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CDH6 cadherin 6 [ Homo sapiens (human) ]

Gene ID: 1004, updated on 2-Nov-2024

Summary

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Official Symbol
CDH6provided by HGNC
Official Full Name
cadherin 6provided by HGNC
Primary source
HGNC:HGNC:1765
See related
Ensembl:ENSG00000113361 MIM:603007; AllianceGenome:HGNC:1765
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
CAD6; KCAD
Summary
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]
Expression
Broad expression in kidney (RPKM 6.1), gall bladder (RPKM 4.1) and 17 other tissues See more
Orthologs
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Genomic context

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See CDH6 in Genome Data Viewer
Location:
5p13.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (31193686..31329146)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (31307253..31442732)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (31193793..31329253)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:30823216-30823800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:30823801-30824385 Neighboring gene NANOG hESC enhancer GRCh37_chr5:30845424-30846002 Neighboring gene VISTA enhancer hs1312 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31018943-31019142 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:31053108-31054307 Neighboring gene ribosomal protein L19 pseudogene 11 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:31119151-31120350 Neighboring gene uncharacterized LOC105374709 Neighboring gene double homeobox 4 like 51 (pseudogene) Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:31342590-31343789 Neighboring gene NANOG hESC enhancer GRCh37_chr5:31427117-31427643 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31452968-31453512 Neighboring gene drosha ribonuclease III Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84469 Neighboring gene Sharpr-MPRA regulatory region 6191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:31493720-31494220 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22433 Neighboring gene chromosome 5 open reading frame 22

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 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. Alterations in expression of cadherin-6 and E-cadherin during kidney development and in renal cell carcinoma. Shimazui T, et al. Eur Urol, 2000 Sep. PMID 10940709
  2. Characterization of the role for cadherin 6 in the regulation of human endometrial receptivity. Zhou W, et al. Reprod Biol Endocrinol, 2020 Jun 29. PMID 32600462, Free PMC Article
  3. Type 2 cadherins in the human endometrium and placenta: their putative roles in human implantation and placentation. MacCalman CD, et al. Am J Reprod Immunol, 1998 Feb. PMID 9506208
  4. Cadherin-6, a cell adhesion molecule specifically expressed in the proximal renal tubule and renal cell carcinoma. Paul R, et al. Cancer Res, 1997 Jul 1. PMID 9205085
  5. Isolation and sequence analysis of human cadherin-6 complementary DNA for the full coding sequence and its expression in human carcinoma cells. Shimoyama Y, et al. Cancer Res, 1995 May 15. PMID 7743525

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cadherin-6 is a novel mediator for the migration of mesenchymal stem cells to glioblastoma cells in response to stromal cell-derived factor-1.
    Title: Cadherin-6 is a novel mediator for the migration of mesenchymal stem cells to glioblastoma cells in response to stromal cell-derived factor-1.
  2. The GLI2/CDH6 axis enhances migration, invasion and mitochondrial fission of stomach adenocarcinoma cells.
    Title: The GLI2/CDH6 axis enhances migration, invasion and mitochondrial fission of stomach adenocarcinoma cells.
  3. Characterization of the role for cadherin 6 in the regulation of human endometrial receptivity.
    Title: Characterization of the role for cadherin 6 in the regulation of human endometrial receptivity.
  4. CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE epsilon4 carriers.
    Title: CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE ε4 carriers.
  5. The low endometrial expression of beta-catenin, E-cadherin and K-cadherin were associated to fertility-related problems, such as primary intertility and recurrent pregnancy loss.
    Title: Low endometrial beta-catenin and cadherins expression patterns are predictive for primary infertility and recurrent pregnancy loss.
  6. our findings demonstrate that CDH6 exerts as an important independent biomarker that could predict human osteosarcoma clinical outcomes. miR-223-3p can inhibit cell invasion, migration, growth, and proliferation in osteosarcoma by directly targeting CDH6
    Title: miR-223-3p Inhibits Human Osteosarcoma Metastasis and Progression by Directly Targeting CDH6.
  7. Tumor suppressor genes deleted in liver cancer 1 (DLC1), F-box/WD-repeat-containing protein 7 (FBXW7), and cadherin-6 (CDH6) were identified as presumed targets in Cholangiocarcinoma (CC).Inverse correlation between promoter methylation and expression suggested miR-129-2 and members of the miR-200 family (miR-200a, miR-200b, and miR-429) as novel tumor suppressors and oncomiRs, respectively, in CC
    Title: Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma.
  8. Data indicate that BRAFV600E, P-cadherin and cadherin 6 protein expressions were correlated with one another.
    Title: Concomitant high expression of BRAFV600E, P-cadherin and cadherin 6 is associated with High TNM stage and lymph node metastasis in conventional papillary thyroid carcinoma.
  9. CDH6 is under the control of the transcription factor RUNX2, which we previously described as a crucial mediator of the Id1 pro-invasive function in thyroid tumor cells.
    Title: Cadherin 6 is a new RUNX2 target in TGF-β signalling pathway.
  10. The chromatin modifications were determined at five PRC2 targets commonly underexpressed in multiple myeloma (CIITA, CXCL12, GATA2, CDH6 and ICSBP/IRF8). The selected genes were confirmed to be underexpressed in MM compared to normal plasma cells.
    Title: Polycomb target genes are silenced in multiple myeloma.
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

