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    CDH6 cadherin 6 [ Homo sapiens (human) ]

    Gene ID: 1004, updated on 27-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
    mouse all
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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
    • 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)

    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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