CDH10
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Summary
CDH10 (cadherin 10, HGNC:1749) is a protein-coding gene on chromosome 5p14.2-p14.1, encoding Cadherin-10 (Q9Y6N8). Cadherins are calcium-dependent cell adhesion proteins.
This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein’s homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin is predominantly expressed in brain and is putatively involved in synaptic adhesions, axon outgrowth and guidance. Mutations in this gene may be associated with lung squamous cell carcinoma and colorectal cancer in human patients.
Source: NCBI Gene 1008 — RefSeq curated summary.
At a glance
- GWAS associations: 11
- Clinical variants (ClinVar): 100 total — 1 pathogenic
- Phenotypes (HPO): 1
- Cancer driver (intOGen): activating (oncogene-like) across 4 cancer types
- MANE Select transcript:
NM_006727
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:1749 |
| Approved symbol | CDH10 |
| Name | cadherin 10 |
| Location | 5p14.2-p14.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000040731 |
| Ensembl biotype | protein_coding |
| OMIM | 604555 |
| Entrez | 1008 |
Gene structure
Transcript identifiers
Ensembl transcripts: 5 — 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay
ENST00000264463, ENST00000502921, ENST00000503958, ENST00000510477, ENST00000965911
RefSeq mRNA: 4 — MANE Select: NM_006727
NM_001317222, NM_001317224, NM_001362460, NM_006727
CCDS: CCDS3892
Canonical transcript exons
ENST00000264463 — 12 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000970943 | 24537380 | 24537674 |
| ENSE00000970946 | 24511327 | 24511514 |
| ENSE00000970947 | 24509566 | 24509819 |
| ENSE00000970948 | 24505112 | 24505248 |
| ENSE00001156334 | 24593260 | 24593613 |
| ENSE00001361706 | 24644594 | 24644978 |
| ENSE00001387472 | 24487100 | 24488153 |
| ENSE00001629749 | 24535112 | 24535279 |
| ENSE00001725744 | 24535703 | 24535822 |
| ENSE00003509431 | 24491576 | 24491827 |
| ENSE00003537047 | 24498398 | 24498519 |
| ENSE00003556727 | 24492817 | 24492925 |
Expression profiles
Bgee: expression breadth ubiquitous, 172 present calls, max score 95.85.
FANTOM5 (CAGE): breadth broad, TPM avg 5.5218 / max 502.3765, expressed in 525 samples.
FANTOM5 promoters (8 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 61121 | 2.9331 | 442 |
| 61122 | 0.9020 | 276 |
| 61117 | 0.5452 | 113 |
| 61120 | 0.4813 | 187 |
| 61119 | 0.3580 | 122 |
| 61118 | 0.1486 | 58 |
| 203506 | 0.0979 | 54 |
| 203505 | 0.0556 | 26 |
Top tissues by expression
270 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| Brodmann (1909) area 23 | UBERON:0013554 | 95.85 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 95.55 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 93.51 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 92.93 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 92.40 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 91.51 | gold quality |
| cerebellar cortex | UBERON:0002129 | 91.48 | gold quality |
| entorhinal cortex | UBERON:0002728 | 91.32 | gold quality |
| cerebellum | UBERON:0002037 | 91.10 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 91.07 | gold quality |
| prefrontal cortex | UBERON:0000451 | 90.12 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 90.08 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 90.01 | gold quality |
| frontal cortex | UBERON:0001870 | 89.59 | gold quality |
| primary visual cortex | UBERON:0002436 | 89.56 | gold quality |
| postcentral gyrus | UBERON:0002581 | 89.41 | gold quality |
| neocortex | UBERON:0001950 | 88.95 | gold quality |
| endothelial cell | CL:0000115 | 88.44 | gold quality |
| parietal lobe | UBERON:0001872 | 88.18 | gold quality |
| cerebral cortex | UBERON:0000956 | 88.14 | gold quality |