EBI GWAS Catalog

Description
Genome-wide association study identifies BICD1 as a susceptibility gene for emphysema.
EBI GWAS Catalog
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
EBI GWAS Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
EBI GWAS Catalog

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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Markers

Homology

Clone Names

  • FLJ14176, DKFZp564N1116

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables beta-catenin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell adhesion mediated by cadherin IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell junction assembly 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
  
involved_in synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
cadherin-6
Names
cadherin 6, type 2, K-cadherin (fetal kidney)

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_001362435.2 → NP_001349364.1  cadherin-6 isoform 2 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' CDS and 3' UTR, compared to variant 1, and encodes a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC091898, AC113386
    UniProtKB/TrEMBL
    D6RF86
    Related
    ENSP00000424843.1, ENST00000514738.5
    Conserved Domains (2) summary
    cd11304
    Location:163 → 264
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:79 → 157
    CA; Cadherin repeats

  2. NM_004932.4 → NP_004923.1  cadherin-6 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_004923.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC091898, D31784, DC353791
    Consensus CDS
    CCDS3894.1
    UniProtKB/Swiss-Prot
    A8K5H5, P55285, Q9BWS0
    Related
    ENSP00000265071.2, ENST00000265071.3
    Conserved Domains (3) summary
    cd11304
    Location:163 → 264
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:79 → 157
    CA; Cadherin repeats
    pfam01049
    Location:645 → 782
    Cadherin_C; Cadherin cytoplasmic region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    31193686..31329146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513921.4 → XP_011512223.1  cadherin-6 isoform X1

    See identical proteins and their annotated locations for XP_011512223.1

    UniProtKB/Swiss-Prot
    A8K5H5, P55285, Q9BWS0
    Conserved Domains (3) summary
    cd11304
    Location:163 → 264
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:79 → 157
    CA; Cadherin repeats
    pfam01049
    Location:645 → 782
    Cadherin_C; Cadherin cytoplasmic region

  2. XM_047416591.1 → XP_047272547.1  cadherin-6 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    31307253..31442732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351375.1 → XP_054207350.1  cadherin-6 isoform X1

    UniProtKB/Swiss-Prot
    A8K5H5, P55285, Q9BWS0

  2. XM_054351377.1 → XP_054207352.1  cadherin-6 isoform X2

  3. XM_054351376.1 → XP_054207351.1  cadherin-6 isoform X1

    UniProtKB/Swiss-Prot
    A8K5H5, P55285, Q9BWS0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55285.1 GenPept UniProtKB/Swiss-Prot:P55285

Gene LinkOut

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

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