2135

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ammonium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables potassium:chloride symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables potassium:chloride symporter activity TAS
    Traceable Author Statement
    more info
     
    enables protein kinase binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in ammonium import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in angiogenesis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell volume homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell volume homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular hypotonic salinity response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chemical synaptic transmission 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 ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in monoatomic ion transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in monoatomic ion transport TAS
    Traceable Author Statement
    more info
     
    involved_in potassium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in potassium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in potassium ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in potassium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    solute carrier family 12 member 6
    Names
    K-Cl cotransporter 3
    electroneutral potassium-chloride cotransporter 3
    potassium chloride cotransporter 3
    potassium chloride cotransporter KCC3a-S3
    potassium-chloride transporter-3a
    potassium-chloride transporter-3b
    solute carrier family 12 (potassium/chloride transporter), member 6
    solute carrier family 12 (potassium/chloride transporters), member 6

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_007951.1 RefSeqGene

      Range
      5001..113069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_270

    mRNA and Protein(s)

    1. NM_001042494.2NP_001035959.1  solute carrier family 12 member 6 isoform c

      See identical proteins and their annotated locations for NP_001035959.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform c) uses a downstream start codon, compared to isoform a.
      Source sequence(s)
      AC021822, AC079203, AF531259
      Consensus CDS
      CCDS42012.1
      UniProtKB/TrEMBL
      Q6NSI7
      Related
      ENSP00000387725.2, ENST00000458406.6
      Conserved Domains (3) summary
      TIGR00930
      Location:501091
      2a30; K-Cl cotransporter
      pfam03522
      Location:7151091
      SLC12; Solute carrier family 12
      cl00456
      Location:150301
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    2. NM_001042495.2NP_001035960.1  solute carrier family 12 member 6 isoform c

      See identical proteins and their annotated locations for NP_001035960.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform c) uses a downstream start codon, compared to isoform a.
      Source sequence(s)
      AC079203, BC070107
      Consensus CDS
      CCDS42012.1
      UniProtKB/TrEMBL
      Q6NSI7
      Related
      ENSP00000380814.2, ENST00000397702.6
      Conserved Domains (3) summary
      TIGR00930
      Location:501091
      2a30; K-Cl cotransporter
      pfam03522
      Location:7151091
      SLC12; Solute carrier family 12
      cl00456
      Location:150301
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    3. NM_001042496.2NP_001035961.1  solute carrier family 12 member 6 isoform d

      See identical proteins and their annotated locations for NP_001035961.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform d) uses a downstream start codon, compared to isoform a.
      Source sequence(s)
      AC021822, AC079203, DQ138323
      Consensus CDS
      CCDS42011.1
      UniProtKB/TrEMBL
      A8K935
      Related
      ENSP00000452776.1, ENST00000558589.5
      Conserved Domains (3) summary
      TIGR00930
      Location:1001141
      2a30; K-Cl cotransporter
      pfam03522
      Location:7651141
      SLC12; Solute carrier family 12
      cl00456
      Location:200351
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    4. NM_001042497.2NP_001035962.1  solute carrier family 12 member 6 isoform e

      See identical proteins and their annotated locations for NP_001035962.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded protein (isoform e) is shorter, compared to isoform a.
      Source sequence(s)
      AC021822, AC079203, AF531258
      Consensus CDS
      CCDS42010.1
      UniProtKB/TrEMBL
      A8K935
      Related
      ENSP00000380819.2, ENST00000397707.6
      Conserved Domains (1) summary
      TIGR00930
      Location:941135
      2a30; K-Cl cotransporter
    5. NM_001365088.1NP_001352017.1  solute carrier family 12 member 6 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC079203, AF116242, AF477977, BC033894, BC051744, BX648195
      Consensus CDS
      CCDS58352.1
      UniProtKB/Swiss-Prot
      A0AV76, Q2VI00, Q7Z2E7, Q7Z4G5, Q8TDD4, Q9UFR2, Q9UHW9, Q9Y642, Q9Y665
      UniProtKB/TrEMBL
      A8K935
      Related
      ENSP00000346112.3, ENST00000354181.8
      Conserved Domains (1) summary
      TIGR00930
      Location:1091150
      2a30; K-Cl cotransporter
    6. NM_005135.2NP_005126.1  solute carrier family 12 member 6 isoform b

      See identical proteins and their annotated locations for NP_005126.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate exon for the 5' UTR and 5' coding region, compared to variant 1. The encoded protein (isoform b) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC021822, AC079203, AF108831
      Consensus CDS
      CCDS10036.1
      UniProtKB/TrEMBL
      Q6NSI7
      Related
      ENSP00000290209.5, ENST00000290209.9
      Conserved Domains (1) summary
      TIGR00930
      Location:581099
      2a30; K-Cl cotransporter
    7. NM_133647.2NP_598408.1  solute carrier family 12 member 6 isoform a

      See identical proteins and their annotated locations for NP_598408.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC021822, AC079203, AF105366
      Consensus CDS
      CCDS58352.1
      UniProtKB/Swiss-Prot
      A0AV76, Q2VI00, Q7Z2E7, Q7Z4G5, Q8TDD4, Q9UFR2, Q9UHW9, Q9Y642, Q9Y665
      UniProtKB/TrEMBL
      A8K935
      Related
      ENSP00000454168.1, ENST00000560611.5
      Conserved Domains (1) summary
      TIGR00930
      Location:1091150
      2a30; K-Cl cotransporter

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      34229784..34338057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006720793.5XP_006720856.1  solute carrier family 12 member 6 isoform X1

      UniProtKB/TrEMBL
      A8K935
      Conserved Domains (3) summary
      TIGR00930
      Location:1091101
      2a30; K-Cl cotransporter
      pfam03522
      Location:7251101
      SLC12; Solute carrier family 12
      cl00456
      Location:184311
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    2. XM_047433396.1XP_047289352.1  solute carrier family 12 member 6 isoform X2

      UniProtKB/TrEMBL
      B3KXX3
      Related
      ENSP00000452705.1, ENST00000560164.5
    3. XM_011522269.4XP_011520571.1  solute carrier family 12 member 6 isoform X3

      Conserved Domains (2) summary
      TIGR00930
      Location:109680
      2a30; K-Cl cotransporter
      cl00456
      Location:209360
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    RNA

    1. XR_931960.4 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791798.1 Reference GRCh38.p14 PATCHES

      Range
      3625..76798 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      32028044..32136362 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379303.1XP_054235278.1  solute carrier family 12 member 6 isoform X1

      UniProtKB/TrEMBL
      A8K935
    2. XM_054379304.1XP_054235279.1  solute carrier family 12 member 6 isoform X2

      UniProtKB/TrEMBL
      B3KXX3
    3. XM_054379305.1XP_054235280.1  solute carrier family 12 member 6 isoform X3

    RNA

    1. XR_008489032.1 RNA Sequence