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Aliases for CDH6 Gene

Aliases for CDH6 Gene

  • Cadherin 6 2 3 5
  • Cadherin 6, Type 2, K-Cadherin (Fetal Kidney) 2 3
  • K-Cadherin 2 4
  • Kidney Cadherin 4
  • Cadherin-6 3
  • CAD6 3
  • KCAD 3

External Ids for CDH6 Gene

Previous GeneCards Identifiers for CDH6 Gene

  • GC05P030978
  • GC05P031640
  • GC05P031193
  • GC05P031239

Summaries for CDH6 Gene

Entrez Gene Summary for CDH6 Gene

  • This gene encodes a member of the cadherin superfamily. Cadherins are membrane glycoproteins that mediate homophilic cell-cell adhesion and play critical roles in cell differentiation and morphogenesis. The encoded protein is a type II cadherin and may play a role in kidney development as well as endometrium and placenta formation. Decreased expression of this gene may be associated with tumor growth and metastasis. [provided by RefSeq, May 2011]

GeneCards Summary for CDH6 Gene

CDH6 (Cadherin 6) is a Protein Coding gene. Diseases associated with CDH6 include Renal Cell Carcinoma, Nonpapillary. 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 CDH10.

UniProtKB/Swiss-Prot for CDH6 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 CDH6 Gene

Additional gene information for CDH6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDH6 Gene

Genomics for CDH6 Gene

GeneHancer (GH) Regulatory Elements for CDH6 Gene

Promoters and enhancers for CDH6 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
GH05J031193 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 650.7 +1.1 1064 3.4 CTCF ZBTB8A RAD21 HIC1 ZNF335 ZFHX2 POLR2A PRDM10 ZNF600 ZBTB26 CDH6 ENSG00000254138 GC05M031204
GH05J031122 Enhancer 0.3 ENCODE 26.2 -70.1 -70067 1.5 POLR2A CDH6 ENSG00000253940 ENSG00000254138
GH05J031218 Enhancer 0.5 ENCODE 11 +25.5 25464 1.2 SOX13 CTCF RFX1 RFX3 ZNF644 CDH6 ENSG00000254138 LOC105374709 GC05M031229
GH05J031105 Enhancer 0.4 ENCODE 11 -86.5 -86537 2.4 NANOG POLR2A EZH2 CDH6 ENSG00000253940 ENSG00000254138
GH05J031224 Enhancer 0.4 ENCODE 10.8 +31.4 31423 1.8 POLR2A FOS ENSG00000254138 CDH6 GC05M031229 LOC105374709
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDH6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDH6 gene promoter:
  • Evi-1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • POU3F2
  • Nkx2-5
  • FOXL1

Genomic Locations for CDH6 Gene

Genomic Locations for CDH6 Gene
chr5:31,193,655-31,329,146
(GRCh38/hg38)
Size:
135,492 bases
Orientation:
Plus strand
chr5:31,193,762-31,329,253
(GRCh37/hg19)
Size:
135,492 bases
Orientation:
Plus strand

Genomic View for CDH6 Gene

Genes around CDH6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDH6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDH6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDH6 Gene

Proteins for CDH6 Gene

  • Protein details for CDH6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55285-CADH6_HUMAN
    Recommended name:
    Cadherin-6
    Protein Accession:
    P55285
    Secondary Accessions:
    • A8K5H5
    • Q9BWS0

    Protein attributes for CDH6 Gene

    Size:
    790 amino acids
    Molecular mass:
    88309 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CDH6 Gene

    Alternative splice isoforms for CDH6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CDH6 Gene

Post-translational modifications for CDH6 Gene

  • Glycosylation at Asn536, posLast=455455, posLast=437437, posLast=399399, Asn255, and Asn49
  • Modification sites at PhosphoSitePlus

Other Protein References for CDH6 Gene

No data available for DME Specific Peptides for CDH6 Gene

Domains & Families for CDH6 Gene

Gene Families for CDH6 Gene

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

Suggested Antigen Peptide Sequences for CDH6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P55285

UniProtKB/Swiss-Prot:

CADH6_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 CDH6: view

Function for CDH6 Gene

Molecular function for CDH6 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 6,K-cadherin,transmembrane glycoprotein component of adherens junction,expressed in fetal kidney

Phenotypes From GWAS Catalog for CDH6 Gene

Gene Ontology (GO) - Molecular Function for CDH6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0008092 cytoskeletal protein binding IBA --
GO:0042803 protein homodimerization activity IBA --
GO:0045296 cadherin binding IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CDH6: view
genes like me logo Genes that share phenotypes with CDH6: view

Animal Models for CDH6 Gene

MGI Knock Outs for CDH6:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDH6 Gene

Localization for CDH6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH6 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 CDH6 gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 2
cytosol 2
cytoskeleton 1
peroxisome 1
nucleus 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CDH6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005913 cell-cell adherens junction IBA --
GO:0009986 cell surface IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CDH6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDH6 Gene

Pathways & Interactions for CDH6 Gene

genes like me logo Genes that share pathways with CDH6: view

Gene Ontology (GO) - Biological Process for CDH6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IBA --
GO:0007043 cell-cell junction assembly IBA --
GO:0007155 cell adhesion TAS 7743525
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007219 Notch signaling pathway IEA --
genes like me logo Genes that share ontologies with CDH6: view

No data available for SIGNOR curated interactions for CDH6 Gene

Drugs & Compounds for CDH6 Gene

(4) Drugs for CDH6 Gene - From: ClinicalTrials and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
Antibodies Pharma 7224
Immunoglobulins Pharma 7224
Maytansine Pharma 86
genes like me logo Genes that share compounds with CDH6: view

Transcripts for CDH6 Gene

Unigene Clusters for CDH6 Gene

Cadherin 6, type 2, K-cadherin (fetal kidney):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDH6 Gene

No ASD Table

Relevant External Links for CDH6 Gene

GeneLoc Exon Structure for
CDH6
ECgene alternative splicing isoforms for
CDH6

Expression for CDH6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDH6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDH6 Gene

This gene is overexpressed in Kidney - Cortex (x7.3) and Artery - Tibial (x5.1).

Protein differential expression in normal tissues from HIPED for CDH6 Gene

This gene is overexpressed in Amniocyte (38.5) and Serum (13.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDH6 Gene



NURSA nuclear receptor signaling pathways regulating expression of CDH6 Gene:

CDH6

SOURCE GeneReport for Unigene cluster for CDH6 Gene:

Hs.124776

mRNA Expression by UniProt/SwissProt for CDH6 Gene:

P55285-CADH6_HUMAN
Tissue specificity: Highly expressed in brain, cerebellum, and kidney. Lung, pancreas, and gastric mucosa show a weak expression. Also expressed in certain liver and kidney carcinomas.

Evidence on tissue expression from TISSUES for CDH6 Gene

  • Kidney(4.7)
  • Nervous system(4.5)
  • Liver(4.2)
  • Bone marrow(4)
genes like me logo Genes that share expression patterns with CDH6: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDH6 Gene

Orthologs for CDH6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CDH6 34 33
  • 98.44 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CDH6 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CDH6 34 33
  • 92.95 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Cdh6 16 34 33
  • 90.51 (n)
rat
(Rattus norvegicus)
Mammalia Cdh6 33
  • 89.52 (n)
dog
(Canis familiaris)
Mammalia CDH6 34
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CDH6 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves CDH6 34 33
  • 80.8 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CDH6 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cdh6 33
  • 74.28 (n)
African clawed frog
(Xenopus laevis)
Amphibia cdh6-A 33
zebrafish
(Danio rerio)
Actinopterygii cdh6 34 33
  • 65.81 (n)
ManyToMany
CABZ01067945.1 34
  • 65 (a)
ManyToMany
cdh10 34
  • 64 (a)
ManyToMany
Species where no ortholog for CDH6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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 squirt (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 CDH6 Gene

ENSEMBL:
Gene Tree for CDH6 (if available)
TreeFam:
Gene Tree for CDH6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDH6: view image

Paralogs for CDH6 Gene

Paralogs for CDH6 Gene

(22) SIMAP similar genes for CDH6 Gene using alignment to 3 proteins:

  • CADH6_HUMAN
  • D6RF86_HUMAN
  • L8EAC6_HUMAN
genes like me logo Genes that share paralogs with CDH6: view

Variants for CDH6 Gene

Sequence variations from dbSNP and Humsavar for CDH6 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000026608 -- 31,286,147(+) A/G intron_variant
rs1000030210 -- 31,248,090(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000045012 -- 31,197,836(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000049449 -- 31,313,151(+) T/C intron_variant
rs1000064624 -- 31,200,591(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDH6 Gene

Variant ID Type Subtype PubMed ID
dgv5619n100 CNV gain 25217958
esv2759336 CNV gain 17122850
esv3368091 CNV insertion 20981092
esv3604572 CNV gain 21293372
esv3604573 CNV loss 21293372
nsv1022392 CNV gain 25217958
nsv1123935 CNV deletion 24896259
nsv830247 CNV gain 17160897

Variation tolerance for CDH6 Gene

Residual Variation Intolerance Score: 6.55% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDH6 Gene

Human Gene Mutation Database (HGMD)
CDH6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDH6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH6 Gene

Disorders for CDH6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CDH6 Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
renal cell carcinoma, nonpapillary
  • rcc
- elite association - COSMIC cancer census association via MalaCards
Search CDH6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDH6

genes like me logo Genes that share disorders with CDH6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDH6 Gene

Publications for CDH6 Gene

  1. Isolation and sequence analysis of human cadherin-6 complementary DNA for the full coding sequence and its expression in human carcinoma cells. (PMID: 7743525) Shimoyama Y … Hirohashi S (Cancer research 1995) 2 3 4 22 58
  2. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T … Smith RD (Journal of proteome research 2005) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Mapping of a cadherin gene cluster to a region of chromosome 5 subject to frequent allelic loss in carcinoma. (PMID: 10191097) Chalmers IJ … Atkinson MJ (Genomics 1999) 2 3 58

Products for CDH6 Gene

Sources for CDH6 Gene

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