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CDH20

gene
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Also known as CDH7L3Cdh7

Summary

CDH20 (cadherin 20, HGNC:1760) is a protein-coding gene on chromosome 18q21.33, encoding Cadherin-20 (Q9HBT6). Cadherins are calcium-dependent cell adhesion proteins.

This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Since disturbance of intracellular adhesion is a prerequisite for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes.

Source: NCBI Gene 28316 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 118 total
  • MANE Select transcript: NM_031891

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1760
Approved symbolCDH20
Namecadherin 20
Location18q21.33
Locus typegene with protein product
StatusApproved
AliasesCDH7L3, Cdh7
Ensembl geneENSG00000101542
Ensembl biotypeprotein_coding
OMIM605807
Entrez28316

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000262717, ENST00000536675, ENST00000538374, ENST00000587582

RefSeq mRNA: 1 — MANE Select: NM_031891 NM_031891

CCDS: CCDS11977

Canonical transcript exons

ENST00000262717 — 12 exons

ExonStartEnd
ENSE000006698976149918661499480
ENSE000008072886150295361503120
ENSE000008072896150737361507560
ENSE000008072906152796761528220
ENSE000008072916153649361536629
ENSE000008072926153902461539145
ENSE000008072936154502761545144
ENSE000010117426154997861550229
ENSE000013832946155419061555779
ENSE000016090196150038361500502
ENSE000022275646133343061333827
ENSE000022843976149040261490799

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 86.16.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6073 / max 77.8897, expressed in 230 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1704931.1062189
1704950.2946104
1704940.117364
1704960.089262

Top tissues by expression

241 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305386.16gold quality
C1 segment of cervical spinal cordUBERON:000646985.25gold quality
amygdalaUBERON:000187683.07gold quality
Brodmann (1909) area 9UBERON:001354082.53gold quality
caudate nucleusUBERON:000187382.46gold quality
anterior cingulate cortexUBERON:000983582.20gold quality
putamenUBERON:000187482.13gold quality
right frontal lobeUBERON:000281081.45gold quality
nucleus accumbensUBERON:000188281.41gold quality
spinal cordUBERON:000224081.21gold quality
prefrontal cortexUBERON:000045180.57gold quality
ganglionic eminenceUBERON:000402379.66gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.64gold quality
hypothalamusUBERON:000189878.49gold quality
dorsolateral prefrontal cortexUBERON:000983475.61gold quality
adrenal tissueUBERON:001830375.23gold quality
substantia nigraUBERON:000203874.90gold quality
neocortexUBERON:000195074.73gold quality
frontal cortexUBERON:000187073.73gold quality
medial globus pallidusUBERON:000247773.46gold quality
right hemisphere of cerebellumUBERON:001489073.11gold quality
forebrainUBERON:000189072.31gold quality
brainUBERON:000095571.44gold quality
cerebellar hemisphereUBERON:000224571.07gold quality
cerebellar cortexUBERON:000212971.04gold quality
cerebral cortexUBERON:000095670.99gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099170.91gold quality
midbrainUBERON:000189170.77gold quality
gastrocnemiusUBERON:000138870.58gold quality
corpus callosumUBERON:000233669.48gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-35yes76.94
E-HCAD-25yes24.12
E-ANND-3yes5.37

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

109 targeting CDH20, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-126-5P100.0072.713180
HSA-MIR-453199.9969.703181
HSA-MIR-607799.9968.042299
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-9-3P99.9670.882068
HSA-MIR-493-5P99.9672.472382
HSA-MIR-302E99.9670.742669
HSA-MIR-96-5P99.9572.802140
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-144-3P99.9473.982698
HSA-MIR-381-3P99.9371.872854

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCdh20ENSMUSG00000050840
rattus_norvegicusCdh20ENSRNOG00000014556

Paralogs (33): CDH1 (ENSG00000039068), CDH10 (ENSG00000040731), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDHR5 (ENSG00000099834), PCDH11X (ENSG00000102290), CDH23 (ENSG00000107736), CDH9 (ENSG00000113100), CDH6 (ENSG00000113361), CDH26 (ENSG00000124215), CDHR3 (ENSG00000128536), CDH15 (ENSG00000129910), CDH24 (ENSG00000139880), CDH11 (ENSG00000140937), CDH13 (ENSG00000140945), CDH18 (ENSG00000145526), CDHR1 (ENSG00000148600), CDH22 (ENSG00000149654), CDH8 (ENSG00000150394), CDH12 (ENSG00000154162), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), PCDH9 (ENSG00000184226), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)

Protein

Protein identifiers

Cadherin-20 — Q9HBT6 (reviewed: Q9HBT6)

All UniProt accessions (1): Q9HBT6

UniProt curated annotations — full annotation on UniProt →

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.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in placenta, adult brain, and fetal brain.

