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    CDH16 cadherin 16 [ Homo sapiens (human) ]

    Gene ID: 1014, updated on 11-Apr-2024

    Summary

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    Official Symbol
    CDH16provided by HGNC
    Official Full Name
    cadherin 16provided by HGNC
    Primary source
    HGNC:HGNC:1755
    See related
    Ensembl:ENSG00000166589 MIM:603118; AllianceGenome:HGNC:1755
    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
    Summary
    This gene is a member of the cadherin superfamily, genes encoding calcium-dependent, membrane-associated glycoproteins. Mapped to a previously identified cluster of cadherin genes on chromosome 16q22.1, the gene localizes with superfamily members CDH1, CDH3, CDH5, CDH8 and CDH11. The protein consists of an extracellular domain containing 6 cadherin domains, a transmembrane region and a truncated cytoplasmic domain but lacks the prosequence and tripeptide HAV adhesion recognition sequence typical of most classical cadherins. Expression is exclusively in kidney, where the protein functions as the principal mediator of homotypic cellular recognition, playing a role in the morphogenic direction of tissue development. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2011]
    Expression
    Restricted expression toward kidney (RPKM 177.1) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    16q22.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66908122..66918885, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72702422..72713185, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66942025..66952788, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933011-66933906 Neighboring gene uncharacterized LOC107984821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933907-66934800 Neighboring gene VISTA enhancer hs1760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66945849-66946350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66955545-66956068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66956069-66956592 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7572 Neighboring gene RRAD, Ras related glycolysis inhibitor and calcium channel regulator Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:66961058-66962257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10946 Neighboring gene cytosolic iron-sulfur assembly component 2B

    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
    • 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. Reduced CDH16 expression is linked to poor prognosis in clear cell renal cell carcinoma 16. Lennartz M, et al. Urol Oncol, 2022 Jul. PMID 35606285
    2. Expression analysis of kidney-specific cadherin in a wide spectrum of traditional and newly recognized renal epithelial neoplasms: diagnostic and histogenetic implications. Kuehn A, et al. Am J Surg Pathol, 2007 Oct. PMID 17895753
    3. Expression of Ksp-cadherin during kidney development and in renal cell carcinoma. Thedieck C, et al. Br J Cancer, 2005 Jun 6. PMID 15886705, Free PMC Article
    4. Histopathological analysis of renal cystic epithelia in the Pkd2WS25/- mouse model of ADPKD. Thomson RB, et al. Am J Physiol Renal Physiol, 2003 Nov. PMID 12851251
    5. Assignment of E-cadherin (CDH1) and KSP-cadherin (CDH16) to chromosome 16q22.1 by radiation hybrid mapping. Baudry D, et al. Cytogenet Cell Genet, 2000. PMID 10828602

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of CDH16 expression is a strong independent predictor for lymph node metastasis in Middle Eastern papillary thyroid cancer.
      Title: Loss of CDH16 expression is a strong independent predictor for lymph node metastasis in Middle Eastern papillary thyroid cancer.
    2. Reduced CDH16 expression is linked to poor prognosis in clear cell renal cell carcinoma 16.
      Title: Reduced CDH16 expression is linked to poor prognosis in clear cell renal cell carcinoma 16.
    3. Our study expands the clinical and allelic spectrum of known Retinal dystrophies genes, and reveals AGBL5, CDH16, and DNAJC17 as novel disease candidates.
      Title: Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies.
    4. In thyroid carcinomas, as determined by quantitative RT-PCR, CDH16 expression decreases in papillary, follicular, and anaplastic thyroid carcinomas, and the decrease is more pronounced than that of CDH1.
      Title: CDH16/Ksp-cadherin is expressed in the developing thyroid gland and is strongly down-regulated in thyroid carcinomas.
    5. The interaction of Ksp-cadherin with alpha B-crystallin is important for the connection of Ksp-cadherin to the cytoskeleton and thus for maintaining tissue integrity in the kidney.
      Title: alpha B-crystallin is a cytoplasmic interaction partner of the kidney-specific cadherin-16.
    6. Ksp-cad is a useful tumor type associated marker for distinguishing chromophobe renal cell carcinoma and renal oncocytoma from the wide range of nonintercalated cell-related adult renal epithelial neoplasms.
      Title: Expression analysis of kidney-specific cadherin in a wide spectrum of traditional and newly recognized renal epithelial neoplasms: diagnostic and histogenetic implications.
    7. These results indicated that LIF induced multi-lineage differentiation of adult stem-like cells in kidney via cadherin 16.
      Title: Leukemia inhibitory factor induces multi-lineage differentiation of adult stem-like cells in kidney via kidney-specific cadherin 16.
    8. Ksp-cadherin expression downregulated inrenal cell carcinoma; this cell adhesion molecule may have role in tumour suppression
      Title: Expression of Ksp-cadherin during kidney development and in renal cell carcinoma.
    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in basolateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-16
    Names
    KSP-cadherin
    cadherin 16, KSP-cadherin
    kidney-specific cadherin

    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_001204744.2 → NP_001191673.1  cadherin-16 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001191673.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AY358911, BC027912
      Consensus CDS
      CCDS56002.1
      UniProtKB/TrEMBL
      B2R7S8
      Related
      ENSP00000377619.3, ENST00000394055.7
      Conserved Domains (2) summary
      cd11304
      Location:342 → 445
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47 → 124
      CA; Cadherin repeats

    2. NM_001204745.2 → NP_001191674.1  cadherin-16 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001191674.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, as compared to variant 1. The resulting isoform (3) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AK298255, BC027912, DC361453
      Consensus CDS
      CCDS58471.1
      UniProtKB/TrEMBL
      B2R7S8
      Related
      ENSP00000454784.1, ENST00000565796.5
      Conserved Domains (2) summary
      cd11304
      Location:342 → 445
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47 → 124
      CA; Cadherin repeats

    3. NM_001204746.2 → NP_001191675.1  cadherin-16 isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame segment in the 5' coding region, as compared to variant 1. The resulting isoform (4) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AK225544, DC361453
      Consensus CDS
      CCDS58472.1
      UniProtKB/TrEMBL
      B2R7S8
      Related
      ENSP00000455263.1, ENST00000568632.5
      Conserved Domains (2) summary
      cd11304
      Location:245 → 348
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47 → 123
      CA; Cadherin repeats

    4. NM_004062.4 → NP_004053.1  cadherin-16 isoform 1 precursor

      See identical proteins and their annotated locations for NP_004053.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF016272, BC027912, DC361453
      Consensus CDS
      CCDS10823.1
      UniProtKB/Swiss-Prot
      B4DPA8, H3BPD3, O75309, Q6UW93
      UniProtKB/TrEMBL
      B2R7S8
      Related
      ENSP00000299752.4, ENST00000299752.9
      Conserved Domains (2) summary
      cd11304
      Location:342 → 445
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47 → 124
      CA; Cadherin repeats

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      66908122..66918885 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433490.1 → XP_047289446.1  cadherin-16 isoform X2

    2. XM_011522807.2 → XP_011521109.1  cadherin-16 isoform X1

      UniProtKB/TrEMBL
      B2R7S8
      Conserved Domains (2) summary
      cd11304
      Location:342 → 445
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:47 → 124
      CA; Cadherin repeats

    3. XM_005255770.3 → XP_005255827.1  cadherin-16 isoform X3

      UniProtKB/TrEMBL
      H3BSG2
      Conserved Domains (1) summary
      cd11304
      Location:164 → 267
      Cadherin_repeat; Cadherin tandem repeat domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72702422..72713185 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379374.1 → XP_054235349.1  cadherin-16 isoform X2

    2. XM_054379373.1 → XP_054235348.1  cadherin-16 isoform X1

    3. XM_054379375.1 → XP_054235350.1  cadherin-16 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75309.1 GenPept UniProtKB/Swiss-Prot:O75309

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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