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 (top 1% of genes corpus-wide)
• Clinical variants (ClinVar): 261 total — 2 likely-pathogenic
• GTEx eGene: eQTL in 20 tissues, sQTL in 21 (q < 0.05)
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.46 (moderately constrained)
• MANE Select transcript: NM_001257
• Interaction hub: 1,742 STRING partners (top 10% of genes corpus-wide)
• Notable: 261 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 16 — 7 protein_coding, 5 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000567109

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 4, TSL 3: 2, TSL 4: 4, TSL 5: 1

ENST00000567109, ENST00000268613, ENST00000428848, ENST00000431540, ENST00000539548, ENST00000562307, ENST00000562601, ENST00000565636, ENST00000566333, ENST00000567445, ENST00000568770, ENST00000569144, ENST00000569454, ENST00000569455, ENST00001017368, ENST00001134889

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
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
ENSE00004785585	83795023	83800640

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.

Highest expression (Bgee): descending thoracic aorta, coronary artery, thoracic aorta, ascending aorta, stromal cell of endometrium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CDH13 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 20 tissues and its splicing (sQTL) in 21 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 41 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Muscle Skeletal	sqtl	7.5e-59	-1.02	16:82638878:G:C
Cells Cultured fibroblasts	sqtl	1.3e-57	-0.60	16:83180875:C:A
Artery Tibial	sqtl	2.2e-57	-0.93	16:83180875:C:A
Artery Aorta	sqtl	4.8e-56	-0.97	16:83180875:C:A
Skin Sun Exposed Lower leg	sqtl	2.7e-40	-0.70	16:83180875:C:A
Skin Not Sun Exposed Suprapubic	sqtl	2.2e-37	-0.76	16:83180875:C:A
Adipose Subcutaneous	sqtl	7.9e-32	-0.85	16:83180875:C:A
Adipose Visceral Omentum	sqtl	1.3e-28	+0.88	16:83180875:C:A
Artery Aorta	eqtl	1.6e-24	-0.46	16:83012185:A:G
Artery Tibial	eqtl	7.5e-24	-0.28	16:83389246:T:C
Breast Mammary Tissue	sqtl	6.7e-15	+0.70	16:83180875:C:A
Lung	sqtl	7.2e-14	-0.66	16:83180875:C:A
Heart Left Ventricle	eqtl	1.5e-12	-0.35	16:82716446:A:G
Esophagus Mucosa	sqtl	4.5e-11	+0.54	16:83180875:C:A
Artery Coronary	sqtl	4.6e-11	+0.85	16:83180875:C:A
Heart Atrial Appendage	eqtl	9.7e-10	-0.35	16:82716446:A:G
Heart Atrial Appendage	sqtl	1.6e-09	+0.53	16:83180875:C:A
Nerve Tibial	sqtl	4.9e-08	+0.42	16:83181822:G:A
Testis	sqtl	5.0e-08	-1.25	16:83260523:A:C
Colon Sigmoid	sqtl	4.2e-07	+0.60	16:83180875:C:A

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

showing 100 of 158 tissues 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
gastrocnemius	UBERON:0001388	88.20	gold quality
right lung	UBERON:0002167	86.93	gold quality
uterus	UBERON:0000995	86.85	gold quality
vagina	UBERON:0000996	86.61	gold quality
skin of leg	UBERON:0001511	86.05	gold quality
frontal cortex	UBERON:0001870	85.86	gold quality
zone of skin	UBERON:0000014	85.63	gold quality
Brodmann (1909) area 10	UBERON:0013541	85.21	gold quality
skin of abdomen	UBERON:0001416	84.86	gold quality
upper lobe of left lung	UBERON:0008952	84.31	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.65	gold quality
lung	UBERON:0002048	83.64	gold quality
subcutaneous adipose tissue	UBERON:0002190	83.35	gold quality
adipose tissue	UBERON:0001013	82.95	gold quality
anterior cingulate cortex	UBERON:0009835	82.83	gold quality
cortical plate	UBERON:0005343	82.67	gold quality
cerebral cortex	UBERON:0000956	82.13	gold quality
omental fat pad	UBERON:0010414	82.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.05	gold quality
frontal pole	UBERON:0002795	81.95	gold quality
primary visual cortex	UBERON:0002436	81.46	gold quality
endometrium	UBERON:0001295	80.76	gold quality
placenta	UBERON:0001987	80.50	gold quality
corpus callosum	UBERON:0002336	80.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.42	gold quality
left uterine tube	UBERON:0001303	80.04	gold quality
gall bladder	UBERON:0002110	79.73	gold quality
thoracic mammary gland	UBERON:0005200	79.59	gold quality
right frontal lobe	UBERON:0002810	78.60	gold quality
rectum	UBERON:0001052	78.36	gold quality
epithelium of bronchus	UBERON:0002031	78.04	gold quality
fallopian tube	UBERON:0003889	77.05	gold quality
layer of synovial tissue	UBERON:0007616	77.03	gold quality
hypothalamus	UBERON:0001898	76.77	gold quality
urinary bladder	UBERON:0001255	76.73	gold quality
dorsal plus ventral thalamus	UBERON:0001897	76.10	gold quality
colonic epithelium	UBERON:0000397	76.01	gold quality
temporal lobe	UBERON:0001871	75.95	gold quality
metanephros cortex	UBERON:0010533	75.70	gold quality
amygdala	UBERON:0001876	75.63	gold quality
esophagus mucosa	UBERON:0002469	74.61	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.25	gold quality
muscle layer of sigmoid colon	UBERON:0035805	74.15	gold quality
sigmoid colon	UBERON:0001159	74.04	gold quality
minor salivary gland	UBERON:0001830	73.86	gold quality
cortex of kidney	UBERON:0001225	73.83	gold quality
material anatomical entity	UBERON:0000465	73.68	gold quality
multicellular organism	UBERON:0000468	73.68	gold quality
anatomical system	UBERON:0000467	73.61	gold quality
esophagus	UBERON:0001043	73.41	gold quality
vermiform appendix	UBERON:0001154	73.36	gold quality
adrenal tissue	UBERON:0018303	72.80	gold quality
saliva-secreting gland	UBERON:0001044	72.72	gold quality
cerebellar vermis	UBERON:0004720	72.59	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.50	gold quality
sural nerve	UBERON:0015488	72.21	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	71.55	gold quality
lower esophagus	UBERON:0013473	71.43	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.41	gold quality
kidney	UBERON:0002113	71.20	gold quality
Ammon’s horn	UBERON:0001954	71.05	gold quality
colon	UBERON:0001155	70.78	gold quality
brain	UBERON:0000955	70.32	gold quality
central nervous system	UBERON:0001017	70.21	gold quality
substantia nigra	UBERON:0002038	69.98	gold quality
dorsal root ganglion	UBERON:0000044	69.95	gold quality
adult mammalian kidney	UBERON:0000082	69.54	gold quality
tibial nerve	UBERON:0001323	69.39	gold quality
intestine	UBERON:0000160	69.19	gold quality
islet of Langerhans	UBERON:0000006	68.56	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

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Caudate putamen	tissue	92.0
Hippocampal formation	tissue	74.1
Skeletal muscle	tissue	64.2	medium
Tongue	tissue	53.9
Heart muscle	tissue	53.5	medium
Cerebral cortex	tissue	48.0	not detected
Motor cortex	tissue	48.0
Prefrontal cortex	tissue	45.5
Somatosensory cortex	tissue	42.7
Frontal cortex	tissue	42.4
Retrosplenial and cingulate cortex	tissue	42.4
Insular cortex	tissue	41.3
Occipital cortex	tissue	40.6
Thalamus	tissue	40.3
Entorhinal cortex	tissue	40.3
Cervix	tissue	39.8	low
Temporal cortex	tissue	39.8
Retrosplenial cortex	tissue	38.9
Endometrium 1	tissue	38.7	not detected
Amygdala	tissue	37.3
Hypothalamus	tissue	35.9
Postcentral gyrus	tissue	34.6
Superior colliculi	tissue	34.5
Periaqueductal gray	tissue	32.3
Smooth muscle	tissue	27.8	medium
Septum	tissue	27.0
Pons	tissue	23.1
Midbrain	tissue	22.5
Medulla oblongata	tissue	22.3
Olfactory bulb	tissue	21.5
Substantia nigra	tissue	21.2
Ventral forebrain	tissue	21.0
Adipose tissue	tissue	19.0	not detected
Skin 1	tissue	17.4	medium
Spinal cord	tissue	17.3
Vagina	tissue	17.2	low
Locus coeruleus	tissue	16.4
Hippocampus	tissue	14.1	not detected
Lung	tissue	13.6	not detected
Cerebellum	tissue	12.1	not detected
Basal ganglia	tissue	11.3	not detected
Putamen	tissue	9.4
Esophagus	tissue	8.8	low
Corpus callosum	tissue	8.7
Seminal vesicle	tissue	6.8	not detected
Nucleus accumbens	tissue	6.8
Urinary bladder	tissue	6.6	not detected
Rectum	tissue	5.8	not detected
Fallopian tube	tissue	5.7	not detected
Choroid plexus	tissue	5.6
Placenta	tissue	5.5	not detected
Thyroid gland	tissue	5.4	not detected
Breast	tissue	4.8	not detected
Gallbladder	tissue	4.7	not detected
Kidney	tissue	4.6	high
Colon	tissue	3.7	not detected
Appendix	tissue	3.6	not detected
Prostate	tissue	3.2	not detected
Epididymis	tissue	3.0	not detected
Ovary	tissue	2.9	not detected

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Blood vessel (140.5), Subiculum (74.1), Ventromedial nucleus (64.7), Olfactory tubercle (64.3), Nucleus of the diagonal band (63.2).

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)

Targeting CDH13 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 90 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 0.998, LOEUF 0.456, missense Z -0.937 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000567109 — one region, missense o/e 1.16.

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:99551) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 5 distinct phenotype terms.

Mouse phenotype (MP)	Records
hyperactivity	1
shortened QT interval	1
retina neovascularization	1
decreased grip strength	1
increased circulating adiponectin level	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5R9X1	99.4%	Diamond
Callithrix jacchus	B0KW95	99.0%	Diamond
Cricetulus griseus	O55075	98.3%	Diamond
Otolemur garnettii	B4USZ0	98.1%	Diamond
Rhinolophus ferrumequinum	B2KI42	97.6%	Diamond
Bos taurus	P19534	97.6%	Diamond
Xenopus laevis	P20310	95.9%	Diamond
Gallus gallus	P24503	94.6%	Diamond
Sus scrofa	O18926	92.4%	Diamond
Canis lupus familiaris	F1PAA9	82.9%	Diamond
Drosophila melanogaster	Q9VJB6	74.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CDH13-AS1	ncRNA	105371368
CEDORA	ncRNA	124903732
MIR8058	ncRNA	102465863
MIR3182	ncRNA	100422853
MLYCD	protein-coding	23417
HSBP1	protein-coding	3281
CDH13-AS2	ncRNA	102724163
SLC38A8	protein-coding	146167
OSGIN1	protein-coding	29948
NECAB2	protein-coding	54550

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 by resolution:

PDB	Title	Method	Resolution (Å)
2V37	Solution structure of the N-terminal extracellular domain of human T- cadherin	SOLUTION NMR

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): plasma membrane

Antibody reliability (HPA): IH enhanced · IF supported

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)

Type	Positions
Gpi-anchor amidated glycine	693

Glycosylation sites (8)

Type	Positions
N-linked (glcnac…) asparagine	52, 86, 382, 500, 530, 598, 638, 671

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

ID	Pathway	Evidence
R-HSA-418990	Adherens junctions interactions	curated
R-HSA-446728	Cell junction organization	—
R-HSA-1500931	Cell-Cell communication	—
R-HSA-421270	Cell-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 (16): extracellular region (GO:0005576), 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

3 top-level categories:

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

GO top-level categories

56 GO namespaces:

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 transport	1
regulation of cellular component organization	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
cell periphery	1
plasma membrane raft	1
cell-cell junction	1
cell-substrate junction	1
plasma membrane	1
cell surface	1
side of membrane	1
extrinsic component of plasma membrane	1
plasma membrane protein complex	1
external encapsulating structure	1
plasma membrane bounded cell projection	1
cytoplasm	1
extracellular vesicle	1
synapse	1
cell junction	1
leaflet of membrane bilayer	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 32 of 57 annotations. The rest are phylogenetic / computational / electronic (IEA).

32 experimentally-supported GO terms:

GO term	NS	Evidence
Rac protein signal transduction	BP	mutant phenotype
Rho protein signal transduction	BP	mutant phenotype
calcium-dependent cell-cell adhesion	BP	direct assay
endothelial cell migration	BP	direct assay
homophilic cell-cell adhesion	BP	direct assay
keratinocyte proliferation	BP	direct assay
lamellipodium assembly	BP	direct assay
localization within membrane	BP	mutant phenotype
low-density lipoprotein particle mediated signaling	BP	direct assay
negative regulation of cell adhesion	BP	direct assay
negative regulation of cell population proliferation	BP	direct assay
positive regulation of calcium-mediated signaling	BP	direct assay
positive regulation of cell migration	BP	direct assay
positive regulation of cell-matrix adhesion	BP	mutant phenotype
positive regulation of endothelial cell proliferation	BP	mutant phenotype
positive regulation of positive chemotaxis	BP	direct assay
positive regulation of smooth muscle cell proliferation	BP	mutant phenotype
positive regulation of transcription by RNA polymerase II	BP	mutant phenotype
regulation of endocytosis	BP	mutant phenotype
regulation of epidermal growth factor receptor signaling pathway	BP	mutant phenotype
sprouting angiogenesis	BP	direct assay
caveola	CC	direct assay
cytoplasm	CC	direct assay
extracellular exosome	CC	high-throughput assay
extracellular matrix	CC	high-throughput assay
extracellular region	CC	high-throughput assay
focal adhesion	CC	high-throughput assay
neuron projection	CC	direct assay
plasma membrane	CC	direct assay
cadherin binding	MF	direct assay
lipoprotein particle binding	MF	direct assay
low-density lipoprotein particle binding	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 1,742 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDH13	RASSF1	Q9NS23	901
CDH13	ADIPOR1	Q96A54	834
CDH13	ADIPOQ	Q15848	757
CDH13	ADIPOR2	Q86V24	753
CDH13	CDKN2A	P42771	741
CDH13	DAPK1	P53355	653
CDH13	RARB	P10826	610
CDH13	MGMT	P16455	575
CDH13	FHIT	P49789	573
CDH13	GSTP1	P09211	569
CDH13	CHFR	Q96EP1	493
CDH13	DLEC1	Q9Y238	478
CDH13	WFDC1	Q9HC57	472
CDH13	MLH1	P40692	470
CDH13	C1QTNF2	Q9BXJ5	453

IntAct

Human interaction partners of CDH13 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

15 partners by confidence:

Partner	Interaction type	MIscore	Records
HTT	physical association	0.560	6
GHITM	physical association	0.560	1
INSIG1	association	0.530	2
ITGB1	physical association	0.460	2
AURKA	physical association	0.370	1
CASP8	physical association	0.370	1
CCND1	physical association	0.370	1
CHEK2	physical association	0.370	1
HMMR	physical association	0.370	1
MAPK6	physical association	0.370	1
PTPN1	physical association	0.370	1
RAD51	physical association	0.370	1
GABRA1	colocalization	0.270	1
ITGB3	colocalization	0.270	1
MTNR1B	physical association	0.000	1

BioGRID (56 interactions; top human partners by supporting records): DNAAF2 (Affinity Capture-MS; 3 records), AGPAT5 (Affinity Capture-MS; 2 records), CHPT1 (Affinity Capture-MS; 2 records), DGUOK (Affinity Capture-MS; 2 records), DSTYK (Affinity Capture-MS; 2 records), ERMP1 (Affinity Capture-MS; 2 records), INSIG1 (Affinity Capture-MS; 2 records), NUFIP1 (Affinity Capture-MS; 2 records), SEC14L1 (Affinity Capture-MS; 2 records), TUBB3 (Affinity Capture-MS; 2 records), TUBB8 (Affinity Capture-MS; 2 records), VMP1 (Affinity Capture-MS; 2 records), ADIPOR1 (Affinity Capture-Western), ANXA1 (Protein-peptide), ARF5 (Affinity Capture-MS)

SIGNOR signaling

3 signaling 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

Genetic variants

Variant evidence for CDH13: 261 ClinVar records (2 pathogenic / likely pathogenic); 1 PharmGKB clinical annotation; 106 GWAS associations. Per-variant detail is on Sugi Variant.

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)

Showing all 2 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
2665080	GRCh38/hg38 16q23.2-23.3(chr16:79568000-83552000)	Likely pathogenic	criteria provided, single submitter	1
393545	GRCh37/hg19 16q23.3(chr16:83414018-83518410)x1	Likely pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore CDH13’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 4,756):

Position(s)	Effect	Δscore	Sites
16:82627138–82627139	donor_loss	1.0000	5
16:82829374	donor_gain	1.0000
16:82858474–82858475	donor_loss	1.0000	6
16:83032000	acceptor_loss	1.0000
16:83032008–83032009	acceptor_loss	1.0000	6
16:83032219–83032220	donor_loss	1.0000	5
16:83217343–83217344	acceptor_loss	1.0000	6
16:83217498	donor_loss	1.0000
16:83344844	acceptor_gain	1.0000
16:83344851	acceptor_gain	1.0000

AlphaMissense

1,335 missense substitutions predicted likely pathogenic (of 4,696 scored), across 348 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
N239	8	0.997	0.999
D271	8	0.996	0.998
D240	8	0.995	0.999
D237	8	0.994	0.998
D273	8	0.994	0.998
D389	8	0.993	0.998
D335	8	0.992	0.998
D387	8	0.990	0.998
D610	8	0.983	0.995
N357	8	0.981	0.998
F299	8	0.978	0.999
D503	8	0.977	0.990
D663	8	0.976	0.993
F411	8	0.974	0.997
D559	8	0.973	0.991
D355	8	0.970	0.993
D608	8	0.970	0.989
F188	8	0.968	0.998
F245	8	0.966	0.996
D505	8	0.965	0.986

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Kidney Renal Clear Cell Carcinoma)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	1.93e-09
Kidney Renal Clear Cell Carcinoma (validation)	favorable	6.97e-05
Breast Invasive Carcinoma (TCGA)	unfavorable	0.000977

Disease associations

OMIM: gene MIM:601364 | disease phenotypes:

GWAS associations

showing 30 of 106 associations:

Study	Trait	p-value
GCST002233_10	Adiponectin levels	7e-165
GCST000828_1	Adiponectin levels	3e-83
GCST001465_4	Adiponectin levels	6e-48
GCST001314_1	Adiponectin levels	5e-40
GCST000812_2	Adiponectin levels	4e-30
GCST007269_141	Pulse pressure	6e-25
GCST007096_165	Pulse pressure	3e-24
GCST004278_17	Pulse pressure	1e-19
GCST010135_51	Oily fish consumption	2e-19
GCST010140_1	Pork consumption	2e-19
GCST010866_42	Coronary artery disease	2e-18
GCST001165_1	Adiponectin levels	6e-17
GCST005194_96	Coronary artery disease	2e-16
GCST005195_44	Coronary artery disease	2e-16
GCST005196_21	Coronary artery disease	2e-16
GCST010321_163	PR interval	2e-16
GCST006902_5	Adolescent idiopathic scoliosis	2e-15
GCST001463_5	Adiponectin levels	1e-14
GCST007268_67	Diastolic blood pressure	2e-12
GCST010142_9	Fish- and plant-related diet	7e-12
GCST010796_444	Electrocardiogram morphology (amplitude at temporal datapoints)	7e-12
GCST010796_447	Electrocardiogram morphology (amplitude at temporal datapoints)	9e-12
GCST010050_19	Adiponectin levels	3e-11
GCST010988_157	Adult body size	3e-11
GCST010796_446	Electrocardiogram morphology (amplitude at temporal datapoints)	6e-11
GCST010796_461	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-10
GCST010796_462	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-10
GCST012490_594	Femur bone mineral density x serum urate levels interaction	2e-10
GCST004775_44	Pulse pressure	3e-10
GCST004787_60	Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)	5e-10

EFO canonical traits (from GWAS)

32 canonical traits:

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
EFO:0007701	spine bone mineral density
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB clinical annotations

1 annotations by evidence level (1 strongest → 4):

Variant	Association	Level	Drugs	Phenotypes
rs17682789	Toxicity	3	sorafenib	Diarrhea

PharmGKB variants

1 variants:

Variant	Genes	Level	Score	#Clin annots	Drugs
rs17682789	CDH13	3	3.00	1	sorafenib

PharmGKB variant annotations

Per-publication pharmacogenomic findings for this gene (significant associations).

5 published findings:

Variant	Drug(s)	Category	Finding	PMID
rs3784943	amphetamine	Efficacy	Genotypes AG + GG is associated with increased response to amphetamine as compared to genotype AA.	PMID:27771748
rs11859453	aspirin, clopidogrel	Efficacy	Genotypes AA + AG is associated with decreased likelihood of Coronary Restenosis or Disease Progression when treated with aspirin and clopidogrel in people with Coronary Disease as compared to genotype GG.	PMID:31854260
rs17682789	sorafenib	Toxicity	Allele C is associated with decreased risk of Diarrhea when treated with sorafenib in people with Carcinoma, Renal Cell as compared to allele T.	PMID:35484400
rs7201829	HMG-CoA reductase inhibitors	Efficacy	Allele T is associated with increased likelihood of Stroke when treated with hmg coa reductase inhibitors as compared to allele C.	PMID:40948399
rs2116971	perphenazine	Efficacy	Allele G is associated with response to perphenazine in people with Schizophrenia.	PMID:22920393

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Decitabine	affects expression, affects methylation, decreases methylation	4
bisphenol A	increases expression, affects cotreatment, increases methylation, decreases methylation	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	increases reaction, affects binding	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)

Via MONDO — disease-level, not drug-specific.

1 trials:

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