Gene Gene information from NCBI Gene database.
Entrez ID 999
Gene name Cadherin 1
Gene symbol CDH1
Synonyms (NCBI Gene)
Arc-1BCDS1CD324CDHEECADLCAMUVO
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 information provided by dbSNP.
231
SNP ID Visualize variation Clinical significance Consequence
rs16260 C>A Risk-factor Upstream transcript variant
rs33935154 G>A,T Benign, pathogenic, benign-likely-benign, uncertain-significance 5 prime UTR variant, missense variant, coding sequence variant
rs34507583 G>A,C Uncertain-significance, conflicting-interpretations-of-pathogenicity Missense variant, coding sequence variant
rs35572355 G>A,C,T Conflicting-interpretations-of-pathogenicity, benign, likely-benign, uncertain-significance, likely-pathogenic Missense variant, coding sequence variant
rs35606263 G>A,C Uncertain-significance, conflicting-interpretations-of-pathogenicity 5 prime UTR variant, missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1076
miRTarBase ID miRNA Experiments Reference
MIRT000029 hsa-miR-9-5p Western blot 19572217
MIRT006029 hsa-miR-92a-3p Luciferase reporter assayNorthern blotqRT-PCR 21148309
MIRT006230 hsa-miR-25-3p Luciferase reporter assayqRT-PCRWestern blot 22450326
MIRT006029 hsa-miR-92a-3p Luciferase reporter assayNorthern blotqRT-PCR 21148309
MIRT006230 hsa-miR-25-3p Luciferase reporter assayqRT-PCRWestern blot 22450326
Transcription factors Transcription factors information provided by TRRUST V2 database.
59
Transcription factor Regulation Reference
AR Repression 18794357
CBX7 Activation 19706751
DNMT1 Repression 18049164
DNMT1 Unknown 21846773
ESR1 Unknown 17893710
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
89
GO ID Ontology Definition Evidence Reference
GO:0000902 Process Cell morphogenesis IBA
GO:0002159 Process Desmosome assembly IMP 29999492
GO:0005509 Function Calcium ion binding IEA
GO:0005515 Function Protein binding IPI 10725230, 11401320, 11790773, 12526809, 15695390, 16212417, 16983094, 17220478, 17237808, 17274640, 17715295, 18093941, 18593713, 19016843, 19038973, 19604117, 19732724, 19822757, 20086044, 21685945, 22056988, 22158051, 22252131, 22294297, 22750944, 23086448, 24189400, 24424122, 246
GO:0005576 Component Extracellular region TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
192090 1748 ENSG00000039068
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P12830
Protein name Cadherin-1 (CAM 120/80) (Epithelial cadherin) (E-cadherin) (Uvomorulin) (CD antigen CD324) [Cleaved into: E-Cad/CTF1; E-Cad/CTF2; E-Cad/CTF3]
Protein function Cadherins are calcium-dependent cell adhesion proteins (PubMed:11976333). They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. CDH1 is
PDB 1O6S , 2O72 , 2OMT , 2OMU , 2OMV , 2OMX , 2OMY , 2OMZ , 3FF7 , 3FF8 , 3L6X , 3L6Y , 4ZT1 , 4ZTE , 6CXY , 6OLE , 6OLF , 6OLG , 6VEL , 7STZ , 8H62
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08758 Cadherin_pro 27 116 Cadherin prodomain like Domain
PF00028 Cadherin 159 253 Cadherin domain Domain
PF00028 Cadherin 267 366 Cadherin domain Domain
PF00028 Cadherin 380 478 Cadherin domain Domain
PF00028 Cadherin 491 585 Cadherin domain Domain
PF00028 Cadherin 598 686 Cadherin domain Domain
PF01049 Cadherin_C 733 879 Cadherin cytoplasmic region Family
Tissue specificity TISSUE SPECIFICITY: Expressed in granuloma macrophages (at protein level) (PubMed:27760340). Expressed in the skin (at protein level) (PubMed:22294297). Expressed in the liver (PubMed:3263290). {ECO:0000269|PubMed:22294297, ECO:0000269|PubMed:27760340, EC
Sequence
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDC
TGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTL
NTVG
HHHRPPPHQASVSGIQAELLTFPNSSPGLRRQKRDWVIPPISCPENEKGPFPKNLVQIKS
NKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGN
AVEDPMEILITVT
DQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAI
AYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTAT
AVITVT
DTNDNPPIFNPTTYKGQVPENEANVVITTLKVTDADAPNTPAWEAVYTILNDDG
GQFVVTTNPVNNDGILKTAKGLDFEAKQQYILHVAVTNVVPFEVSLTTSTATVTVDVL
DV
NEAPIFVPPEKRVEVSEDFGVGQEITSYTAQEPDTFMEQKITYRIWRDTANWLEINPDTG
AISTRAELDREDFEHVKNSTYTALIIATDNGSPVATGTGTLLLIL
SDVNDNAPIPEPRTI
FFCERNPKPQVINIIDADLPPNTSPFTAELTHGASANWTIQYNDPTQESIILKPKMALEV
GDYKINLKLMDNQNKDQVTTLEVSVC
DCEGAAGVCRKAQPVEAGLQIPAILGILGGILAL
LILILLLLLFLRRRAVVKEPLLPPEDDTRDNVYYYDEEGGGEEDQDFDLSQLHRGLDARP
EVTRNDVAPTLMSVPRYLPRPANPDEIGNFIDENLKAADTDPTAPPYDSLLVFDYEGSGS
EAASLSSLNSSESDKDQDYDYLNEWGNRFKKLADMYGGG
EDD
Sequence length 882
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
87
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 Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Blepharocheilodontic syndrome 1 Likely pathogenic; Pathogenic rs2152134773, rs886039685, rs1555515925, rs1555515445, rs765929630 RCV001731127
RCV000505772
RCV000505716
RCV000505743
RCV005021486
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Breast carcinoma Likely pathogenic rs2152129697 RCV001667852
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Breast lobular carcinoma Pathogenic rs121964873 RCV000013021
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Carcinoma of parotid gland Pathogenic rs2543816786 RCV006254365
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Anophthalmia-microphthalmia syndrome Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BENIGN NEOPLASM GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BLEPHARO-CHEILO-DONTIC SYNDROME Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations