CDH12

gene
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Also known as Br-cadherinCDHB

Summary

CDH12 (cadherin 12, HGNC:1751) is a protein-coding gene on chromosome 5p14.3, encoding Cadherin-12 (P55289). Cadherins are calcium-dependent cell adhesion proteins.

This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin appears to be expressed specifically in the brain and its temporal pattern of expression would be consistent with a role during a critical period of neuronal development, perhaps specifically during synaptogenesis.

Source: NCBI Gene 1010 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 166 total — 1 pathogenic
  • MANE Select transcript: NM_004061

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1751
Approved symbolCDH12
Namecadherin 12
Location5p14.3
Locus typegene with protein product
StatusApproved
AliasesBr-cadherin, CDHB
Ensembl geneENSG00000154162
Ensembl biotypeprotein_coding
OMIM600562
Entrez1010

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000382254, ENST00000504376, ENST00000517378, ENST00000518209, ENST00000520668, ENST00000521384, ENST00000521745, ENST00000522262, ENST00000880753, ENST00000954356

RefSeq mRNA: 9 — MANE Select: NM_004061 NM_001317227, NM_001317228, NM_001364104, NM_001364105, NM_001364106, NM_001364107, NM_001364108, NM_001364109, NM_004061

CCDS: CCDS3890, CCDS82991

Canonical transcript exons

ENST00000382254 — 15 exons

ExonStartEnd
ENSE000014026562221249822212643
ENSE000014047362250527022505364
ENSE000014062752240525722405351
ENSE000014914332285305822853344
ENSE000020723062175067321752236
ENSE000034629502184216121842328
ENSE000034629892180216721802420
ENSE000034657652176055821760675
ENSE000035253762207844622078862
ENSE000035299862176497821765099
ENSE000035351592197509121975385
ENSE000036259352178335821783494
ENSE000036320462175559121755842
ENSE000036757612181694521817132
ENSE000036942642185467121854790

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 78.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7445 / max 229.6578, expressed in 127 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
611040.6135113
611050.131061

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.25gold quality
middle temporal gyrusUBERON:000277177.10gold quality
postcentral gyrusUBERON:000258176.00gold quality
adrenal tissueUBERON:001830375.78gold quality
cortical plateUBERON:000534375.33gold quality
Brodmann (1909) area 23UBERON:001355475.02gold quality
parietal lobeUBERON:000187274.82gold quality
right uterine tubeUBERON:000130274.75gold quality
primary visual cortexUBERON:000243674.32gold quality
frontal poleUBERON:000279573.36gold quality
occipital lobeUBERON:000202173.19gold quality
Brodmann (1909) area 10UBERON:001354173.06gold quality
superior frontal gyrusUBERON:000266172.58gold quality
paraflocculusUBERON:000535172.54gold quality
middle frontal gyrusUBERON:000270271.95gold quality
prefrontal cortexUBERON:000045171.89gold quality
entorhinal cortexUBERON:000272871.34gold quality
Brodmann (1909) area 46UBERON:000648371.33gold quality
cerebellar vermisUBERON:000472069.57silver quality
endometrium epitheliumUBERON:000481169.57gold quality
right adrenal glandUBERON:000123368.70gold quality
ventricular zoneUBERON:000305368.64gold quality
frontal cortexUBERON:000187068.54gold quality
right adrenal gland cortexUBERON:003582768.52gold quality
ganglionic eminenceUBERON:000402368.08gold quality
upper leg skinUBERON:000426267.43gold quality
adrenal glandUBERON:000236966.96gold quality
neocortexUBERON:000195066.88gold quality
left adrenal glandUBERON:000123466.55gold quality
orbitofrontal cortexUBERON:000416766.49silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-35yes92.01
E-MTAB-7606no3.96
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting CDH12, 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-6867-5P100.0082.213464
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-574-5P100.0066.01989
HSA-MIR-223-3P99.9970.141140
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-511-3P99.9968.851467
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-314899.9775.066478
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-365899.9673.874379
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-335-3P99.9373.364958
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-430299.8967.941187
HSA-MIR-4697-3P99.8967.091123
HSA-MIR-129-5P99.8870.263273
HSA-MIR-612499.8769.783551
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-130B-5P99.8368.501888
HSA-MIR-3681-5P99.8266.88387
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248

