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 regi... See more...

Aliases for CDH16 Gene

Aliases for CDH16 Gene

  • Cadherin 16 2 3 5
  • Cadherin 16, KSP-Cadherin 2 3
  • Kidney-Specific Cadherin 3 4
  • Cadherin-16 3 4
  • KSP-Cadherin 3
  • Ksp-Cadherin 4
  • CDH16 5

External Ids for CDH16 Gene

Previous GeneCards Identifiers for CDH16 Gene

  • GC16M057636
  • GC16M067319
  • GC16M066677
  • GC16M066718
  • GC16M065499
  • GC16M066942
  • GC16M052816

Summaries for CDH16 Gene

Entrez Gene Summary for CDH16 Gene

  • 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]

GeneCards Summary for CDH16 Gene

CDH16 (Cadherin 16) is a Protein Coding gene. Diseases associated with CDH16 include Oncocytoma and Renal Oncocytoma. Among its related pathways are ERK Signaling and Presenilin-Mediated Signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA2.

UniProtKB/Swiss-Prot Summary for CDH16 Gene

  • Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.

Gene Wiki entry for CDH16 Gene

Additional gene information for CDH16 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDH16 Gene

Genomics for CDH16 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CDH16 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J066918 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 600.7 +0.9 916 2.8 GATAD2A IKZF1 ZKSCAN1 ZNF205 ZNF189 GABPB1 HDAC2 KDM1A KDM3A XRCC5 CDH16 lnc-CES2-3 CA7 B3GNT9 LRRC29 TMEM208 CES3 ELMO3 NAE1 LOC107984821
GH16J066879 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 12.1 +38.1 38116 2.8 SP1 HNRNPL PRDM10 REST TFE3 LEF1 IKZF1 NFKBIZ POLR2A ZNF692 PDP2 lnc-PDP2-3 CES2 B3GNT9 CTCF ENSG00000260465 CDH16 RRAD NAE1 ZDHHC1
GH16J066749 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 9.6 +167.7 167717 3.2 GATAD2A CTCF PRDM10 POLR2A ZNF7 BACH1 JUND LARP7 PRDM1 ZNF143 DYNC1LI2 LOC106699570 CES2 TERB1 NAE1 ACD CTCF CA7 LOC107984813 CDH16
GH16J066894 Enhancer 1.1 Ensembl ENCODE 18.4 +22.7 22718 2.8 GATAD2A CTCF PRDM10 TFE3 NFKBIZ ZNF143 RFX1 RXRB REST RAD21 piR-30188-073 piR-30188-074 piR-60246-067 CES2 CDH16 RRAD CIAO2B FBXL8 TRADD HSF4
GH16J066960 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 11.6 -42.3 -42293 1.2 HNRNPL GATAD2A CTCF TEAD4 PRDM10 REST ZNF512 ZNF692 MTA2 ZNF143 CES3 FBXL8 TRADD HSF4 CES2 RRAD CDH16 CIAO2B B3GNT9 CBFB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDH16 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDH16

Top Transcription factor binding sites by QIAGEN in the CDH16 gene promoter:
  • AML1a

Genomic Locations for CDH16 Gene

Genomic Locations for CDH16 Gene
chr16:66,908,122-66,918,917
(GRCh38/hg38)
Size:
10,796 bases
Orientation:
Minus strand
chr16:66,942,025-66,952,887
(GRCh37/hg19)
Size:
10,863 bases
Orientation:
Minus strand

Genomic View for CDH16 Gene

Genes around CDH16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDH16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDH16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDH16 Gene

Proteins for CDH16 Gene

  • Protein details for CDH16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75309-CAD16_HUMAN
    Recommended name:
    Cadherin-16
    Protein Accession:
    O75309
    Secondary Accessions:
    • B4DPA8
    • H3BPD3
    • Q6UW93

    Protein attributes for CDH16 Gene

    Size:
    829 amino acids
    Molecular mass:
    89923 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CDH16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CDH16 Gene

Post-translational modifications for CDH16 Gene

  • Glycosylation at Asn517, Asn602, and Asn722
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CDH16 Gene

Domains & Families for CDH16 Gene

Gene Families for CDH16 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CDH16 Gene

InterPro:
Blocks:
  • Cadherin
ProtoNet:

Suggested Antigen Peptide Sequences for CDH16 Gene

GenScript: Design optimal peptide antigens:
  • Kidney-specific cadherin (CAD16_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75309

UniProtKB/Swiss-Prot:

CAD16_HUMAN :
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
Domain:
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
genes like me logo Genes that share domains with CDH16: view

Function for CDH16 Gene

Molecular function for CDH16 Gene

UniProtKB/Swiss-Prot Function:
Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.
GENATLAS Biochemistry:
cadherin 16,Ksp-cadherin,130kDa,transmembrane glycoprotein component of adherens junction,kidney specific,wsith three alternatively spliced isoforms

Phenotypes From GWAS Catalog for CDH16 Gene

Gene Ontology (GO) - Molecular Function for CDH16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CDH16: view
genes like me logo Genes that share phenotypes with CDH16: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CDH16

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH16

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CDH16 Gene

Localization for CDH16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH16 Gene

Cell membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CDH16 gene
Compartment Confidence
plasma membrane 4
extracellular 4
cytoskeleton 2
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CDH16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016323 basolateral plasma membrane IEA --
genes like me logo Genes that share ontologies with CDH16: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDH16 Gene

Pathways & Interactions for CDH16 Gene

PathCards logo

SuperPathways for CDH16 Gene

SuperPathway Contained pathways
1 ERK Signaling
.61
.49
2 Regulation of activated PAK-2p34 by proteasome mediated degradation
3 G12-G13 in Cellular Signaling
-
4 Nanog in Mammalian ESC Pluripotency
.62
5 Presenilin-Mediated Signaling
-
genes like me logo Genes that share pathways with CDH16: view

Pathways by source for CDH16 Gene

1 Sino Biological pathway for CDH16 Gene
7 Qiagen pathways for CDH16 Gene
  • G12-G13 in Cellular Signaling
  • GSK3 Signaling
  • ILK Signaling
  • Presenilin-Mediated Signaling
  • Rho Family GTPases

Gene Ontology (GO) - Biological Process for CDH16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS,IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IEA --
genes like me logo Genes that share ontologies with CDH16: view

No data available for SIGNOR curated interactions for CDH16 Gene

Drugs & Compounds for CDH16 Gene

(3) Drugs for CDH16 Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ispinesib (SB-715992) Pharma Kinesin spindle protein (KSP)inhibitor 0
SB743921 Pharma Potent KSP inhibitor 0
Calcium Nutra 6556

(2) ApexBio Compounds for CDH16 Gene

Compound Action Cas Number
Ispinesib (SB-715992) Kinesin spindle protein (KSP)inhibitor 336113-53-2
SB743921 Potent KSP inhibitor 940929-33-9
genes like me logo Genes that share compounds with CDH16: view

Transcripts for CDH16 Gene

mRNA/cDNA for CDH16 Gene

4 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH16

Alternative Splicing Database (ASD) splice patterns (SP) for CDH16 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^
SP1: - -
SP2: -
SP3: -
SP4: - - - - - -
SP5: - -
SP6: - - -

ExUns: 18a · 18b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for CDH16 Gene

GeneLoc Exon Structure for
CDH16

Expression for CDH16 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CDH16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDH16 Gene

This gene is overexpressed in Kidney - Cortex (x49.0).

Protein differential expression in normal tissues from HIPED for CDH16 Gene

This gene is overexpressed in Kidney (57.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDH16 Gene



Protein tissue co-expression partners for CDH16 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDH16

SOURCE GeneReport for Unigene cluster for CDH16 Gene:

Hs.513660

mRNA Expression by UniProt/SwissProt for CDH16 Gene:

O75309-CAD16_HUMAN
Tissue specificity: Kidney specific.

Evidence on tissue expression from TISSUES for CDH16 Gene

  • Kidney(4.9)
  • Spleen(4.4)
  • Lung(4.2)
  • Thyroid gland(3.3)
genes like me logo Genes that share expression patterns with CDH16: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CDH16 Gene

Orthologs for CDH16 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH16 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CDH16 30 31
  • 98.75 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CDH16 30 31
  • 84.48 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CDH16 30 31
  • 83.35 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cdh16 30 17 31
  • 80.27 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cdh16 30
  • 80.15 (n)
Oppossum
(Monodelphis domestica)
Mammalia CDH16 31
  • 57 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CDH16 31
  • 47 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cdh16 30
  • 47.58 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC101886380 30
  • 48.09 (n)
CDH16 31
  • 35 (a)
OneToOne
Species where no ortholog for CDH16 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CDH16 Gene

ENSEMBL:
Gene Tree for CDH16 (if available)
TreeFam:
Gene Tree for CDH16 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDH16: view image

Paralogs for CDH16 Gene

(2) SIMAP similar genes for CDH16 Gene using alignment to 5 proteins:

  • CAD16_HUMAN
  • H3BSG2_HUMAN
  • H3BSV3_HUMAN
  • I3L418_HUMAN
  • J3QLA1_HUMAN
genes like me logo Genes that share paralogs with CDH16: view

Variants for CDH16 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDH16 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
720839 Benign: not provided 66,912,815(-) G/A SYNONYMOUS_VARIANT
727735 Benign: not provided 66,917,634(-) C/T INTRON_VARIANT
743166 Likely Benign: not provided 66,913,545(-) A/G SYNONYMOUS_VARIANT
784344 Benign: not provided 66,910,277(-) C/T MISSENSE_VARIANT
rs2271023 - p.His257Tyr

Additional dbSNP identifiers (rs#s) for CDH16 Gene

Structural Variations from Database of Genomic Variants (DGV) for CDH16 Gene

Variant ID Type Subtype PubMed ID
nsv1113815 CNV deletion 24896259
nsv572904 CNV loss 21841781
nsv827706 CNV loss 20364138

Variation tolerance for CDH16 Gene

Residual Variation Intolerance Score: 14.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.09; 75.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDH16 Gene

Human Gene Mutation Database (HGMD)
CDH16
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDH16

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH16 Gene

Disorders for CDH16 Gene

MalaCards: The human disease database

(13) MalaCards diseases for CDH16 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
oncocytoma
  • oxyphilic adenoma
renal oncocytoma
  • oncocytoma of kidney
chromophobe renal cell carcinoma
  • chromophobe adenocarcinoma
fetal adenoma
  • microfollicular adenoma
eosinophilic variant of chromophobe renal cell carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search CDH16 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with CDH16: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDH16 Gene

Publications for CDH16 Gene

  1. cDNA cloning and chromosomal localization of the human and mouse isoforms of Ksp-cadherin. (PMID: 9721215) Thomson RB … Aronson PS (Genomics 1998) 2 3 4 23
  2. Isolation and cDNA cloning of Ksp-cadherin, a novel kidney-specific member of the cadherin multigene family. (PMID: 7615566) Thomson RB … Aronson PS (The Journal of biological chemistry 1995) 2 3 23
  3. alpha B-crystallin is a cytoplasmic interaction partner of the kidney-specific cadherin-16. (PMID: 18343407) Thedieck C … Klein G (Journal of molecular biology 2008) 3 23
  4. Expression analysis of kidney-specific cadherin in a wide spectrum of traditional and newly recognized renal epithelial neoplasms: diagnostic and histogenetic implications. (PMID: 17895753) Kuehn A … Amin MB (The American journal of surgical pathology 2007) 3 23
  5. Expression of Ksp-cadherin during kidney development and in renal cell carcinoma. (PMID: 15886705) Thedieck C … Klein G (British journal of cancer 2005) 3 23

Products for CDH16 Gene

Sources for CDH16 Gene