CDH3 cadherin 3 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Alteration of Cadherin 3 Expression and DNA Methylation in Association with Aggressive Renal Cell Carcinoma.
Title: Alteration of Cadherin 3 Expression and DNA Methylation in Association with Aggressive Renal Cell Carcinoma.
CDH3 is associated with poor prognosis by promoting the malignancy and chemoresistance in oral squamous cell carcinoma.
Title: CDH3 is associated with poor prognosis by promoting the malignancy and chemoresistance in oral squamous cell carcinoma.
Novel compound heterozygous cadherin 3 mutations in hypotrichosis and juvenile macular dystrophy.
Title: Novel compound heterozygous cadherin 3 mutations in hypotrichosis and juvenile macular dystrophy.
Cadherin-3 is a novel oncogenic biomarker with prognostic value in glioblastoma.
Title: Cadherin-3 is a novel oncogenic biomarker with prognostic value in glioblastoma.
Placental-Cadherin, a biomarker for local immune status and poor prognosis among patients with tongue squamous cell carcinoma.
Title: Placental-Cadherin, a biomarker for local immune status and poor prognosis among patients with tongue squamous cell carcinoma.
P-Cadherin Regulates Intestinal Epithelial Cell Migration and Mucosal Repair, but Is Dispensable for Colitis Associated Colon Cancer.
Title: P-Cadherin Regulates Intestinal Epithelial Cell Migration and Mucosal Repair, but Is Dispensable for Colitis Associated Colon Cancer.
P-Cadherin and WNT5A expression in assessment of lymph node metastasis in oral squamous cell carcinoma.
Title: P-Cadherin and WNT5A expression in assessment of lymph node metastasis in oral squamous cell carcinoma.
Phase I Study of P-cadherin-targeted Radioimmunotherapy with (90)Y-FF-21101 Monoclonal Antibody in Solid Tumors.
Title: Phase I Study of P-cadherin-targeted Radioimmunotherapy with (90)Y-FF-21101 Monoclonal Antibody in Solid Tumors.
Aberrant Expression of E-cadherin, N-cadherin, and P-cadherin in Clear Cell Renal Cell Carcinoma: Association With Adverse Clinicopathologic Factors and Poor Prognosis.
Title: Aberrant Expression of E-cadherin, N-cadherin, and P-cadherin in Clear Cell Renal Cell Carcinoma: Association With Adverse Clinicopathologic Factors and Poor Prognosis.
E-cadherin to P-cadherin switching in lobular breast cancer with tubular elements.
Title: E-cadherin to P-cadherin switching in lobular breast cancer with tubular elements.

Submit: New GeneRIF Correction See all GeneRIFs (100)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital hypotrichosis with juvenile macular dystrophy MedGen: C1832162 OMIM: 601553 GeneReviews: Not available	not available
EEM syndrome MedGen: C1857041 OMIM: 225280 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-61141 (e-PCR)
- UniSTS:33812

D16S3206 (e-PCR)
- UniSTS:10818

SHGC-146481 (e-PCR)
- UniSTS:175244

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 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

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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

NG_009096.2 RefSeqGene

Range

5002..59984

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001317195.3 → NP_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:219 → 324

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:687 → 765

Cadherin_C; Cadherin cytoplasmic region

cl07391
Location:26 → 96

Cadherin_pro; Cadherin prodomain like

cl09101
Location:113 → 211

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
NM_001317196.2 → NP_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:164 → 269

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:632 → 769

Cadherin_C; Cadherin cytoplasmic region

cl09101
Location:58 → 156

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
NM_001793.6 → NP_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:219 → 324

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:687 → 824

Cadherin_C; Cadherin cytoplasmic region

cl07391
Location:26 → 96

Cadherin_pro; Cadherin prodomain like

cl09101
Location:113 → 211

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

68645310..68733771

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047433450.1 → XP_047289406.1 cadherin-3 isoform X1
XM_011522800.4 → XP_011521102.1 cadherin-3 isoform X1

UniProtKB/TrEMBL

B4DLF0

Conserved Domains (4) summary

cd11304
Location:219 → 324

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:687 → 762

Cadherin_C; Cadherin cytoplasmic region

cl07391
Location:26 → 96

Cadherin_pro; Cadherin prodomain like

cl09101
Location:113 → 211

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus