CDH13

Summary

CDH13 (cadherin 13, HGNC:1753) is a protein-coding gene on chromosome 16q23.3, encoding Cadherin-13 (P55290). Cadherins are calcium-dependent cell adhesion proteins.

This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 1012 — RefSeq curated summary.

At a glance

• GWAS associations: 106
• Clinical variants (ClinVar): 261 total — 2 likely-pathogenic
• MANE Select transcript: NM_001257

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1753
Approved symbol	CDH13
Name	cadherin 13
Location	16q23.3
Locus type	gene with protein product
Status	Approved
Aliases	CDHH
Ensembl gene	ENSG00000140945
Ensembl biotype	protein_coding
OMIM	601364
Entrez	1012

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 6 protein_coding, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000268613, ENST00000428848, ENST00000431540, ENST00000539548, ENST00000562307, ENST00000562601, ENST00000565636, ENST00000566333, ENST00000567109, ENST00000567445, ENST00000568770, ENST00000569144, ENST00000569454, ENST00000569455

RefSeq mRNA: 6 — MANE Select: NM_001257 NM_001220488, NM_001220489, NM_001220490, NM_001220491, NM_001220492, NM_001257

CCDS: CCDS56009, CCDS56010, CCDS58485, CCDS58486, CCDS58487

Canonical transcript exons

ENST00000567109 — 14 exons

Exon	Start	End
ENSE00002617620	82626969	82627137
ENSE00002630405	83795023	83800640
ENSE00003462150	82858362	82858473
ENSE00003476797	83217345	83217497
ENSE00003478206	83602454	83602594
ENSE00003491569	83748108	83748250
ENSE00003509460	83125385	83125501
ENSE00003525857	83670790	83670972
ENSE00003529170	83783254	83783472
ENSE00003537631	83486477	83486655
ENSE00003599006	83779968	83780201
ENSE00003605534	83032010	83032218
ENSE00003619059	83344862	83345006
ENSE00003653345	83678208	83678461

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 98.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.9716 / max 1108.7204, expressed in 1081 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155243	12.2990	1021
155245	12.1749	977
155244	2.4976	713

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
descending thoracic aorta	UBERON:0002345	98.27	gold quality
right coronary artery	UBERON:0001625	98.22	gold quality
thoracic aorta	UBERON:0001515	97.86	gold quality
ascending aorta	UBERON:0001496	97.81	gold quality
stromal cell of endometrium	CL:0002255	97.39	gold quality
popliteal artery	UBERON:0002250	95.81	gold quality
tibial artery	UBERON:0007610	95.79	gold quality
artery	UBERON:0001637	95.61	gold quality
calcaneal tendon	UBERON:0003701	95.11	gold quality
quadriceps femoris	UBERON:0001377	94.67	gold quality
vastus lateralis	UBERON:0001379	94.40	gold quality
left coronary artery	UBERON:0001626	93.78	gold quality
skeletal muscle tissue	UBERON:0001134	93.26	gold quality
smooth muscle tissue	UBERON:0001135	93.16	gold quality
superior frontal gyrus	UBERON:0002661	92.77	gold quality
heart left ventricle	UBERON:0002084	92.13	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.10	gold quality
heart	UBERON:0000948	91.67	gold quality
muscle tissue	UBERON:0002385	91.38	gold quality
myometrium	UBERON:0001296	90.79	gold quality
body of uterus	UBERON:0009853	90.50	gold quality
prefrontal cortex	UBERON:0000451	90.22	gold quality
uterine cervix	UBERON:0000002	89.72	gold quality
muscle organ	UBERON:0001630	89.72	gold quality
skeletal muscle organ	UBERON:0014892	89.72	gold quality
right atrium auricular region	UBERON:0006631	89.59	gold quality
muscle of leg	UBERON:0001383	89.45	gold quality
ectocervix	UBERON:0012249	89.28	gold quality
endocervix	UBERON:0000458	89.21	gold quality
apex of heart	UBERON:0002098	88.95	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	4710.52
E-ENAD-20	yes	500.00
E-MTAB-6075	yes	60.67
E-CURD-119	yes	23.88
E-MTAB-8271	yes	14.76
E-ANND-3	yes	8.02
E-GEOD-124858	no	891.35
E-MTAB-5061	no	3.45

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AHR, AP1, CEBPA, CUX1, DNMT3B, EGR1, ETS1, FLCN, GATA5, HIF1A, POU3F2, SP1, TAL1, TOP2B, TP53, ZEB1

miRNA regulators (miRDB)

90 targeting CDH13, 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-6867-5P	100.00	82.21	3464
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4698	99.84	71.41	4303

Literature-anchored findings (GeneRIF, showing 40)

• cadherin cell adhesion molecule anchored to the cell surface membrane through a glycosyl phosphatidyl inositol moiety (PMID:11642747)
• There is aberrant methylation of the CDH13 (H-cadherin) promoter region in colorectal cancers and adenomas. (PMID:12067979)
• combination of deletion and aberrant methylation of the T-cadherin gene may play a role in loss of gene expression in a considerable number of invasive cutaneous squamous cell carcinomas (PMID:12177241)
• downregulation is caused by a combination of allelic loss and hypermethylation of the T-cadherin promoter region and is related to cancer invasion (PMID:12489108)
• Our data indicate that the silencing of CDH13 expression by aberrant promoter methylation occurs at an early stage in CML pathogenesis and probably influences the clinical behavior of the disease. (PMID:12697869)
• T-cadherin is not required for maintenance of intercellular adhesion, but may rather function as a signalling molecule involved in cell-cell recognition and sensing of the environment in processes where cell detachment occurs. (PMID:14579115)
• Coating of culture plates with recombinant T-cad protein or with antibody against the first amino-terminal domain of T-cad (anti-EC1) significantly decreased adhesion and spreading of smooth muscle cells and HUVEC. (PMID:14729458)
• Aberrant methylation of CDH13 is associated with recurrent cervical cancer (PMID:14750164)
• CDH13 promoter methylation is associated with poorly differentiated colorectal cancer (PMID:14997203)
• Hypermethylation of CDH13 is statistically significantly associated with poor disease outcome in cervical cancer. (PMID:15251938)
• Digestive tract neoplasms may show abnormal DNA methylation of this protein. (PMID:15292927)
• T-cadherin acts as an endogenous negative regulator of keratinocyte proliferation and its inactivation is the cause for keratinocyte hyperproliferation in squamous cell carcinoma or in psoriasis vulgaris. (PMID:15816843)
• T-cad mediates low-density lipoprotein-initiated cell proliferation via the Ca(2+)-tyrosine kinase-Erk1/2 pathway. (PMID:15821437)
• T-cad overexpression in vascular endothelial cells protects against stress-induced apoptosis through activation of the PI3K/Akt/mTOR survival signal pathway and concomitant suppression of the p38 MAPK proapoptotic pathway (PMID:16099944)
• Data suggest a functional role of T-/H-cadherin for the differentiation of the podocytes and the formation of the glomerular capillary network. (PMID:16133358)
• The frequency of p16INK4A or CDH13 hypermethylation in patient serum and the total lack of methylation in serum from healthy individuals, offer a promising tool for non invasive early detection of lung cancer. (PMID:16222700)
• T-cadherin was selectively expressed in intratumoral capillary endothelial cells of hepatocellular carcinomas and increasingly expressed with tumor progression. (PMID:16273386)
• T-cadherin expression in tumor cells might occur by cadherin-switching during epithelial-mesenchymal transition and may represent an additional mechanism contributing to hepatoma metastasis. (PMID:17077306)
• Methylation of H-cadherin is associated with advanced esophageal squamous cell carcinoma (PMID:17094449)
• T-cadherin may modulate cell-matrix adhesion in basal keratinocytes as well as invasive potency in squamous cell carcinoma by regulating surface level of beta1 integrin (PMID:17573778)
• Results show that T-cadherin upregulation on endothelial cells may potentiate intratumoral angiogenesis. (PMID:17765896)
• tumor-specific downregulation of expression and methylation of CDH13 and CDH1, alone or in combination, may be involved in the development and invasive growth of pituitary adenomas. (PMID:17873891)
• The current findings suggested that simultaneous methylation of the E-cadherin and H-cadherin genes occurs in a subset of NSCLCs (PMID:17960794)
• Results identified CDH13 loci showing significant differential DNA methylation levels between tumor and non-tumor lung and highly significant hypermethylation in adenocarcinoma. (PMID:17967182)
• Susceptibility genes CPNE3, IL16 and CDH13 with moderate effects associated with susceptibility to prostate cancer. (PMID:18264096)
• Methylation of the promoter region of CDH13 in patients with stage I NSCLC treated with curative intent by means of surgery is associated with early recurrence. (PMID:18337602)
• Methylation of CDH13 was present in 80% of NSCLC tissues but only in 14% of noncancerous tissues. (PMID:18349282)
• Grp78/BiP has a role in T-cadherin-dependent cell survival (PMID:18411300)
• T-cadherin down-regulation by promoter methylation is associated with the development and progression of hepatocellular carcinoma. Suggest that T-cadherin is an important tumor suppressor in liver cancer. (PMID:18425332)
• methylation status of CDH13 may help predict clinical outcome in patients with endometrial cancer. (PMID:18519763)
• T-cadherin may be involved in reversible and dynamic cellular adhesion-deadhesion processes, which are consistent with its role in cell growth and migration (PMID:18550521)
• The underexpression of T-cadherin in HCC cells suggests it may be another critical event in addition to T-cadherin-mediated angiogenesis during HCC development. (PMID:18553387)
• thioredoxin-1 is an important determinant of redox-sensitive transcriptional up-regulation of T-cad in vascular endothelial cells. (PMID:18627351)
• In the tubular breast carcinoma samples, the highest frequencies for DNA sequence copy number losses were detected for CDH13 (in 86% of the samples) (PMID:18656243)
• hypermethylation of CDH13 is a common, tissue-specific event in esophageal adenocarcinoma, occurs early during Barrett esophagus-associated neoplastic progression, and correlates with known clinical neoplastic progression risk factors (PMID:18729198)
• These findings suggest that Zeb1 represses T-cadherin expression and thus increases the invasive activity of gallbladder cancer. (PMID:19116147)
• ADIPOQ and CDH13 single-nucleotide polymorphisms are associated with variation in adiponectin levels. (PMID:19165155)
• The study showed that the reduction of the CDH13 expression at different clinical stage of CML may account for the defective cell adhesion in CML, and the expression of the CDH13 gene was probably down-regulated by the BCR/ABL fusion gene. (PMID:19199263)
• CDH13 as a novel susceptibility locus contributes to high blood pressure in European populations. (PMID:19304780)
• Results show that H-cadherin expression is lost in nearly 80% of the analyzed melanoma cell lines. (PMID:19368692)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdh13	ENSDARG00000014215
mus_musculus	Cdh13	ENSMUSG00000031841
rattus_norvegicus	Cdh13	ENSRNOG00000014371

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), 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-13 — P55290 (reviewed: P55290)

Alternative names: Heart cadherin, P105, Truncated cadherin

All UniProt accessions (6): P55290, F5H7W7, H3BQH4, H3BRL7, H3BTF2, H3BV21

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. May act as a negative regulator of neural cell growth.

Subunit / interactions. By contrast to classical cadherins, homodimerization in trans is not mediated by cadherin EC1 domain strand-swapping, but instead through a homophilic adhesive interface which joins two elongated EC1-EC2 domains through a region near their Ca2+-binding sites to form a tetrahedral, X-like shape.

