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    CDH6 cadherin 6 [ Homo sapiens (human) ]

    Gene ID: 1004, updated on 18-Sep-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001362435.2NP_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:163264
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:79157
      CA; Cadherin repeats
    2. NM_004932.4NP_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:163264
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:79157
      CA; Cadherin repeats
      pfam01049
      Location:645782
      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_011513921.4XP_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:163264
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:79157
      CA; Cadherin repeats
      pfam01049
      Location:645782
      Cadherin_C; Cadherin cytoplasmic region
    2. XM_047416591.1XP_047272547.1  cadherin-6 isoform X2

      UniProtKB/TrEMBL
      D6RF86

    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_054351375.1XP_054207350.1  cadherin-6 isoform X1

      UniProtKB/Swiss-Prot
      A8K5H5, P55285, Q9BWS0
    2. XM_054351377.1XP_054207352.1  cadherin-6 isoform X2

      UniProtKB/TrEMBL
      D6RF86
    3. XM_054351376.1XP_054207351.1  cadherin-6 isoform X1

      UniProtKB/Swiss-Prot
      A8K5H5, P55285, Q9BWS0