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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
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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

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