CDH24

Summary

CDH24 (cadherin 24, HGNC:14265) is a protein-coding gene on chromosome 14q11.2, encoding Cadherin-24 (Q86UP0). Cadherins are calcium-dependent cell adhesion proteins.

Enables several functions, including alpha-catenin binding activity; beta-catenin binding activity; and delta-catenin binding activity. Acts upstream of or within cell-cell adhesion. Located in cell-cell junction.

Source: NCBI Gene 64403 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 160 total
• MANE Select transcript: NM_144985

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14265
Approved symbol	CDH24
Name	cadherin 24
Location	14q11.2
Locus type	gene with protein product
Status	Approved
Aliases	CDH11L
Ensembl gene	ENSG00000139880
Ensembl biotype	protein_coding
OMIM	618599
Entrez	64403

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000267383, ENST00000397359, ENST00000485922, ENST00000487137, ENST00000554034

RefSeq mRNA: 2 — MANE Select: NM_144985 NM_022478, NM_144985

CCDS: CCDS9585, CCDS9586

Canonical transcript exons

ENST00000487137 — 13 exons

Exon	Start	End
ENSE00001901992	23047067	23047374
ENSE00002106471	23054747	23054866
ENSE00002110144	23053496	23053749
ENSE00002112576	23054506	23054673
ENSE00002113912	23054141	23054328
ENSE00002125806	23055059	23055353
ENSE00002130509	23052473	23052609
ENSE00002137040	23049822	23049943
ENSE00002141751	23055533	23055857
ENSE00003484180	23049627	23049738
ENSE00003610748	23049027	23049275
ENSE00003679414	23047461	23048479
ENSE00003919204	23057403	23057520

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 90.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.1985 / max 402.7891, expressed in 1546 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
142297	5.0317	1356
142298	4.0614	1358
142296	0.1053	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	90.59	gold quality
ganglionic eminence	UBERON:0004023	89.93	gold quality
kidney epithelium	UBERON:0004819	89.27	gold quality
left ventricle myocardium	UBERON:0006566	89.18	gold quality
upper arm skin	UBERON:0004263	88.30	gold quality
stromal cell of endometrium	CL:0002255	86.46	gold quality
cortical plate	UBERON:0005343	84.57	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.40	gold quality
cerebellar hemisphere	UBERON:0002245	84.25	gold quality
cerebellar cortex	UBERON:0002129	84.19	gold quality
ventricular zone	UBERON:0003053	83.92	gold quality
cerebellum	UBERON:0002037	83.32	gold quality
body of uterus	UBERON:0009853	82.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.77	gold quality
mucosa of transverse colon	UBERON:0004991	81.04	gold quality
myocardium	UBERON:0002349	80.72	gold quality
cerebellar vermis	UBERON:0004720	80.64	gold quality
epithelial cell of pancreas	CL:0000083	80.60	gold quality
ectocervix	UBERON:0012249	80.02	gold quality
right lung	UBERON:0002167	79.97	gold quality
left uterine tube	UBERON:0001303	78.59	gold quality
ventral tegmental area	UBERON:0002691	78.58	silver quality
vena cava	UBERON:0004087	78.50	gold quality
right lobe of thyroid gland	UBERON:0001119	78.44	gold quality
putamen	UBERON:0001874	78.10	gold quality
metanephros cortex	UBERON:0010533	78.01	gold quality
left lobe of thyroid gland	UBERON:0001120	77.65	gold quality
endocervix	UBERON:0000458	77.35	gold quality
cortex of kidney	UBERON:0001225	77.00	gold quality
gall bladder	UBERON:0002110	76.93	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting CDH24, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-3612	99.45	66.02	1333

Literature-anchored findings (GeneRIF, showing 2)

• cadherin-24 is a novel alternatively spliced type II cadherin (PMID:12734196)
• Unconventional CDH10, CDH24 and DCHS2 genes harbored frameshift mutations. (PMID:24898286)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdh24a	ENSDARG00000075960
danio_rerio	cdh24b	ENSDARG00000077996
mus_musculus	Cdh24	ENSMUSG00000059674
rattus_norvegicus	Cdh24	ENSRNOG00000013503

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), 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-24 — Q86UP0 (reviewed: Q86UP0)

All UniProt accessions (1): Q86UP0

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. Cadherin-24 mediate strong cell-cell adhesion.

Subunit / interactions. Associates with alpha-, beta- and delta-catenins.

Subcellular location. Cell membrane.

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 (3)

UniProt ID	Names	Canonical?
Q86UP0-1	1, Long form	yes
Q86UP0-2	2, Short form
Q86UP0-3	3

RefSeq proteins (2): NP_071923, NP_659422* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000233	Cadherin_Y-type_LIR	Domain
IPR002126	Cadherin-like_dom	Domain
IPR015919	Cadherin-like_sf	Homologous_superfamily
IPR020894	Cadherin_CS	Conserved_site
IPR027397	Catenin-bd_sf	Homologous_superfamily
IPR039808	Cadherin	Family

Pfam: PF00028, PF01049

UniProt features (19 total): domain 5, glycosylation site 3, splice variant 3, topological domain 2, signal peptide 1, propeptide 1, region of interest 1, compositionally biased region 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86UP0-F1	76.54	0.46

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 (3): 446, 548, 563

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-418990	Adherens junctions interactions
R-HSA-9833576	CDH11 homotypic and heterotypic interactions
R-HSA-1500931	Cell-Cell communication
R-HSA-421270	Cell-cell junction organization
R-HSA-446728	Cell junction organization
R-HSA-9759475	Regulation of CDH11 Expression and Function
R-HSA-9759476	Regulation of Homotypic Cell-Cell Adhesion
R-HSA-9762292	Regulation of CDH11 function
R-HSA-9764260	Regulation of Expression and Function of Type II Classical Cadherins

MSigDB gene sets: 88 (showing top): FISCHER_G1_S_CELL_CYCLE, TGACCTY_ERR1_Q2, AP2_Q3, SP1_Q2_01, GOBP_CALCIUM_DEPENDENT_CELL_CELL_ADHESION, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_CELL_JUNCTION_ASSEMBLY, DOUGLAS_BMI1_TARGETS_UP, 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-cell adhesion (GO:0098609), cell adhesion (GO:0007155)

GO Molecular Function (6): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), alpha-catenin binding (GO:0045294), cadherin binding (GO:0045296), delta-catenin binding (GO:0070097), metal ion binding (GO:0046872)

GO Cellular Component (5): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), adherens junction (GO:0005912), catenin complex (GO:0016342), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
Cell-cell junction organization	1
Regulation of CDH11 function	1
Cell junction organization	1
Cell-Cell communication	1
Regulation of Expression and Function of Type II Classical Cadherins	1
Adherens junctions interactions	1
Regulation of CDH11 Expression and Function	1
Regulation of Homotypic Cell-Cell Adhesion	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-cell adhesion	3
protein binding	3
cell-cell junction organization	2
anatomical structure morphogenesis	1
cell junction assembly	1
cell motility	1
cell adhesion	1
cellular process	1
metal ion binding	1
cell adhesion molecule binding	1
cation binding	1
membrane	1
cell periphery	1
anchoring junction	1
cell-cell junction	1
extrinsic component of plasma membrane	1
plasma membrane protein complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDH24	KNDC1	Q76NI1	579
CDH24	CTNND1	O60716	530
CDH24	ADGRA1	Q86SQ6	518
CDH24	ANKDD1B	A6NHY2	518
CDH24	LGALSL	Q3ZCW2	461
CDH24	ZNF787	Q6DD87	460
CDH24	CTNNB1	P35222	453
CDH24	ACVR2B	Q13705	406
CDH24	ANKAR	Q7Z5J8	392
CDH24	FOXN1	O15353	380
CDH24	PTPRT	O14522	374
CDH24	ITGB1BP1	O14713	357
CDH24	SLC15A1	P46059	353
CDH24	GPR183	P32249	348
CDH24	USF3	Q68DE3	326

IntAct

8 interactions, top by confidence:

A	B	Type	Score
TAX1BP3	ARVCF	psi-mi:“MI:0914”(association)	0.690
DKKL1	DENND11	psi-mi:“MI:0914”(association)	0.640
CTNNA3	ARVCF	psi-mi:“MI:0914”(association)	0.350
CDH12	ARVCF	psi-mi:“MI:0914”(association)	0.350
CEACAM8	VGF	psi-mi:“MI:0914”(association)	0.350
MMP3	VGF	psi-mi:“MI:0914”(association)	0.350
PPP1R16A	CDH24	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): CDH24 (Affinity Capture-RNA), CDH24 (Affinity Capture-RNA), CDH24 (Affinity Capture-MS), CDH24 (Two-hybrid), CDH24 (Affinity Capture-MS), CDH24 (Affinity Capture-MS), CDH24 (Proximity Label-MS)

ESM2 similar proteins: A0A140LHF2, A6H8M9, D3YX43, O08644, O15197, O55134, O70394, O70540, O75309, O88338, P0C091, P0C0K6, P0C0K7, P0DP72, P21709, P40223, P59862, P70289, Q00657, Q04912, Q0V8J4, Q28634, Q501P1, Q53RD9, Q58Y75, Q5DRE2, Q5H8B9, Q5R6F5, Q5SZK8, Q60750, Q63315, Q64612, Q6MG64, Q6NVD0, Q6PFX6, Q6UVK1, Q76MJ5, Q7TN88, Q7Z442, Q86UP0

Diamond homologs: A0A8M9PFP2, B0S5G3, F1R520, O02840, O55111, O88278, O94985, P30944, P33151, P55287, P55288, Q0VCN6, Q14517, Q5DRC8, Q5R9Q9, Q63418, Q6Q0N0, Q6URK6, Q6V1P9, Q86UP0, Q8BNA6, Q8R553, Q8VDA1, Q96JQ0, Q99JH7, Q9BQT9, Q9EPL2, Q9ER65, Q9H4D0, Q9HCU4, Q9NYQ6, Q9R0M0, A0A8M2BIB6, B0KW95, B2KI42, B4USZ0, F1PAA9, F1QSQ0, O35902, O54800

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
calcium(2+)	“up-regulates activity”	CDH24	“chemical activation”
CDH24	“up-regulates activity”	CTNNB1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	144
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2322 predictions. Top by Δscore:

Variant	Effect	Δscore
14:23049625:A:AC	donor_gain	1.0000
14:23049625:A:AT	donor_loss	1.0000
14:23049626:C:CC	donor_gain	1.0000
14:23049626:CCT:C	donor_gain	1.0000
14:23049734:ATCAG:A	acceptor_gain	1.0000
14:23049735:TCAG:T	acceptor_gain	1.0000
14:23049736:CAG:C	acceptor_gain	1.0000
14:23049736:CAGC:C	acceptor_gain	1.0000
14:23049737:A:T	acceptor_gain	1.0000
14:23049737:AG:A	acceptor_gain	1.0000
14:23049739:C:CC	acceptor_gain	1.0000
14:23049818:TCA:T	donor_loss	1.0000
14:23049819:CA:C	donor_loss	1.0000
14:23049821:C:A	donor_loss	1.0000
14:23049939:ACTGT:A	acceptor_loss	1.0000
14:23049940:CTGT:C	acceptor_gain	1.0000
14:23049941:TGT:T	acceptor_gain	1.0000
14:23049942:GTCT:G	acceptor_loss	1.0000
14:23049943:TC:T	acceptor_loss	1.0000
14:23049944:C:A	acceptor_loss	1.0000
14:23049944:C:CC	acceptor_gain	1.0000
14:23049945:T:G	acceptor_loss	1.0000
14:23049951:C:CT	acceptor_gain	1.0000
14:23049952:A:T	acceptor_gain	1.0000
14:23052610:C:CC	acceptor_gain	1.0000
14:23053491:CCTA:C	donor_gain	1.0000
14:23053492:CTA:C	donor_loss	1.0000
14:23053494:A:AC	donor_gain	1.0000
14:23053495:C:CC	donor_gain	1.0000
14:23053748:GG:G	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000145646 (14:23058398 G>A), RS1000365059 (14:23058214 C>T), RS1000554642 (14:23053516 G>A), RS1001095751 (14:23047946 C>A,G,T), RS1001112030 (14:23052243 G>A), RS1001580649 (14:23047190 G>A), RS1001936379 (14:23053007 G>A,T), RS1002053721 (14:23046841 G>C), RS1002166817 (14:23053300 G>A), RS1002625509 (14:23050158 G>A,C), RS1002730254 (14:23049526 C>G,T), RS1003555780 (14:23049472 A>T), RS1004598424 (14:23055899 C>A,T), RS1005026378 (14:23051012 G>A), RS1005126769 (14:23058302 G>T)

Disease associations

OMIM: gene MIM:618599 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004621_65	Red cell distribution width	2.000000e-20
GCST90002404_388	Red cell distribution width	3.000000e-23

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, increases expression	3
sodium arsenite	affects cotreatment, decreases expression, increases abundance, increases expression	2
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases oxidation	2
Arsenic	affects methylation, affects cotreatment, decreases expression, increases abundance	2
Tretinoin	decreases expression	2
Aflatoxin B1	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
eprenetapopt	affects reaction, affects expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Acrolein	increases abundance, affects cotreatment, increases oxidation	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects expression	1
Okadaic Acid	increases expression	1
Lactic Acid	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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