CDH3 (cadherin 3)

Gene

• Entrez ID: 1001
• Gene name: Cadherin 3
• Gene symbol: CDH3
• Synonyms (NCBI Gene): CDHP, HJMD, PCAD
• Chromosome: 16
• Chromosome location: 16q22.1
• 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 cal

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs36038900	A>C,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs121434542	G>A	Pathogenic	Coding sequence variant, missense variant
rs121434543	A>G,T	Pathogenic	Coding sequence variant, missense variant
rs138190335	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Coding sequence variant, missense variant
rs144403828	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs201521473	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs376302917	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs724159984	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs724159985	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs752131891	G>C,T	Pathogenic	Splice donor variant
rs755910254	G>A	Pathogenic	Coding sequence variant, stop gained
rs758614807	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs775268226	C>A,G,T	Likely-pathogenic	Coding sequence variant, 3 prime UTR variant, intron variant, missense variant
rs775541873	G>A,C,T	Likely-pathogenic	Coding sequence variant, missense variant
rs866290802	C>T	Pathogenic	Coding sequence variant, stop gained
rs1238109100	G>A	Likely-pathogenic	Initiator codon variant, 5 prime UTR variant, missense variant
rs1597807758	C>A	Pathogenic	Coding sequence variant, stop gained
rs1597807897	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1597809479	G>T	Pathogenic	Coding sequence variant, missense variant
rs1597817636	T>G	Likely-pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017451	hsa-miR-335-5p	Microarray	18185580
MIRT021364	hsa-miR-9-5p	Microarray	17612493
MIRT021719	hsa-miR-132-3p	Microarray	17612493
MIRT733635	hsa-miR-665	ELISA, Luciferase reporter assay, Western blotting	33968210
MIRT879841	hsa-miR-1286	CLIP-seq
MIRT879842	hsa-miR-133a	CLIP-seq
MIRT879843	hsa-miR-133b	CLIP-seq
MIRT879844	hsa-miR-2355-5p	CLIP-seq
MIRT879845	hsa-miR-296-5p	CLIP-seq
MIRT879846	hsa-miR-3163	CLIP-seq
MIRT879847	hsa-miR-3622a-5p	CLIP-seq
MIRT879848	hsa-miR-3689a-3p	CLIP-seq
MIRT879849	hsa-miR-3689c	CLIP-seq
MIRT879850	hsa-miR-4281	CLIP-seq
MIRT879851	hsa-miR-4423-3p	CLIP-seq
MIRT879852	hsa-miR-4714-3p	CLIP-seq
MIRT879853	hsa-miR-4722-5p	CLIP-seq
MIRT879854	hsa-miR-4728-5p	CLIP-seq
MIRT879855	hsa-miR-4756-3p	CLIP-seq
MIRT879856	hsa-miR-4797-3p	CLIP-seq
MIRT879857	hsa-miR-548ac	CLIP-seq
MIRT879858	hsa-miR-548ae	CLIP-seq
MIRT879859	hsa-miR-548aj	CLIP-seq
MIRT879860	hsa-miR-548am	CLIP-seq
MIRT879861	hsa-miR-548d-3p	CLIP-seq
MIRT879862	hsa-miR-548x	CLIP-seq
MIRT879863	hsa-miR-548z	CLIP-seq
MIRT1960704	hsa-miR-1197	CLIP-seq
MIRT1960705	hsa-miR-1299	CLIP-seq
MIRT1960706	hsa-miR-1827	CLIP-seq
MIRT1960707	hsa-miR-214	CLIP-seq
MIRT1960708	hsa-miR-296-3p	CLIP-seq
MIRT1960709	hsa-miR-3619-5p	CLIP-seq
MIRT1960710	hsa-miR-3921	CLIP-seq
MIRT1960711	hsa-miR-4261	CLIP-seq
MIRT1960712	hsa-miR-4436a	CLIP-seq
MIRT1960713	hsa-miR-4649-3p	CLIP-seq
MIRT1960714	hsa-miR-4653-5p	CLIP-seq
MIRT1960715	hsa-miR-4690-5p	CLIP-seq
MIRT1960716	hsa-miR-4704-3p	CLIP-seq
MIRT1960717	hsa-miR-4757-5p	CLIP-seq
MIRT1960718	hsa-miR-761	CLIP-seq
MIRT1960719	hsa-miR-875-3p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
BRCA1	Repression	22120723
BRCA1	Unknown	19882246
GATA3	Repression	22120723
HOXA9	Unknown	25023983
MYC	Unknown	19882246
SP1	Unknown	19882246

