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CDH3 cadherin 3 [ Homo sapiens (human) ]

Gene ID: 1001, updated on 9-Jun-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
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Genomic context

See CDH3 in Genome Data Viewer
Location:
16q22.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68645310..68733771)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74441601..74531453)
105.20220307 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
 
enables molecular_function ND
No biological Data available
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 multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
 
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)

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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.

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_2023_10

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