Domain organisation. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.

RefSeq proteins (1): NP_114097* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000233Cadherin_Y-type_LIRDomain
IPR002126Cadherin-like_domDomain
IPR015919Cadherin-like_sfHomologous_superfamily
IPR020894Cadherin_CSConserved_site
IPR027397Catenin-bd_sfHomologous_superfamily
IPR039808CadherinFamily

Pfam: PF00028, PF01049

UniProt features (26 total): sequence variant 6, domain 5, sequence conflict 5, glycosylation site 4, topological domain 2, signal peptide 1, propeptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HBT6-F177.330.46

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (4): 261, 420, 461, 542

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 206 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, BENPORATH_ES_WITH_H3K27ME3, GU_PDEF_TARGETS_DN, TGACCTY_ERR1_Q2, CHX10_01, GOBP_CALCIUM_DEPENDENT_CELL_CELL_ADHESION, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, AACTTT_UNKNOWN, MYB_Q3, chr18q22, HNF1_C, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_ADHERENS_JUNCTION_ORGANIZATION

GO Biological Process (9): cell morphogenesis (GO:0000902), cell-cell junction assembly (GO:0007043), homophilic cell-cell adhesion (GO:0007156), calcium-dependent cell-cell adhesion (GO:0016339), cell migration (GO:0016477), adherens junction organization (GO:0034332), cell-cell adhesion mediated by cadherin (GO:0044331), cell adhesion (GO:0007155), cell-cell adhesion (GO:0098609)

GO Molecular Function (4): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), cadherin binding (GO:0045296), metal ion binding (GO:0046872)

GO Cellular Component (4): adherens junction (GO:0005912), catenin complex (GO:0016342), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell-cell adhesion3
cell-cell junction organization2
anatomical structure morphogenesis1
cell junction assembly1
cell motility1
cellular process1
cell adhesion1
metal ion binding1
protein binding1
cell adhesion molecule binding1
cation binding1
cell-cell junction1
extrinsic component of plasma membrane1
plasma membrane protein complex1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

1134 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDH20CDH15P55291659
CDH20CDH2P19022637
CDH20CDH10Q9Y6N8626
CDH20CDH6P55285571
CDH20SMARCA4P51532511
CDH20CDH4P55283507
CDH20CTNNB1P35222464
CDH20CDH3P22223452
CDH20CDH8P55286451
CDH20CDH12P55289446
CDH20CDH9Q9ULB4417
CDH20CDH18Q13634413
CDH20CDH11P55287407
CDH20RNF152Q8N8N0396
CDH20ABT1Q9ULW3396

IntAct

2 interactions, top by confidence:

ABTypeScore
FMR1CDH20psi-mi:“MI:0915”(physical association)0.000

BioGRID (3): CDH20 (Affinity Capture-MS), CDH20 (Biochemical Activity), CDH20 (Protein-peptide)

ESM2 similar proteins: A0A8M2BIB6, F1QSQ0, F8W3X3, H2EQR6, O35902, O54800, O55111, O93319, P32926, P33545, P55280, P55285, P55286, P55287, P55288, P55289, P55292, P55849, P55850, P70407, P70408, P79995, P97291, P97326, Q01107, Q02413, Q02487, Q08554, Q08DJ5, Q13634, Q14126, Q14574, Q28060, Q3SWX5, Q5DWV1, Q5RJH3, Q61495, Q68SP4, Q6W3B0, Q7TMD7

Diamond homologs: A0A8M2BIB6, B0KW95, B2KI42, B4USZ0, F1PAA9, F1QSQ0, O02840, O35902, O54800, O55075, O55111, O93319, P08641, P09803, P10287, P10288, P12830, P15116, P19022, P19534, P19535, P20310, P22223, P24503, P30944, P32926, P33145, P33146, P33147, P33148, P33150, P33151, P33152, P33545, P39038, P55280, P55283, P55284, P55285, P55286

SIGNOR signaling

2 interactions.