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000902	Process	Cell morphogenesis	IBA
GO:0001895	Process	Retina homeostasis	IMP	23143461
GO:0005509	Function	Calcium ion binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005886	Component	Plasma membrane	IDA	10460003
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0005912	Component	Adherens junction	IBA
GO:0005912	Component	Adherens junction	IEA
GO:0007043	Process	Cell-cell junction assembly	IBA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	TAS	2793940
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IEA
GO:0007601	Process	Visual perception	IEA
GO:0008013	Function	Beta-catenin binding	IBA
GO:0010628	Process	Positive regulation of gene expression	IMP	23334344
GO:0010838	Process	Positive regulation of keratinocyte proliferation	IMP	22696062
GO:0016020	Component	Membrane	IEA
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IBA
GO:0016342	Component	Catenin complex	IBA
GO:0016477	Process	Cell migration	IBA
GO:0022405	Process	Hair cycle process	IMP	23143461
GO:0030054	Component	Cell junction	IDA
GO:0030054	Component	Cell junction	IEA
GO:0030512	Process	Negative regulation of transforming growth factor beta receptor signaling pathway	IMP	22696062
GO:0031424	Process	Keratinization	IMP	22696062
GO:0032773	Process	Positive regulation of tyrosinase activity	IMP	23334344
GO:0034332	Process	Adherens junction organization	IBA
GO:0043568	Process	Positive regulation of insulin-like growth factor receptor signaling pathway	IMP	22696062
GO:0044331	Process	Cell-cell adhesion mediated by cadherin	IBA
GO:0045296	Function	Cadherin binding	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0048023	Process	Positive regulation of melanin biosynthetic process	IMP	23334344
GO:0051049	Process	Regulation of transport	IEA
GO:0051796	Process	Negative regulation of timing of catagen	IMP	22696062
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IMP	22696062, 23334344
GO:0098609	Process	Cell-cell adhesion	IEA
GO:0098609	Process	Cell-cell adhesion	IEA
GO:1902910	Process	Positive regulation of melanosome transport	IMP	23334344

Other IDs

• MIM: 114021
• HGNC: 1762
• e!Ensembl: ENSG00000062038

Protein

• UniProt ID: P22223
• Protein name: Cadherin-3 (Placental cadherin) (P-cadherin)
• Protein function: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.
• PDB: 4OY9, 4ZML, 4ZMN, 4ZMO, 4ZMP, 4ZMQ, 4ZMT, 4ZMV, 4ZMW, 4ZMX, 4ZMY, 4ZMZ, 5JYL, 5JYM, 6ZTB, 6ZTR, 7CME, 7CMF, 8HYI
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00028	Cadherin	112 → 206	Cadherin domain	Domain
  PF00028	Cadherin	220 → 319	Cadherin domain	Domain
  PF00028	Cadherin	333 → 432	Cadherin domain	Domain
  PF00028	Cadherin	445 → 539	Cadherin domain	Domain
  PF01049	Cadherin_C	678 → 826	Cadherin cytoplasmic region	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in some normal epithelial tissues and in some carcinoma cell lines. {ECO:0000269|PubMed:2702654}.
• Sequence:

  MGLPRGPLASLLLLQVCWLQCAASEPCRAVFREAEVTLEAGGAEQEPGQALGKVFMGCPG
  QEPALFSTDNDDFTVRNGETVQERRSLKERNPLKIFPSKRILRRHKRDWVVAPISVPENG
  KGPFPQRLNQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAK
  YELFGHAVSENGASVEDPMNISIIVTDQNDHKPKFTQDTFRGSVLEGVLPGTSVMQVTAT
  DEDDAIYTYNGVVAYSIHSQEPKDPHDLMFTIHRSTGTISVISSGLDREKVPEYTLTIQA
  TDMDGDGSTTTAVAVVEILDANDNAPMFDPQKYEAHVPENAVGHEVQRLTVTDLDAPNSP
  AWRATYLIMGGDDGDHFTITTHPESNQGILTTRKGLDFEAKNQHTLYVEVTNEAPFVLKL
  PTSTATIVVHVEDVNEAPVFVPPSKVVEVQEGIPTGEPVCVYTAEDPDKENQKISYRILR
  DPAGWLAMDPDSGQVTAVGTLDREDEQFVRNNIYEVMVLAMDNGSPPTTGTGTLLLTLID
  VNDHGPVPEPRQITICNQSPVRQVLNITDKDLSPHTSPFQAQLTDDSDIYWTAEVNEEGD
  TVVLSLKKFLKQDTYDVHLSLSDHGNKEQLTVIRATVCDCHGHVETCPGPWKGGFILPVL
  GAVLALLFLLLVLLLLVRKKRKIKEPLLLPEDDTRDNVFYYGEEGGGEEDQDYDITQLHR
  GLEARPEVVLRNDVAPTIIPTPMYRPRPANPDEIGNFIIENLKAANTDPTAPPYDTLLVF
  DYEGSGSDAASLSSLTSSASDQDQDYDYLNEWGSRFKKLADMYGGGEDD

• Sequence length: 829

Pathways

KEGG:

Cell adhesion molecules

Reactome:

Adherens junctions interactions

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
CDH3-related disorder	Likely pathogenic	rs1437616632	RCV003894681	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital hypotrichosis with juvenile macular dystrophy	Pathogenic; Likely pathogenic	rs1474181679, rs761941770, rs779888126, rs724159984, rs121434542, rs724159985, rs752131891, rs1597809479, rs1597817636, rs1157108621	RCV002300590 RCV002300633 RCV002464042 RCV000019205 RCV000019206 RCV002243655 RCV000824709 RCV000824812 RCV000985062 RCV004813151	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
EEM syndrome	Pathogenic; Likely pathogenic	rs121434543, rs724159985, rs1961688932	RCV000019207 RCV000019208 RCV001196535	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypotrichosis	Pathogenic	rs866290802	RCV004798861	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypotrichosis simplex	Pathogenic	rs2152100234	RCV002248476	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypotrichosis with juvenile macular dystrophy	Pathogenic; Likely pathogenic	rs724159984, rs1597807758, rs1597807897	RCV001002926 RCV001002924 RCV001002925	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Macular dystrophy	Pathogenic	rs724159985	RCV000505148	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs1961376390, rs1474181679, rs779888126, rs1157340043, rs1437616632, rs121434542, rs1157108621	RCV004815518 RCV004815631 RCV004816834 RCV004816796 RCV004818437 RCV004814909 RCV001073805	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis pigmentosa	Likely pathogenic	rs1238109100	RCV000787809	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC LEFT-SIDED ULCERATIVE COLITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLITIS, ULCERATIVE	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL ADENOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
concomitant exotropia	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS MELANOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ECTODERMAL DYSPLASIA, ECTRODACTYLY, AND MACULAR DYSTROPHY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ECTODERMAL DYSPLASIA, ECTRODACTYLY, AND MACULAR DYSTROPHY SYNDROME	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE MACULAR DEGENERATION AND HYPOTRICHOSIS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CYSTS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous cell carcinoma of the head and neck	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations