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    CLDN16 claudin 16 [ Homo sapiens (human) ]

    Gene ID: 10686, updated on 7-Sep-2023

    Summary

    Official Symbol
    CLDN16provided by HGNC
    Official Full Name
    claudin 16provided by HGNC
    Primary source
    HGNC:HGNC:2037
    See related
    Ensembl:ENSG00000113946 MIM:603959; AllianceGenome:HGNC:2037
    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
    HOMG3; PCLN1
    Summary
    Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. These junctions are comprised of sets of continuous networking strands in the outwardly facing cytoplasmic leaflet, with complementary grooves in the inwardly facing extracytoplasmic leaflet. The protein encoded by this gene, a member of the claudin family, is an integral membrane protein and a component of tight junction strands. It is found primarily in the kidneys, specifically in the thick ascending limb of Henle, where it acts as either an intercellular pore or ion concentration sensor to regulate the paracellular resorption of magnesium ions. Defects in this gene are a cause of primary hypomagnesemia, which is characterized by massive renal magnesium wasting with hypomagnesemia and hypercalciuria, resulting in nephrocalcinosis and renal failure. This gene and the CLDN1 gene are clustered on chromosome 3q28. [provided by RefSeq, Jun 2010]
    Expression
    Biased expression in kidney (RPKM 20.4), thyroid (RPKM 4.2) and 1 other tissue See more
    Orthologs
    NEW
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    Genomic context

    See CLDN16 in Genome Data Viewer
    Location:
    3q28
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (190290361..190412138)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (193106655..193228453)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (190008150..190129927)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:189894452-189894952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:189894953-189895453 Neighboring gene RNA, U6 small nuclear 1109, pseudogene Neighboring gene NMNAT1 pseudogene 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:189949260-189950459 Neighboring gene claudin 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:190080003-190080564 Neighboring gene Sharpr-MPRA regulatory region 3521 Neighboring gene Sharpr-MPRA regulatory region 14389 Neighboring gene transmembrane protein 207 Neighboring gene Sharpr-MPRA regulatory region 15127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:190232063-190232564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:190232565-190233064 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:190258615-190259497 Neighboring gene interleukin 1 receptor accessory protein Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:190283646-190284845 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:190302729-190303262 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:190303263-190303796 Neighboring gene glucosaminyl (N-acetyl) transferase 1 pseudogene 3

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables magnesium ion transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in bicellular tight junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in intercellular transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in intracellular monoatomic cation homeostasis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in magnesium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metal ion transport TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in bicellular tight junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in bicellular tight junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    claudin-16
    Names
    hypomagnesemia 3, with hypercalciuria and nephrocalcinosis
    paracellin-1

    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_008149.2 RefSeqGene

      Range
      102803..126778
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001378492.1NP_001365421.1  claudin-16

      Status: REVIEWED

      Source sequence(s)
      AC009520, AC080006
      Consensus CDS
      CCDS3296.2
      UniProtKB/Swiss-Prot
      Q9Y5I7
      Conserved Domains (1) summary
      cl21598
      Location:11183
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family
    2. NM_001378493.1NP_001365422.1  claudin-16

      Status: REVIEWED

      Source sequence(s)
      AC009520, AC080006
      Consensus CDS
      CCDS3296.2
      UniProtKB/Swiss-Prot
      Q9Y5I7
      Conserved Domains (1) summary
      cl21598
      Location:11183
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family
    3. NM_006580.4NP_006571.2  claudin-16

      Status: REVIEWED

      Source sequence(s)
      AC009520
      Consensus CDS
      CCDS3296.2
      UniProtKB/Swiss-Prot
      Q9Y5I7
      Related
      ENSP00000264734.3, ENST00000264734.3
      Conserved Domains (1) summary
      cl21598
      Location:11183
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      190290361..190412138
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447333.1XP_047303289.1  claudin-16 isoform X1

      UniProtKB/Swiss-Prot
      Q9Y5I7
      Conserved Domains (1) summary
      cl21598
      Location:11183
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      193106655..193228453
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344990.1XP_054200965.1  claudin-16 isoform X1

      UniProtKB/Swiss-Prot
      Q9Y5I7