Literature-anchored findings (GeneRIF, showing 6)

  • E2F4, PHACTR3, PRAME family member and CDH12 most probably play important role in non-small-cell lung cancer geneses (PMID:19473719)
  • CDH12 may play an important role in the invasion and metastasis of salivary adenoid cystic carcinoma (PMID:21573496)
  • CDH12 may influence CRC cell progression. (PMID:26762412)
  • Identification of a CDH12 potential candidate genetic variant for an autosomal dominant form of transgrediens and progrediens palmoplantar keratoderma in a Tunisian family. (PMID:31911611)
  • An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer. (PMID:34385456)
  • The Role of Cadherin 12 (CDH12) in the Peritoneal Fluid among Patients with Endometriosis and Endometriosis-Related Infertility. (PMID:36141853)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCdh12ENSMUSG00000040452
rattus_norvegicusCdh12ENSRNOG00000026392

Paralogs (33): CDH1 (ENSG00000039068), CDH10 (ENSG00000040731), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDHR5 (ENSG00000099834), CDH20 (ENSG00000101542), 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), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), PCDH9 (ENSG00000184226), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)

Protein

Protein identifiers

Cadherin-12P55289 (reviewed: P55289)

Alternative names: Brain cadherin, Neural type cadherin 2

All UniProt accessions (1): P55289

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. 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.

Isoforms (2)

UniProt IDNamesCanonical?
P55289-11yes
P55289-22

RefSeq proteins (9): NP_001304156, NP_001304157, NP_001351033, NP_001351034, NP_001351035, NP_001351036, NP_001351037, NP_001351038, NP_004052* (*=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 (25 total): domain 5, sequence conflict 5, glycosylation site 4, sequence variant 3, topological domain 2, signal peptide 1, propeptide 1, modified residue 1, splice variant 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P55289-F177.190.47

Functional residue map

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

Post-translational modifications (1): 787

Glycosylation sites (4): 256, 456, 537, 545

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-418990Adherens junctions interactions
R-HSA-1500931Cell-Cell communication
R-HSA-421270Cell-cell junction organization
R-HSA-446728Cell junction organization

MSigDB gene sets: 100 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE45365_NK_CELL_VS_CD8_TCELL_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_CALCIUM_DEPENDENT_CELL_CELL_ADHESION, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, MCLACHLAN_DENTAL_CARIES_DN, HOOI_ST7_TARGETS_DN, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_ADHERENS_JUNCTION_ORGANIZATION, GOBP_CELL_CELL_JUNCTION_ASSEMBLY, GOCC_CELL_CELL_JUNCTION, GOCC_MEMBRANE_PROTEIN_COMPLEX, GOCC_ANCHORING_JUNCTION

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

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Cell-cell junction organization1
Cell junction organization1
Cell-Cell communication1

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
membrane1
cell periphery1
cell-cell junction1
extrinsic component of plasma membrane1
plasma membrane protein complex1
cellular anatomical structure1

Protein interactions and networks

STRING

694 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDH12CDH9Q9ULB4540
CDH12CDH15P55291481
CDH12CDH1P12830477
CDH12CDH2P19022475
CDH12CDH13P55290471
CDH12CDH19Q9H159459
CDH12CDH20Q9HBT6446
CDH12CDH6P55285438
CDH12CDH7Q9ULB5438
CDH12CDH18Q13634415
CDH12CDH10Q9Y6N8413
CDH12CRACDQ6ZU35411
CDH12CTNNB1P35222401
CDH12CDH8P55286399
CDH12DRC4O95995389

IntAct

7 interactions, top by confidence:

ABTypeScore
IGHG1PDPK1psi-mi:“MI:0914”(association)0.350
CTNNA3ARVCFpsi-mi:“MI:0914”(association)0.350
CDH12ARVCFpsi-mi:“MI:0914”(association)0.350
CDC20BDHX16psi-mi:“MI:0914”(association)0.350

BioGRID (17): CDH12 (Affinity Capture-MS), PKP4 (Affinity Capture-MS), FRMD4A (Affinity Capture-MS), CTNNA1 (Affinity Capture-MS), CTNNB1 (Affinity Capture-MS), CDH12 (Affinity Capture-MS), CTNNA2 (Affinity Capture-MS), ARVCF (Affinity Capture-MS), CDH8 (Affinity Capture-MS), PSEN1 (Affinity Capture-MS), CDH12 (Affinity Capture-MS), CHEK2 (Affinity Capture-MS), CDH24 (Affinity Capture-MS), PCDH1 (Affinity Capture-MS), RBM14-RBM4 (Affinity Capture-MS)

ESM2 similar proteins: A0A1S4GGP7, B1Q236, B8V7Q1, B8VIW9, F1QSQ0, F8W3X3, G5EDK5, H2A0L8, O02466, O15943, O44386, O44730, P28827, P34616, P35822, P55289, P70408, Q02763, Q02858, Q03600, Q03763, Q06807, Q09165, Q15262, Q19319, Q24247, Q24298, Q5RJH3, Q60ZN5, Q61495, Q68SP4, Q6W3B0, Q7TMD7, Q7TSF0, Q7TSF1, Q86SJ6, Q86WI1, Q8JHW2, Q8VHN7, Q8WXG9

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”CDH12“chemical activation”
CDH12“up-regulates activity”CTNNB1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance126
Likely benign15
Benign11

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1809200GRCh37/hg19 5p15.33-14.1(chr5:113577-26164852)x1Pathogenic

SpliceAI

5423 predictions. Top by Δscore:

VariantEffectΔscore
5:21752232:TATGG:Tacceptor_gain1.0000
5:21752234:TGG:Tacceptor_gain1.0000
5:21752237:C:CCacceptor_gain1.0000
5:21755665:T:TAdonor_gain1.0000
5:21760556:A:ACdonor_gain1.0000
5:21760557:C:CCdonor_gain1.0000
5:21760557:CTT:Cdonor_gain1.0000
5:21783356:A:ACdonor_gain1.0000
5:21783357:C:CCdonor_gain1.0000
5:21783357:CTA:Cdonor_gain1.0000
5:21783357:CTAA:Cdonor_gain1.0000
5:21816941:ATACC:Adonor_loss1.0000
5:21816942:TACC:Tdonor_loss1.0000
5:21816943:A:Tdonor_loss1.0000
5:21816944:C:CAdonor_loss1.0000
5:21816964:C:CAdonor_gain1.0000
5:21817143:A:Cacceptor_gain1.0000
5:21842157:ATAC:Adonor_loss1.0000
5:21842158:TA:Tdonor_loss1.0000
5:21842159:A:ACdonor_gain1.0000
5:21842159:ACTTT:Adonor_loss1.0000
5:21842160:C:CCdonor_gain1.0000
5:21842160:CT:Cdonor_gain1.0000
5:21842160:CTT:Cdonor_gain1.0000
5:21842326:CAC:Cacceptor_gain1.0000
5:21842327:ACC:Aacceptor_loss1.0000
5:21842328:CC:Cacceptor_loss1.0000
5:21842329:CTTAA:Cacceptor_loss1.0000
5:21842330:T:Cacceptor_gain1.0000
5:21975090:CCCA:Cdonor_gain1.0000

AlphaMissense

5230 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:21975153:T:GD155A1.000
5:21975162:T:GD152A1.000
5:21975163:C:GD152H1.000
5:21975291:C:AG109V1.000
5:21975291:C:TG109E1.000
5:21975292:C:AG109W1.000
5:21975312:A:GF102S1.000
5:21755609:A:GC623R0.999
5:21783369:G:TA461E0.999
5:21802200:G:TA408D0.999
5:21802206:A:TV406D0.999
5:21802380:A:TV348D0.999
5:21842169:A:GF269S0.999
5:21842175:G:TP267H0.999
5:21842184:T:GD264A0.999
5:21842199:A:GL259P0.999
5:21842211:A:TV255D0.999
5:21842253:T:GD241A0.999
5:21842254:C:GD241H0.999
5:21842259:G:TA239D0.999
5:21842260:C:GA239P0.999
5:21842322:A:TI218N0.999
5:21842328:C:TG216D0.999
5:21854691:A:GF209S0.999
5:21854719:A:CY200D0.999
5:21854754:T:AD188V0.999
5:21854754:T:GD188A0.999
5:21854755:C:GD188H0.999
5:21854761:C:GD186H0.999
5:21975137:A:CF160L0.999

dbSNP variants (sampled 300 via entrez): RS1000001454 (5:22834207 G>C), RS1000005121 (5:22744349 A>G), RS1000005366 (5:22316733 A>G), RS1000009781 (5:21750554 G>C,T), RS1000010667 (5:22717500 A>G), RS1000014089 (5:22598430 G>A), RS1000018705 (5:22597664 A>G), RS1000022651 (5:22143821 A>G), RS1000025179 (5:22377516 A>G), RS1000025225 (5:22522017 G>A), RS1000025419 (5:21949013 C>T), RS1000031537 (5:22476158 C>A,G,T), RS1000032561 (5:22390413 A>C,G,T), RS1000033243 (5:21843328 C>T), RS1000035371 (5:21805212 A>C)

Disease associations

OMIM: gene MIM:600562 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST000427_5Waist circumference2.000000e-06
GCST004558_85Body mass index (joint analysis main effects and physical activity interaction)7.000000e-07
GCST004568_1Body mass index (physical activity interaction)3.000000e-08
GCST004568_2Body mass index (physical activity interaction)3.000000e-07
GCST004863_143Mosquito bite size9.000000e-06
GCST005578_4Low white blood cell count (conditioned on rs2814778)4.000000e-07
GCST005578_5Low white blood cell count (conditioned on rs2814778)2.000000e-07
GCST005760_5Dimensional psychopathology (Cognitive)4.000000e-07
GCST007603_35Smoking initiation5.000000e-08
GCST007678_2Brooding (response to stress)5.000000e-07
GCST008810_93Smoking initiation (ever regular vs never regular)1.000000e-08

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008002physical activity measurement
EFO:0003940physical activity
EFO:0008378mosquito bite reaction size measurement
EFO:0009098cognitive domain measurement
EFO:0005670smoking initiation
EFO:0009858brooding stress response

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1decreases methylation, increases methylation, affects expression, decreases expression4
sodium arseniteaffects methylation, decreases expression, increases reaction, decreases methylation2
Resveratrolaffects cotreatment, decreases expression, increases expression2
Copperaffects cotreatment, decreases expression, affects binding2
Valproic Aciddecreases expression2
methyleugenoldecreases expression1
bisphenol Aaffects methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
aflatoxin B2decreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
glycidamidedecreases expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
NSC 689534affects binding, decreases expression1
Sunitinibdecreases expression1
Benzo(a)pyreneaffects methylation1
Coumestrolaffects cotreatment, increases expression1
Leadaffects methylation1
Lipopolysaccharidesincreases expression, affects cotreatment1
Niclosamidedecreases reaction, increases expression1
Silicon Dioxideincreases expression1
Tetrachlorodibenzodioxinincreases expression1
Tretinoinincreases expression1
Triclosanincreases expression1
Cyclosporinedecreases expression1
Silver Compoundsincreases expression1
Cadmium Chlorideincreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.