AEffectBMechanism
calcium(2+)“up-regulates activity”CDH20“chemical activation”
CDH20“up-regulates activity”CTNNB1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

118 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance110
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2730 predictions. Top by Δscore:

VariantEffectΔscore
18:61500377:CCCCA:Cacceptor_loss1.0000
18:61500378:CCCAG:Cacceptor_loss1.0000
18:61500379:CCAGG:Cacceptor_loss1.0000
18:61500380:CA:Cacceptor_loss1.0000
18:61500381:A:ACacceptor_loss1.0000
18:61500449:T:TAdonor_gain1.0000
18:61500450:G:GAdonor_gain1.0000
18:61500499:ACAG:Adonor_loss1.0000
18:61500501:AGGT:Adonor_loss1.0000
18:61500502:GG:Gdonor_loss1.0000
18:61503119:GA:Gdonor_gain1.0000
18:61536628:GA:Gdonor_gain1.0000
18:61536630:G:GGdonor_gain1.0000
18:61539022:A:AGacceptor_gain1.0000
18:61539023:G:GGacceptor_gain1.0000
18:61539023:GAC:Gacceptor_gain1.0000
18:61539023:GACA:Gacceptor_gain1.0000
18:61539142:ACAG:Adonor_loss1.0000
18:61539143:CAG:Cdonor_loss1.0000
18:61539144:AG:Adonor_loss1.0000
18:61539145:GG:Gdonor_loss1.0000
18:61539146:G:GTdonor_loss1.0000
18:61539147:T:TCdonor_loss1.0000
18:61550230:G:GCdonor_loss1.0000
18:61550231:T:Gdonor_loss1.0000
18:61554184:T:Aacceptor_gain1.0000
18:61333822:TGCC:Tdonor_gain0.9900
18:61333825:CAGGT:Cdonor_loss0.9900
18:61333826:AGGTA:Adonor_loss0.9900
18:61333828:G:GCdonor_loss0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001072 (18:61359640 A>G), RS1000006175 (18:61355076 G>A), RS1000014985 (18:61527226 T>C), RS1000028495 (18:61533656 T>C), RS1000040628 (18:61476700 A>G), RS1000049353 (18:61399079 G>A), RS1000065179 (18:61343649 C>G,T), RS1000068948 (18:61398644 C>G), RS1000069512 (18:61358921 C>T), RS1000072670 (18:61483349 T>C), RS1000087201 (18:61520924 G>A,C), RS1000104667 (18:61483924 T>A), RS1000119286 (18:61397684 A>C), RS1000121578 (18:61358548 C>T), RS1000152756 (18:61405734 G>A)

Disease associations

OMIM: gene MIM:605807 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): non-syndromic syndactyly (MONDO:0019530)

Orphanet (1): Non-syndromic syndactyly (Orphanet:90025)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001762_750Obesity-related traits6.000000e-06
GCST002930_15Cobalt levels7.000000e-06
GCST004370_9Deep ovarian and/or rectovaginal disease with dense adhesions1.000000e-06
GCST007094_69Diastolic blood pressure1.000000e-08
GCST007482_1Handedness4.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:0006336diastolic blood pressure
EFO:0009902handedness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1decreases methylation2
aristolochic acid Iincreases expression1
bisphenol Aaffects methylation, decreases methylation, affects cotreatment1
ethyl-p-hydroxybenzoatedecreases expression1
benzo(e)pyrenedecreases methylation1
ferrous chloridedecreases expression1
tetrachlorodiandecreases expression1
Fulvestrantaffects cotreatment, affects methylation1
Acetaminophendecreases expression1
Benzo(a)pyreneincreases methylation1
Diethylhexyl Phthalatedecreases expression1
Methapyrilenedecreases methylation1
Triclosandecreases expression1
Asbestos, Crocidoliteaffects expression1

Clinical trials (associated diseases)

4 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04564430PHASE4UNKNOWNClonidine for Tourniquet-related Pain in Children
NCT03107546Not specifiedCOMPLETEDComparison of Scar Formation in Syndactyly Release Surgery With Full Thickness Skin Graft Versus Skin Graft Substitute
NCT06239064Not specifiedACTIVE_NOT_RECRUITINGEarly Genetic Identification of Obesity
NCT07596862Not specifiedCOMPLETEDRemote Assesment of Functional Sequelae in Patients Operated for Congenital Syndactyly
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): endometriosis, non-syndromic syndactyly

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot