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    CDH3 cadherin 3 [ Homo sapiens (human) ]

    Gene ID: 1001, updated on 9-Dec-2024

    Summary

    Official Symbol
    CDH3provided by HGNC
    Official Full Name
    cadherin 3provided by HGNC
    Primary source
    HGNC:HGNC:1762
    See related
    Ensembl:ENSG00000062038 MIM:114021; AllianceGenome:HGNC:1762
    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
    CDHP; HJMD; PCAD
    Summary
    This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. This gene is located in a gene cluster in a region on the long arm of chromosome 16 that is involved in loss of heterozygosity events in breast and prostate cancer. In addition, aberrant expression of this protein is observed in cervical adenocarcinomas. Mutations in this gene are associated with hypotrichosis with juvenile macular dystrophy and ectodermal dysplasia, ectrodactyly, and macular dystrophy syndrome (EEMS). [provided by RefSeq, Nov 2015]
    Expression
    Broad expression in skin (RPKM 13.2), ovary (RPKM 12.3) and 15 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDH3 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68645310..68733771)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74441601..74531453)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68679213..68734195)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U109 Neighboring gene uncharacterized LOC124903809 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68679193-68679717 Neighboring gene calponin 2 pseudogene Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68688677 Neighboring gene CDH3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68691962-68692462 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68710737 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68733646 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68737269-68737769 Neighboring gene Sharpr-MPRA regulatory region 3013 Neighboring gene Sharpr-MPRA regulatory region 1210 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68741769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68744771-68745272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68745273-68745772 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68748223 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68749055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11024 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68757572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68762277-68762796 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68766493-68767168 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68770288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7650 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68776246 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68778919-68779504 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68780069 Neighboring gene RNA, 5S ribosomal pseudogene 429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68787439-68788396 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68790502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11025 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68791231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11026 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68792712 Neighboring gene cadherin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11029 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68799944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68800316-68800990 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 16:68802068 and 16:68802072 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68803726 Neighboring gene Sharpr-MPRA regulatory region 4224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68808283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813037-68813640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813641-68814242 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68814316 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68815000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11032 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818245 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818709 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68820718 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68825333-68825902 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68826109 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68827591-68828091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829108-68829608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829609-68830109 Neighboring gene ferritin light chain pseudogene 14

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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 hair cycle process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in keratinization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of timing of catagen IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within_negative_effect negative regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_positive_effect positive regulation of insulin-like growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of keratinocyte proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of melanin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of melanosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of tyrosinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    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
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    cadherin-3
    Names
    cadherin 3, type 1, P-cadherin (placental)
    calcium-dependent adhesion protein, placental

    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.

    Genomic

    1. NG_009096.2 RefSeqGene

      Range
      5002..59984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317195.3NP_001304124.1  cadherin-3 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift and an early stop codon. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform (1).
      Source sequence(s)
      AW339148, BC014462, BQ945506, BU543746, CA489015, CN365479
      Consensus CDS
      CCDS82004.1
      UniProtKB/TrEMBL
      B4DLF0
      Related
      ENSP00000398485.2, ENST00000429102.6
      Conserved Domains (4) summary
      cd11304
      Location:219324
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:687765
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:2696
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:113211
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_001317196.2NP_001304125.1  cadherin-3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in its 5' UTR, resulting in the use of a downstream translation start site compared to variant 1. The encoded isoform (3) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1.
      Source sequence(s)
      AC099314, AK296968, AW339148, BQ945506, BU543746, CA489015, CN365479
      UniProtKB/TrEMBL
      B4DLF0
      Conserved Domains (3) summary
      cd11304
      Location:164269
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:632769
      Cadherin_C; Cadherin cytoplasmic region
      cl09101
      Location:58156
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    3. NM_001793.6NP_001784.2  cadherin-3 isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_001784.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC099314, AW339148, BC014462, BC041846, BQ945506, BU543746, CA489015, CN365479
      Consensus CDS
      CCDS10868.1
      UniProtKB/Swiss-Prot
      B2R6F4, P22223, Q05DI6
      UniProtKB/TrEMBL
      B4DLF0
      Related
      ENSP00000264012.4, ENST00000264012.9
      Conserved Domains (4) summary
      cd11304
      Location:219324
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:687824
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:2696
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:113211
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      68645310..68733771
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433450.1XP_047289406.1  cadherin-3 isoform X1

      UniProtKB/TrEMBL
      B4DLF0
    2. XM_011522800.4XP_011521102.1  cadherin-3 isoform X1

      UniProtKB/TrEMBL
      B4DLF0
      Conserved Domains (4) summary
      cd11304
      Location:219324
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:687762
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:2696
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:113211
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      74441601..74531453
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379318.1XP_054235293.1  cadherin-3 isoform X1

      UniProtKB/TrEMBL
      B4DLF0
    2. XM_054379317.1XP_054235292.1  cadherin-3 isoform X1

      UniProtKB/TrEMBL
      B4DLF0