Subcellular location. Cell membrane. Cytoplasm.

Tissue specificity. Highly expressed in heart. In the CNS, expressed in cerebral cortex, medulla, hippocampus, amygdala, thalamus and substantia nigra. No expression detected in cerebellum or spinal cord.

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 (5)

UniProt ID	Names	Canonical?
P55290-1	1	yes
P55290-2	2
P55290-3	3
P55290-4	4
P55290-5	5

RefSeq proteins (6): NP_001207417, NP_001207418, NP_001207419, NP_001207420, NP_001207421, NP_001248* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002126	Cadherin-like_dom	Domain
IPR014868	Cadherin_pro_dom	Domain
IPR015919	Cadherin-like_sf	Homologous_superfamily
IPR020894	Cadherin_CS	Conserved_site
IPR039808	Cadherin	Family

Pfam: PF00028, PF08758

UniProt features (49 total): strand 10, glycosylation site 8, sequence variant 8, splice variant 6, domain 5, sequence conflict 4, turn 3, propeptide 2, signal peptide 1, chain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2V37	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P55290-F1	85.19	0.61

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): 693

Glycosylation sites (8): 52, 86, 382, 500, 530, 598, 638, 671

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

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

MSigDB gene sets: 298 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GOBP_CELLULAR_RESPONSE_TO_LIPOPROTEIN_PARTICLE_STIMULUS, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, YAATNRNNNYNATT_UNKNOWN, GOBP_REGULATION_OF_CALCIUM_MEDIATED_SIGNALING, GOBP_REGULATION_OF_ERBB_SIGNALING_PATHWAY, MODULE_545, GOBP_KERATINOCYTE_PROLIFERATION, GCANCTGNY_MYOD_Q6, LI_PROSTATE_CANCER_EPIGENETIC, GOCC_CELL_SURFACE, MODULE_128, AREB6_01, SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER, TGACCTY_ERR1_Q2

GO Biological Process (31): cell morphogenesis (GO:0000902), positive regulation of endothelial cell proliferation (GO:0001938), positive regulation of cell-matrix adhesion (GO:0001954), sprouting angiogenesis (GO:0002040), cell-cell junction assembly (GO:0007043), homophilic cell-cell adhesion (GO:0007156), negative regulation of cell adhesion (GO:0007162), Rho protein signal transduction (GO:0007266), negative regulation of cell population proliferation (GO:0008285), calcium-dependent cell-cell adhesion (GO:0016339), cell migration (GO:0016477), Rac protein signal transduction (GO:0016601), lamellipodium assembly (GO:0030032), regulation of endocytosis (GO:0030100), positive regulation of cell migration (GO:0030335), adherens junction organization (GO:0034332), regulation of epidermal growth factor receptor signaling pathway (GO:0042058), endothelial cell migration (GO:0043542), keratinocyte proliferation (GO:0043616), cell-cell adhesion mediated by cadherin (GO:0044331), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of smooth muscle cell proliferation (GO:0048661), positive regulation of calcium-mediated signaling (GO:0050850), positive regulation of positive chemotaxis (GO:0050927), localization within membrane (GO:0051668), low-density lipoprotein particle mediated signaling (GO:0055096), cellular response to xenobiotic stimulus (GO:0071466), cellular response to toxic substance (GO:0097237), cell adhesion (GO:0007155), regulation of transport (GO:0051049), cell-cell adhesion (GO:0098609)

GO Molecular Function (9): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), low-density lipoprotein particle binding (GO:0030169), identical protein binding (GO:0042802), cadherin binding (GO:0045296), adiponectin binding (GO:0055100), lipoprotein particle binding (GO:0071813), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (17): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), plasma membrane (GO:0005886), caveola (GO:0005901), adherens junction (GO:0005912), focal adhesion (GO:0005925), external side of plasma membrane (GO:0009897), catenin complex (GO:0016342), extracellular matrix (GO:0031012), neuron projection (GO:0043005), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), GABA-ergic synapse (GO:0098982), membrane (GO:0016020), synapse (GO:0045202), side of membrane (GO:0098552)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Cell-cell junction organization	1
Cell junction organization	1
Cell-Cell communication	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cell-cell adhesion	3
protein binding	3
cell-cell junction organization	2
negative regulation of cellular process	2
small GTPase-mediated signal transduction	2
cell migration	2
membrane	2
anatomical structure morphogenesis	1
endothelial cell proliferation	1
regulation of endothelial cell proliferation	1
positive regulation of epithelial cell proliferation	1
regulation of cell-matrix adhesion	1
cell-matrix adhesion	1
positive regulation of cell-substrate adhesion	1
angiogenesis	1
cell junction assembly	1
cell adhesion	1
regulation of cell adhesion	1
cell population proliferation	1
regulation of cell population proliferation	1
cell motility	1
lamellipodium organization	1
plasma membrane bounded cell projection assembly	1
endocytosis	1
regulation of cellular component organization	1
regulation of vesicle-mediated transport	1
regulation of cell migration	1
positive regulation of cell motility	1
epidermal growth factor receptor signaling pathway	1
regulation of ERBB signaling pathway	1
epithelial cell proliferation	1
metal ion binding	1
lipoprotein particle binding	1
cell adhesion molecule binding	1
hormone binding	1
protein-lipid complex binding	1
binding	1
cation binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

2030 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDH13	ADIPOQ	Q15848	996
CDH13	RASSF1	Q9NS23	906
CDH13	ADIPOR1	Q96A54	904
CDH13	ADIPOR2	Q86V24	869
CDH13	CDKN2A	P42771	746
CDH13	CTNNB1	P35222	674
CDH13	DAPK1	P53355	669
CDH13	RARB	P10826	652
CDH13	MGMT	P16455	620
CDH13	FHIT	P49789	599
CDH13	GSTP1	P09211	591
CDH13	INS	P01308	586
CDH13	AKT1	P31749	574
CDH13	NAALADL2	Q58DX5	569
CDH13	CALR	P27797	525

IntAct

46 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
SCGB1D1	MANBA	psi-mi:“MI:0914”(association)	0.640
HTT	CDH13	psi-mi:“MI:0915”(physical association)	0.560
GHITM	CDH13	psi-mi:“MI:0915”(physical association)	0.560
CDH13	INSIG1	psi-mi:“MI:0914”(association)	0.530
GPIHBP1	ADAM10	psi-mi:“MI:0914”(association)	0.530
LGALS1	PODXL	psi-mi:“MI:0914”(association)	0.530
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
CFTR	CNOT1	psi-mi:“MI:0914”(association)	0.480
CDH13	ITGB1	psi-mi:“MI:0915”(physical association)	0.460
CDH13	ITGB1	psi-mi:“MI:0403”(colocalization)	0.460
CDH13	MAPK6	psi-mi:“MI:0915”(physical association)	0.370
AURKA	CDH13	psi-mi:“MI:0915”(physical association)	0.370
CDH13	CASP8	psi-mi:“MI:0915”(physical association)	0.370
CDH13	CCND1	psi-mi:“MI:0915”(physical association)	0.370
CDH13	CHEK2	psi-mi:“MI:0915”(physical association)	0.370
CDH13	HMMR	psi-mi:“MI:0915”(physical association)	0.370
CDH13	PTPN1	psi-mi:“MI:0915”(physical association)	0.370
CDH13	RAD51	psi-mi:“MI:0915”(physical association)	0.370
APBB1	SSPOP	psi-mi:“MI:0914”(association)	0.350

BioGRID (56): CDH13 (Affinity Capture-MS), CDH13 (Affinity Capture-MS), CDH13 (Affinity Capture-MS), CDH13 (Affinity Capture-MS), CDH13 (Two-hybrid), CDH13 (Two-hybrid), CDH13 (Two-hybrid), CDH13 (Two-hybrid), CDH13 (Two-hybrid), CDH13 (Two-hybrid), CDH13 (Two-hybrid), SEC14L1 (Affinity Capture-MS), AGPAT5 (Affinity Capture-MS), INSIG1 (Affinity Capture-MS), DSTYK (Affinity Capture-MS)

ESM2 similar proteins: B0KW95, B2KI42, B4USZ0, F1PAA9, O18926, O55075, P08641, P09803, P10287, P10288, P12830, P12960, P14781, P15116, P19022, P19534, P20310, P22223, P24503, P33145, P33147, P33148, P33150, P33152, P39038, P55283, P55290, P79883, Q12860, Q24292, Q28106, Q3B7N0, Q5DRB6, Q5DRB8, Q5DRC2, Q5R5W6, Q5R9X1, Q5RAX1, Q63198, Q6R8F2

Diamond homologs: A0A8M2BIB6, B0KW95, B2KI42, B4USZ0, F1PAA9, H2EQR6, O18926, O35902, O55075, O55111, O88277, P08641, P09803, P10287, P10288, P12830, P15116, P19022, P19534, P19535, P20310, P22223, P24503, P30944, P32926, P33145, P33146, P33147, P33148, P33150, P33152, P33545, P39038, P55283, P55290, P55291, P55292, P55849, P55850, P79883

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
TOP2B	“up-regulates quantity by expression”	CDH13	“transcriptional regulation”
calcium(2+)	“up-regulates activity”	CDH13	“chemical activation”
CDH13	“up-regulates activity”	CTNNB1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	2
Uncertain significance	151
Likely benign	34
Benign	55

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2665080	GRCh38/hg38 16q23.2-23.3(chr16:79568000-83552000)	Likely pathogenic
393545	GRCh37/hg19 16q23.3(chr16:83414018-83518410)x1	Likely pathogenic

SpliceAI

4871 predictions. Top by Δscore:

Variant	Effect	Δscore
16:82627134:CCAG:C	donor_loss	1.0000
16:82627135:CAGGT:C	donor_loss	1.0000
16:82627136:AG:A	donor_loss	1.0000
16:82627137:GGT:G	donor_loss	1.0000
16:82627138:GTAGG:G	donor_loss	1.0000
16:82829374:T:G	donor_gain	1.0000
16:82858469:AAACT:A	donor_gain	1.0000
16:82858470:AACT:A	donor_gain	1.0000
16:82858470:AACTG:A	donor_loss	1.0000
16:82858471:ACT:A	donor_gain	1.0000
16:82858472:CT:C	donor_gain	1.0000
16:82858472:CTG:C	donor_loss	1.0000
16:82858473:TGTA:T	donor_loss	1.0000
16:82858474:G:GG	donor_gain	1.0000
16:82858474:GTAAG:G	donor_loss	1.0000
16:82858475:TA:T	donor_loss	1.0000
16:82858476:AA:A	donor_loss	1.0000
16:83031996:C:CA	acceptor_gain	1.0000
16:83032005:CCCA:C	acceptor_loss	1.0000
16:83032007:CAGT:C	acceptor_loss	1.0000
16:83032008:A:AG	acceptor_gain	1.0000
16:83032008:AGT:A	acceptor_gain	1.0000
16:83032009:G:GT	acceptor_gain	1.0000
16:83032009:GT:G	acceptor_gain	1.0000
16:83032009:GTG:G	acceptor_gain	1.0000
16:83032009:GTGA:G	acceptor_gain	1.0000
16:83032009:GTGAC:G	acceptor_gain	1.0000
16:83032214:TGCAG:T	donor_loss	1.0000
16:83032215:GCAGG:G	donor_loss	1.0000
16:83032216:CAG:C	donor_loss	1.0000

AlphaMissense

4696 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:83344941:A:T	N239I	0.999
16:83344942:T:A	N239K	0.999
16:83344942:T:G	N239K	0.999
16:83344943:G:C	D240H	0.999
16:83344944:A:C	D240A	0.999
16:83344944:A:T	D240V	0.999
16:83344953:C:A	P243Q	0.999
16:83486591:T:C	F299S	0.999
16:83602479:T:C	L329P	0.999
16:83678242:T:C	L440P	0.999
16:83678314:T:A	V464D	0.999
16:83217424:T:C	F188S	0.998
16:83217478:A:T	E206V	0.998
16:83344935:A:T	D237V	0.998
16:83344941:A:C	N239T	0.998
16:83344943:G:T	D240Y	0.998
16:83344944:A:G	D240G	0.998
16:83344952:C:T	P243S	0.998
16:83344953:C:G	P243R	0.998
16:83486507:A:C	D271A	0.998
16:83486512:G:C	D273H	0.998
16:83486513:A:T	D273V	0.998
16:83486591:T:G	F299C	0.998
16:83602496:G:C	D335H	0.998
16:83602497:A:C	D335A	0.998
16:83602539:C:A	A349D	0.998
16:83602545:T:A	I351N	0.998
16:83602564:T:A	N357K	0.998
16:83602564:T:G	N357K	0.998
16:83602581:T:C	F363S	0.998

dbSNP variants (sampled 300 via entrez): RS1000000746 (16:83744465 A>C), RS1000004061 (16:83392357 A>G), RS1000005433 (16:83567734 T>G), RS1000005447 (16:82960689 A>C), RS1000008472 (16:83103119 A>G), RS1000008805 (16:83677047 G>C), RS1000009685 (16:83204915 C>A,T), RS1000010030 (16:82734783 T>C), RS1000011200 (16:82640779 T>C), RS1000012263 (16:82709228 C>G), RS1000023435 (16:83440766 C>G,T), RS1000023610 (16:83231229 C>T), RS1000024699 (16:83268524 A>G), RS1000027021 (16:83098751 A>C,G), RS1000027569 (16:83339205 C>G)

Disease associations

OMIM: gene MIM:601364 | disease phenotypes: MIM:192350

GenCC curated gene-disease

Mondo (1): VACTERL/vater association (MONDO:0008642)

Orphanet (1): VACTERL/VATER association (Orphanet:887)

HPO phenotypes

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

GWAS associations

106 associations (top):

Study	Trait	p-value
GCST000094_4	Blood pressure	1.000000e-09
GCST000246_15	Attention deficit hyperactivity disorder	7.000000e-06
GCST000361_1	Hypertension	8.000000e-06
GCST000611_2	Height	6.000000e-06
GCST000618_8	Response to antipsychotic treatment	1.000000e-06
GCST000779_9	Depression (quantitative trait)	5.000000e-06
GCST000812_2	Adiponectin levels	4.000000e-30
GCST000828_1	Adiponectin levels	3.000000e-83
GCST001049_1	D-dimer levels	4.000000e-06
GCST001165_1	Adiponectin levels	6.000000e-17
GCST001314_1	Adiponectin levels	5.000000e-40
GCST001463_5	Adiponectin levels	1.000000e-14
GCST001465_19	Adiponectin levels	6.000000e-48
GCST001651_22	Response to amphetamines	5.000000e-08
GCST001738_10	Response to fenofibrate (adiponectin levels)	6.000000e-06
GCST001839_2	Schizophrenia	1.000000e-06
GCST002125_2	IgE levels in asthmatics (D.f. specific)	8.000000e-06
GCST002127_14	Periodontitis (Mean PAL)	9.000000e-06
GCST002178_7	Adverse response to chemotherapy in breast cancer (alopecia) (cyclophosphamide+doxorubicin+/-5FU)	8.000000e-06
GCST002179_2	Adverse response to chemotherapy in breast cancer (alopecia) (paclitaxel)	4.000000e-07
GCST002233_4	Adiponectin levels	7.000000e-165
GCST002251_12	Homeostasis model assessment of beta-cell function (dietary factor interaction)	7.000000e-06
GCST002664_4	Maximal oxygen uptake response	9.000000e-06
GCST002726_59	Glucose homeostasis traits	8.000000e-06
GCST003264_848	Post bronchodilator FEV1/FVC ratio	1.000000e-06
GCST003518_49	Daytime sleep phenotypes	4.000000e-06
GCST003542_145	Night sleep phenotypes	6.000000e-06
GCST003542_86	Night sleep phenotypes	2.000000e-06
GCST003830_1	Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)	5.000000e-09
GCST003830_18	Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)	1.000000e-08

EFO canonical traits (32, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0004502	adiponectin measurement
EFO:0004507	D dimer measurement
EFO:0004469	HOMA-B
EFO:0008111	diet measurement
EFO:0004887	maximal oxygen uptake measurement
EFO:0006833	glucose effectiveness measurement
EFO:0004713	FEV/FVC ratio
EFO:0007828	daytime rest measurement
EFO:0005921	FEV change measurement
EFO:0007943	response to platinum-based neoadjuvant chemotherapy
EFO:0005763	pulse pressure measurement
EFO:0009096	negative domain measurement
EFO:0009099	arousal domain measurement
EFO:0009599	feeling emotionally hurt measurement
EFO:0009596	feeling tense measurement
EFO:0006336	diastolic blood pressure
EFO:0006876	seasonality measurement
EFO:0008579	risk-taking behaviour
EFO:0005301	reading and spelling ability
EFO:0004335	short-term memory
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0005035	hippocampal volume
EFO:0004462	PR interval
EFO:0005257	response to anthracycline-based chemotherapy
EFO:1001482	cardiotoxicity
EFO:0004327	electrocardiography
EFO:0600027	hemoglobin change measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs17682789	Toxicity	3	sorafenib	Diarrhea

PharmGKB variants

5 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2116971	CDH13		0.00	0
rs3784943	CDH13		0.00	0
rs11859453	CDH13		0.00	0
rs17682789	CDH13	3	3.00	1	sorafenib
rs7201829	CDH13		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Decitabine	affects expression, affects methylation, decreases methylation	4
bisphenol A	affects cotreatment, increases methylation, decreases methylation, increases expression	3
sodium arsenite	affects methylation, decreases expression	3
mercuric bromide	increases expression, affects cotreatment	2
Temozolomide	affects response to substance, decreases expression	2
Air Pollutants	decreases expression, increases abundance, increases response to substance	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Estradiol	increases expression, affects response to substance, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	affects expression, increases methylation	2
Valproic Acid	affects expression, decreases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
Particulate Matter	decreases expression, increases abundance, increases response to substance	2
bisphenol F	increases expression	1
methylmercuric chloride	increases expression	1
deoxynivalenol	decreases expression	1
domiphen	affects response to substance	1
decabromobiphenyl ether	decreases expression	1
trichostatin A	affects acetylation, affects expression	1
beta-lapachone	increases expression	1
aflatoxin B2	increases methylation	1
nickel sulfate	decreases expression	1
1-nitropyrene	increases expression	1
epigallocatechin gallate	decreases expression	1
3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone	affects response to substance	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1

Cellosaurus cell lines

2 cell lines: 2 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A4YD	UKWMPi002-A-1	Induced pluripotent stem cell	Female
CVCL_A4YE	UKWMPi002-A-2	Induced pluripotent stem cell	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03799705	Not specified	COMPLETED	Genetic Variants in Nicotinamide Adenine Dinucleotide (NAD) Synthesis Pathway