| cerebellar vermis | UBERON:0004720 | 88.01 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 87.68 | gold quality |
| cingulate cortex | UBERON:0003027 | 87.62 | gold quality |
| right frontal lobe | UBERON:0002810 | 87.19 | gold quality |
| temporal lobe | UBERON:0001871 | 87.01 | gold quality |
| CA1 field of hippocampus | UBERON:0003881 | 86.71 | gold quality |
| occipital lobe | UBERON:0002021 | 86.26 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 84.82 | gold quality |
| amygdala | UBERON:0001876 | 84.64 | gold quality |
| telencephalon | UBERON:0001893 | 84.63 | gold quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-35 | yes | 62.68 |
| E-ANND-3 | no | 5.22 |
| E-MTAB-6058 | no | 2.08 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
56 targeting CDH10, 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-25-3P | 99.98 | 74.60 | 1817 |
| HSA-MIR-32-5P | 99.98 | 75.21 | 1964 |
| HSA-MIR-363-3P | 99.98 | 74.72 | 1821 |
| HSA-MIR-367-3P | 99.98 | 74.83 | 1819 |
| HSA-MIR-92A-3P | 99.98 | 75.21 | 1960 |
| HSA-MIR-92B-3P | 99.98 | 75.25 | 1955 |
| HSA-MIR-548AJ-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-548X-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-3658 | 99.96 | 73.87 | 4379 |
| HSA-MIR-548J-3P | 99.94 | 72.61 | 4881 |
| HSA-MIR-548AE-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-548AH-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AM-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AQ-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-6721-5P | 99.93 | 68.92 | 2981 |
| HSA-MIR-7-1-3P | 99.91 | 71.53 | 4384 |
| HSA-MIR-7-2-3P | 99.91 | 71.40 | 4394 |
| HSA-MIR-589-3P | 99.91 | 69.62 | 2088 |
| HSA-MIR-3671 | 99.90 | 73.04 | 3897 |
| HSA-MIR-380-3P | 99.89 | 70.18 | 1978 |
| HSA-MIR-8062 | 99.88 | 68.43 | 995 |
| HSA-LET-7A-2-3P | 99.87 | 70.53 | 1921 |
| HSA-MIR-579-3P | 99.86 | 71.66 | 3628 |
| HSA-LET-7G-3P | 99.85 | 70.43 | 1929 |
| HSA-MIR-664B-3P | 99.84 | 71.65 | 3590 |
| HSA-MIR-4524A-3P | 99.72 | 66.85 | 2406 |
| HSA-MIR-4699-3P | 99.71 | 70.15 | 3142 |
| HSA-MIR-6086 | 99.70 | 65.38 | 699 |
| HSA-MIR-377-5P | 99.70 | 65.28 | 712 |
| HSA-MIR-587 | 99.64 | 70.86 | 2611 |
Literature-anchored findings (GeneRIF, showing 4)
- The CC genotype of rs4307059 located in the region between CDH9 and CDH10 is associated with completed suicide in a Polish cohort (PMID:22846907)
- Unconventional CDH10, CDH24 and DCHS2 genes harbored frameshift mutations. (PMID:24898286)
- Loss of CDH10 gene is associated with pancreatic ductal adenocarcinomas. (PMID:28124395)
- G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome. (PMID:32292512)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cdh10a | ENSDARG00000055843 |
| danio_rerio | ENSDARG00000103903 | |
| mus_musculus | Cdh10 | ENSMUSG00000022321 |
| rattus_norvegicus | Cdh10 | ENSRNOG00000009771 |
Paralogs (33): CDH1 (ENSG00000039068), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDHR5 (ENSG00000099834), CDH20 (ENSG00000101542), PCDH11X (ENSG00000102290), CDH23 (ENSG00000107736), CDH9 (ENSG00000113100), CDH6 (ENSG00000113361), CDH26 (ENSG00000124215), CDHR3 (ENSG00000128536), CDH15 (ENSG00000129910), CDH24 (ENSG00000139880), CDH11 (ENSG00000140937), CDH13 (ENSG00000140945), CDH18 (ENSG00000145526), CDHR1 (ENSG00000148600), CDH22 (ENSG00000149654), CDH8 (ENSG00000150394), CDH12 (ENSG00000154162), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), PCDH9 (ENSG00000184226), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)
Protein
Protein identifiers
Cadherin-10 — Q9Y6N8 (reviewed: Q9Y6N8)
Alternative names: T2-cadherin
All UniProt accessions (4): D6RJG0, Q9Y6N8, X5D8X5, X5DNG6
UniProt curated annotations — full annotation on UniProt →
Function. Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.
Subcellular location. Cell membrane.
Tissue specificity. Predominantly expressed in brain. Also found in adult and fetal kidney. Very low levels detected in prostate and fetal lung.
Domain organisation. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
RefSeq proteins (4): NP_001304151, NP_001304153, NP_001349389, NP_006718* (*=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 (21 total): domain 5, glycosylation site 4, modified residue 2, sequence variant 2, sequence conflict 2, topological domain 2, signal peptide 1, propeptide 1, chain 1, transmembrane region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9Y6N8-F1 | 78.29 | 0.49 |
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 (2): 784, 788
Glycosylation sites (4): 256, 438, 456, 534
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: 165 (showing top):
FISCHER_G1_S_CELL_CYCLE, GCANCTGNY_MYOD_Q6, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, CHANDRAN_METASTASIS_DN, GOBP_CALCIUM_DEPENDENT_CELL_CELL_ADHESION, NKX61_01, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, CATTTCA_MIR203, NF1_Q6_01, TGCTGAY_UNKNOWN, TGIF_01, FOXJ2_01, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN
GO Biological Process (10): 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), synaptic membrane adhesion (GO:0099560), cell adhesion (GO:0007155)
GO Molecular Function (4): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), cadherin binding (GO:0045296), metal ion binding (GO:0046872)
GO Cellular Component (9): plasma membrane (GO:0005886), adherens junction (GO:0005912), catenin complex (GO:0016342), presynaptic active zone membrane (GO:0048787), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), postsynaptic specialization membrane (GO:0099634), membrane (GO:0016020), synapse (GO:0045202)
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 |
|---|---|
| cell-cell adhesion | 4 |
| cell-cell junction organization | 2 |
| synaptic membrane | 2 |
| synapse | 2 |
| anatomical structure morphogenesis | 1 |
| cell junction assembly | 1 |
| cell motility | 1 |
| cell adhesion | 1 |
| synapse organization | 1 |
| cellular process | 1 |
| metal ion binding | 1 |
| protein binding | 1 |
| cell adhesion molecule binding | 1 |
| cation binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| cell-cell junction | 1 |
| extrinsic component of plasma membrane | 1 |
| plasma membrane protein complex | 1 |
| presynaptic membrane | 1 |
| presynaptic active zone | 1 |
| postsynaptic membrane | 1 |
| postsynaptic specialization | 1 |
| cellular anatomical structure | 1 |
| cell junction | 1 |
Protein interactions and networks
STRING
1304 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CDH10 | TAS2R1 | Q9NYW7 | 788 |
| CDH10 | SEMA5A | Q13591 | 741 |
| CDH10 | NLGN4X | Q8N0W4 | 739 |
| CDH10 | NLGN3 | Q9NZ94 | 711 |
| CDH10 | CNTN4 | Q8IWV2 | 707 |
| CDH10 | NLGN1 | Q8N2Q7 | 668 |
| CDH10 | ASTN2 | O75129 | 661 |
| CDH10 | CDH15 | P55291 | 656 |
| CDH10 | NRXN1 | Q9ULB1 | 641 |
| CDH10 | CDH2 | P19022 | 635 |
| CDH10 | CDH19 | Q9H159 | 632 |
| CDH10 | FBXO40 | Q9UH90 | 631 |
| CDH10 | CDH20 | Q9HBT6 | 626 |
| CDH10 | CDH7 | Q9ULB5 | 626 |
| CDH10 | COP1 | Q8NHY2 | 596 |
IntAct
7 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CTNNB1 | JUP | psi-mi:“MI:0914”(association) | 0.610 |
| Cdh1 | ARVCF | psi-mi:“MI:0914”(association) | 0.350 |
| CTNNA3 | ARVCF | psi-mi:“MI:0914”(association) | 0.350 |
| CTNNB1 | IGLL5 | psi-mi:“MI:0914”(association) | 0.350 |
| CDH10 | COPS6 | psi-mi:“MI:0915”(physical association) | 0.000 |
| CDH10 | PTN | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (11): CDH10 (Affinity Capture-MS), CDH10 (Affinity Capture-MS), CDH10 (Affinity Capture-MS), COPS6 (Two-hybrid), PTN (Two-hybrid), CDH10 (Affinity Capture-Western), CDH10 (Affinity Capture-MS), CDH10 (Affinity Capture-MS), CDH10 (Affinity Capture-MS), CDH10 (Protein-peptide), JUP (Two-hybrid)
ESM2 similar proteins: A0A8M2BIB6, F1QSQ0, F8W3X3, H2EQR6, O35902, O54800, O55111, O93319, P32926, P33545, P55280, P55285, P55286, P55287, P55288, P55289, P55292, P55849, P55850, P70407, P70408, P79995, P97291, P97326, Q01107, Q02413, Q02487, Q08554, Q08DJ5, Q13634, Q14126, Q14574, Q28060, Q3SWX5, Q5DWV1, Q5RJH3, Q61495, Q68SP4, Q6W3B0, Q7TMD7
Diamond homologs: A0A8M2BIB6, B0KW95, B2KI42, B4USZ0, F1PAA9, F1QSQ0, O02840, O35902, O54800, O55075, O55111, O93319, P08641, P09803, P10287, P10288, P12830, P15116, P19022, P19534, P19535, P20310, P22223, P24503, P30944, P32926, P33145, P33146, P33147, P33148, P33150, P33151, P33152, P33545, P39038, P55280, P55283, P55284, P55285, P55286
SIGNOR signaling
2 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| calcium(2+) | “up-regulates activity” | CDH10 | “chemical activation” |
| CDH10 | “up-regulates activity” | CTNNB1 | binding |
Disease & clinical
Cancer significance
From intOGen — cancer-driver classification: activating (oncogene-like) across 4 cancer types — LUAD, LUSC, PAAD, UCEC.
Clinical variants and AI predictions
ClinVar
100 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 79 |
| Likely benign | 4 |
| Benign | 4 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 59605 | GRCh38/hg38 5p14.3-14.1(chr5:23279693-26849830)x1 | Pathogenic |
SpliceAI
2711 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 5:24488149:TATAA:T | acceptor_gain | 1.0000 |
| 5:24488150:ATAA:A | acceptor_gain | 1.0000 |
| 5:24488151:TAA:T | acceptor_gain | 1.0000 |
| 5:24488152:AA:A | acceptor_gain | 1.0000 |
| 5:24488154:C:CC | acceptor_gain | 1.0000 |
| 5:24488155:T:C | acceptor_gain | 1.0000 |
| 5:24488155:T:G | acceptor_loss | 1.0000 |
| 5:24488155:T:TC | acceptor_gain | 1.0000 |
| 5:24491574:AC:A | donor_gain | 1.0000 |
| 5:24491575:CC:C | donor_gain | 1.0000 |
| 5:24498391:GGCTT:G | donor_loss | 1.0000 |
| 5:24498392:GCTTA:G | donor_loss | 1.0000 |
| 5:24498393:CTTA:C | donor_loss | 1.0000 |
| 5:24498394:TTA:T | donor_loss | 1.0000 |
| 5:24498395:T:TG | donor_loss | 1.0000 |
| 5:24498396:AC:A | donor_loss | 1.0000 |
| 5:24498516:TTGT:T | acceptor_gain | 1.0000 |
| 5:24498517:TGT:T | acceptor_gain | 1.0000 |
| 5:24498520:C:CC | acceptor_gain | 1.0000 |
| 5:24505110:A:AC | donor_gain | 1.0000 |
| 5:24505111:C:CC | donor_gain | 1.0000 |
| 5:24509816:GTGG:G | acceptor_gain | 1.0000 |
| 5:24509817:TGG:T | acceptor_gain | 1.0000 |
| 5:24509817:TGGCT:T | acceptor_loss | 1.0000 |
| 5:24509818:GG:G | acceptor_gain | 1.0000 |
| 5:24509818:GGCTG:G | acceptor_loss | 1.0000 |
| 5:24509819:GC:G | acceptor_loss | 1.0000 |
| 5:24509820:C:CC | acceptor_gain | 1.0000 |
| 5:24509820:CT:C | acceptor_loss | 1.0000 |
| 5:24509822:G:C | acceptor_gain | 1.0000 |
AlphaMissense
5198 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 5:24535204:T:G | D241A | 1.000 |
| 5:24535205:C:G | D241H | 1.000 |
| 5:24535210:G:T | A239D | 1.000 |
| 5:24535211:C:G | A239P | 1.000 |
| 5:24535216:A:T | I237N | 1.000 |
| 5:24535273:A:T | I218N | 1.000 |
| 5:24535723:A:G | F209S | 1.000 |
| 5:24535751:A:C | Y200D | 1.000 |
| 5:24537433:G:T | P158Q | 1.000 |
| 5:24537442:T:A | D155V | 1.000 |
| 5:24537442:T:C | D155G | 1.000 |
| 5:24537442:T:G | D155A | 1.000 |
| 5:24537443:C:G | D155H | 1.000 |
| 5:24537444:A:C | N154K | 1.000 |
| 5:24537444:A:T | N154K | 1.000 |
| 5:24537450:A:C | D152E | 1.000 |
| 5:24537450:A:T | D152E | 1.000 |
| 5:24537451:T:A | D152V | 1.000 |
| 5:24537451:T:G | D152A | 1.000 |
| 5:24537452:C:G | D152H | 1.000 |
| 5:24537463:A:T | I148N | 1.000 |
| 5:24537468:A:C | F146L | 1.000 |
| 5:24537468:A:T | F146L | 1.000 |
| 5:24537469:A:G | F146S | 1.000 |
| 5:24537470:A:G | F146L | 1.000 |
| 5:24537526:A:G | L127P | 1.000 |
| 5:24537547:T:A | E120V | 1.000 |
| 5:24537550:C:A | R119M | 1.000 |
| 5:24537550:C:G | R119T | 1.000 |
| 5:24537574:A:C | I111S | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000001711 (5:24564180 C>A), RS1000039864 (5:24604015 T>C), RS1000055521 (5:24633745 T>C,G), RS1000081298 (5:24531300 C>T), RS1000087877 (5:24552248 T>A,C), RS1000088976 (5:24616547 T>C,G), RS1000129782 (5:24637231 A>G), RS1000137333 (5:24546264 C>T), RS1000156677 (5:24506582 A>G), RS1000160486 (5:24492527 G>A), RS1000172009 (5:24529867 A>G), RS1000174471 (5:24490965 T>C), RS1000230621 (5:24570664 G>GTA), RS1000241390 (5:24610311 G>A,T), RS1000248041 (5:24609182 T>C)
Disease associations
OMIM: gene MIM:604555 | disease phenotypes:
GenCC curated gene-disease
Mondo (2): hyperopia (MONDO:0004891), obesity disorder (MONDO:0011122)
Orphanet (2): Obesity due to melanocortin 4 receptor deficiency (Orphanet:71529), NON RARE IN EUROPE: Non rare obesity (Orphanet:521399)
HPO phenotypes
1 total (1 of 1 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0001513 | Obesity |
GWAS associations
11 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000382_1 | Autism | 2.000000e-10 |
| GCST001800_8 | β2-Glycoprotein I (β2-GPI) plasma levels | 2.000000e-06 |
| GCST002451_2 | Obsessive-compulsive disorder | 2.000000e-06 |
| GCST003944_28 | Hepcidin/ferritin ratio | 6.000000e-06 |
| GCST005588_26 | Idiopathic dilated cardiomyopathy | 3.000000e-06 |
| GCST005956_56 | Waist-to-hip ratio adjusted for BMI | 2.000000e-06 |
| GCST005959_31 | Waist-to-hip ratio adjusted for BMI x sex interaction | 4.000000e-06 |
| GCST007325_71 | General risk tolerance (MTAG) | 5.000000e-10 |
| GCST008465_7 | Anorexia nervosa | 3.000000e-08 |
| GCST010570_4 | Polycystic ovary syndrome (reproductive subtype) | 1.000000e-08 |
| GCST011743_73 | HDL cholesterol levels in HIV infection | 4.000000e-06 |
EFO canonical traits (7, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004555 | glycoprotein measurement |
| EFO:0007901 | hepcidin:ferritin ratio |
| EFO:0009094 | idiopathic dilated cardiomyopathy |
| EFO:0007788 | BMI-adjusted waist-hip ratio |
| EFO:0008343 | sex interaction measurement |
| EFO:0008579 | risk-taking behaviour |
| EFO:0004612 | high density lipoprotein cholesterol measurement |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D006956 | Hyperopia | C11.744.479 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
46 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, decreases expression, decreases methylation, affects cotreatment, increases expression | 8 |
| Benzo(a)pyrene | increases expression | 3 |
| mercuric bromide | increases expression, affects cotreatment | 2 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 2 |
| Panobinostat | affects cotreatment, increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| Rotenone | decreases expression | 2 |
| Aflatoxin B1 | affects expression, decreases methylation | 2 |
| methylmercuric chloride | decreases expression | 1 |
| ascorbate-2-phosphate | affects binding, affects cotreatment, increases expression | 1 |
| trichostatin A | increases expression | 1 |
| sulforaphane | decreases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| potassium chromate(VI) | increases expression | 1 |
| 4-(2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acid | affects cotreatment, increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| deguelin | decreases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| fenpyroximate | decreases expression | 1 |
| 4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide | decreases expression | 1 |
| Chir 99021 | increases expression, affects binding, affects cotreatment | 1 |
| pyrimidifen | decreases expression | 1 |
| thifluzamide | decreases expression | 1 |
| pyrachlostrobin | decreases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| XAV939 | affects binding, affects cotreatment, increases expression | 1 |
| LDN 193189 | affects cotreatment, increases expression | 1 |
| picoxystrobin | decreases expression | 1 |
| 3-(4-pyridyl)-1H-indole | affects cotreatment, increases expression | 1 |
| Temozolomide | increases expression | 1 |
Clinical trials (associated diseases)
300 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00347204 | PHASE4 | COMPLETED | Comparison of Acular LS Versus Nevanac for Pain Control in Eyes Undergoing PRK |
| NCT00455455 | PHASE4 | COMPLETED | Corneal and Conjunctival Sensitivity and Staining Study |
| NCT00937105 | PHASE4 | COMPLETED | Daily Wear Corneal Infiltrative Event Study |
| NCT01387360 | PHASE4 | COMPLETED | Presbyopic Supracor Treatment for Near Myopic/Hyperopic Pseudophakic Eyes |
| NCT01977807 | PHASE4 | UNKNOWN | A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser in Asian Eyes Using LASIK |
| NCT02071576 | PHASE4 | UNKNOWN | A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser Using LASIK |
| NCT02112968 | PHASE4 | UNKNOWN | A Prospective Safety and Effectiveness Study of a New High Repetition Rate Excimer Laser Using LASIK for the Correction of Ammetropia and Presbyopia |
| NCT03881670 | PHASE4 | COMPLETED | On-Eye Optical Quality of Lotrafilcon B Lenses Over 12 Hours |
| NCT04208750 | PHASE4 | COMPLETED | Clinical Investigation of the Vision-R800 Device. |
| NCT04283331 | PHASE4 | UNKNOWN | Anesthetic Impregnated Bandage Soft Contact Lens (BSCL) in Pain Management After Photorefractive Keratectomy (PRK) |
| NCT00076362 | PHASE4 | COMPLETED | Pediatric Hypothalamic Obesity |
| NCT00079547 | PHASE4 | COMPLETED | The Safety and Effectiveness of Low and High Carbohydrate Diets |
| NCT00115063 | PHASE4 | TERMINATED | LOSS- Louisiana Obese Subjects Study |
| NCT00134303 | PHASE4 | COMPLETED | Trial Comparing Metformin Versus Placebo in Non Alcoholic Steatohepatitis (NASH) Patients Receiving Bariatric Surgery for Obesity |
| NCT00143936 | PHASE4 | COMPLETED | The Safety and Efficacy of Low and High Carbohydrate Diets |
| NCT00143962 | PHASE4 | COMPLETED | Comparison of Two Approaches to Weight Loss Follow-Up Study |
| NCT00152360 | PHASE4 | COMPLETED | The Effect of Xenical on Weight and Risk Factors |
| NCT00176306 | PHASE4 | COMPLETED | Levofloxacin Pharmacokinetics (PK) in the Severely Obese |
| NCT00203450 | PHASE4 | COMPLETED | Zonegran for the Treatment of Weight Gain Associated With Psychotropic Medication Use: A Placebo-Controlled Trial |
| NCT00205504 | PHASE4 | COMPLETED | Oral Contraceptives in the Metabolic Syndrome |
| NCT00229229 | PHASE4 | TERMINATED | Comparison of 4 Diets in the Management of Overweight Patients With Vascular Disease |
| NCT00234988 | PHASE4 | COMPLETED | A Phase IV, Multi-Center, Open-Label Trial of Sibutramine in Combination With a Hypocaloric Diet in Obese and Overweight Thai Subjects. |
| NCT00264589 | PHASE4 | COMPLETED | Exercise Training and Cardiovascular Function in Obesity and in Type 2 Diabetes |
| NCT00288873 | PHASE4 | COMPLETED | Characterization of Hyperparathyroidism and Vitamin D Deficiency in Obesity |
| NCT00298857 | PHASE4 | TERMINATED | A Pharmacokinetic Study to Compare the Dosing of Valproic Acid in Subjects With Different Body Weights |
| NCT00315146 | PHASE4 | COMPLETED | Optimizing Body Composition for Function in Older Adults |
| NCT00319202 | PHASE4 | TERMINATED | Clinical Trial to Assess the Effects of Candesartan on the Carbohydrate Metabolism of Obese Subjects |
| NCT00327912 | PHASE4 | UNKNOWN | Laparoscopic Roux-en-Y Gastric Bypass Versus Laparoscopic Biliopancreatic Diversion (BPD)- Duodenal Switch for Superobesity |
| NCT00352287 | PHASE4 | COMPLETED | Study to Determine the Effects of Human Growth Hormone and Pioglitazone in Overweight, Prediabetic Adults |
| NCT00353054 | PHASE4 | COMPLETED | Effect of Calcium/Vitamin D Supplementation on Body Weight and Fat Loss. |
| NCT00390637 | PHASE4 | COMPLETED | Diet, Obesity and Genes (DiOGenes) |
| NCT00415688 | PHASE4 | COMPLETED | Lifestyle Modification for Obesity-Related Type 2 Diabetes |
| NCT00433641 | PHASE4 | COMPLETED | Weight Loss in Response to Sibutramine (MERIDIA) is Influenced by the Inherited Genes |
| NCT00440375 | PHASE4 | COMPLETED | Effects of Rosiglitazone on Bone in Postmenopausal Diabetic Women |
| NCT00453557 | PHASE4 | COMPLETED | Mechanism of Growth Hormone Effects on Adipose Tissue |
| NCT00456885 | PHASE4 | COMPLETED | The Effect of Exenatide on Weight and Hunger in Obese, Healthy Women |
| NCT00463112 | PHASE4 | COMPLETED | Effect of Diet Plus Sibutramine on Hormonal and Metabolic Features in Overweight and Obese Women With PCOS |
| NCT00512187 | PHASE4 | COMPLETED | Moderate Weight Loss Makes Obese Patients With Severe Chronic Plaque Psoriasis Responsive to Sub-Optimal Dose of Cyclosporine: an Investigator Blinded, Controlled, Randomized Clinical Trial |
| NCT00516919 | PHASE4 | COMPLETED | Study of Behavioral Weight Loss Therapy for Obesity and Binge Eating in Monolingual Hispanic Persons |
| NCT00522470 | PHASE4 | COMPLETED | Effects of Rosiglitazone on Serum Ghrelin and Peptide YY Levels |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): anorexia nervosa, hyperopia, obesity disorder, obsessive-compulsive disorder, polycystic ovary syndrome