CDH3 (cadherin 3)

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Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

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 Show/Hide all (20)

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 Show/Hide all (43)

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 Show/Hide all (6)

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) Show/Hide all (39)

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	220 → 319	Cadherin domain	Domain
  PF00028	Cadherin	333 → 432	Cadherin domain	Domain
  PF00028	Cadherin	445 → 539	Cadherin domain	Domain
  PF00028	Cadherin	112 → 206	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 Pathway:

Cell adhesion molecules

Reactome Pathway:

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 Show/Hide Causal Diseases (9)
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 Show/Hide Unknown Diseases (26)
Phenotype Name	Clinical Significance	Source	Reference	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	19915572	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL ADENOMA	—	GWAS catalog	30510241	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	30510241, 36539618, 38872215	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
concomitant exotropia	Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	37156999	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS MELANOMA	—	GWAS catalog	32341527	★★☆☆☆ 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	37156999	★★☆☆☆ 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	24076602	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CYSTS	—	CTD	21239663	★★☆☆☆ 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	37340002	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
PROSTATE CARCINOMA	—	GWAS catalog	37340002	★★☆☆☆ 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	21297633, 37156999	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Genes

Sort by: Blended Diseases Pathways Evidence source

KRT74 3 shared diseasesEctodermal dysplasia, Hypotrichosis, Hypotrichosis simplex 5 shared evidence sourcesCTD (Ectodermal dysplasia), Disgenet (Ectodermal dysplasia), HPO (Ectodermal dysplasia), Disgenet (Hypotrichosis), Disgenet (Hypotrichosis simplex) Related via 3 shared diseases including Ectodermal dysplasia, Hypotrichosis — evidence mostly Disgenet. CDH4 2 shared pathwaysCell adhesion molecules, Adherens junctions interactions Related via 2 shared pathways including Cell adhesion molecules, Adherens junctions interactions. CDH15 2 shared pathwaysCell adhesion molecules, Adherens junctions interactions 1 shared evidence sourceGWAS catalog (Melanoma) Related via 2 shared pathways including Cell adhesion molecules, Adherens junctions interactions — evidence mostly GWAS catalog. CADM1 2 shared pathwaysCell adhesion molecules, Adherens junctions interactions Related via 2 shared pathways including Cell adhesion molecules, Adherens junctions interactions. CADM3 2 shared pathwaysCell adhesion molecules, Adherens junctions interactions Related via 2 shared pathways including Cell adhesion molecules, Adherens junctions interactions.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
KRT74	3	["Ectodermal dysplasia","Hypotrichosis","Hypotrichosis simplex"]	0	[]	5	["CTD (Ectodermal dysplasia)","Disgenet (Ectodermal dysplasia)","HPO (Ectodermal dysplasia)","Disgenet (Hypotrichosis)","Disgenet (Hypotrichosis simplex)"]
CDH4	0	[]	2	["Cell adhesion molecules","Adherens junctions interactions"]	0	[]
CDH15	0	[]	2	["Cell adhesion molecules","Adherens junctions interactions"]	1	["GWAS catalog (Melanoma)"]
CADM1	0	[]	2	["Cell adhesion molecules","Adherens junctions interactions"]	0	[]
CADM3	0	[]	2	["Cell adhesion molecules","Adherens junctions interactions"]	0	[]

Diseases Linked via Similar Genes

Alzheimer disease Linked via 2 of 5 related genesCDH4, CDH15 Bipolar disorder Linked via 2 of 5 related genesCDH4, CADM3 Major depressive disorder Linked via 2 of 5 related genesCDH4, CADM1 Obesity Linked via 2 of 5 related genesCDH4, CADM1 Willis-ekbom disease Linked via 2 of 5 related genesCDH4, CADM1

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Alzheimer disease	2	["CDH4","CDH15"]
Bipolar disorder	2	["CDH4","CADM3"]
Major depressive disorder	2	["CDH4","CADM1"]
Obesity	2	["CDH4","CADM1"]
Willis-ekbom disease	2	["CDH4","CADM1"]