CDH12
gene geneOn this page
Also known as Br-cadherinCDHB
Summary
CDH12 (cadherin 12, HGNC:1751) is a protein-coding gene on chromosome 5p14.3, encoding Cadherin-12 (P55289). Cadherins are calcium-dependent cell adhesion proteins.
This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin appears to be expressed specifically in the brain and its temporal pattern of expression would be consistent with a role during a critical period of neuronal development, perhaps specifically during synaptogenesis.
Source: NCBI Gene 1010 — RefSeq curated summary.
At a glance
- GWAS associations: 11
- Clinical variants (ClinVar): 166 total — 1 pathogenic
- MANE Select transcript:
NM_004061
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:1751 |
| Approved symbol | CDH12 |
| Name | cadherin 12 |
| Location | 5p14.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | Br-cadherin, CDHB |
| Ensembl gene | ENSG00000154162 |
| Ensembl biotype | protein_coding |
| OMIM | 600562 |
| Entrez | 1010 |
Gene structure
Transcript identifiers
Ensembl transcripts: 10 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron
ENST00000382254, ENST00000504376, ENST00000517378, ENST00000518209, ENST00000520668, ENST00000521384, ENST00000521745, ENST00000522262, ENST00000880753, ENST00000954356
RefSeq mRNA: 9 — MANE Select: NM_004061
NM_001317227, NM_001317228, NM_001364104, NM_001364105, NM_001364106, NM_001364107, NM_001364108, NM_001364109, NM_004061
CCDS: CCDS3890, CCDS82991
Canonical transcript exons
ENST00000382254 — 15 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001402656 | 22212498 | 22212643 |
| ENSE00001404736 | 22505270 | 22505364 |
| ENSE00001406275 | 22405257 | 22405351 |
| ENSE00001491433 | 22853058 | 22853344 |
| ENSE00002072306 | 21750673 | 21752236 |
| ENSE00003462950 | 21842161 | 21842328 |
| ENSE00003462989 | 21802167 | 21802420 |
| ENSE00003465765 | 21760558 | 21760675 |
| ENSE00003525376 | 22078446 | 22078862 |
| ENSE00003529986 | 21764978 | 21765099 |
| ENSE00003535159 | 21975091 | 21975385 |
| ENSE00003625935 | 21783358 | 21783494 |
| ENSE00003632046 | 21755591 | 21755842 |
| ENSE00003675761 | 21816945 | 21817132 |
| ENSE00003694264 | 21854671 | 21854790 |
Expression profiles
Bgee: expression breadth ubiquitous, 133 present calls, max score 78.25.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7445 / max 229.6578, expressed in 127 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 61104 | 0.6135 | 113 |
| 61105 | 0.1310 | 61 |
Top tissues by expression
262 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 78.25 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 77.10 | gold quality |
| postcentral gyrus | UBERON:0002581 | 76.00 | gold quality |
| adrenal tissue | UBERON:0018303 | 75.78 | gold quality |
| cortical plate | UBERON:0005343 | 75.33 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 75.02 | gold quality |
| parietal lobe | UBERON:0001872 | 74.82 | gold quality |
| right uterine tube | UBERON:0001302 | 74.75 | gold quality |
| primary visual cortex | UBERON:0002436 | 74.32 | gold quality |
| frontal pole | UBERON:0002795 | 73.36 | gold quality |
| occipital lobe | UBERON:0002021 | 73.19 | gold quality |
| Brodmann (1909) area 10 | UBERON:0013541 | 73.06 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 72.58 | gold quality |
| paraflocculus | UBERON:0005351 | 72.54 | gold quality |
| middle frontal gyrus | UBERON:0002702 | 71.95 | gold quality |
| prefrontal cortex | UBERON:0000451 | 71.89 | gold quality |
| entorhinal cortex | UBERON:0002728 | 71.34 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 71.33 | gold quality |
| cerebellar vermis | UBERON:0004720 | 69.57 | silver quality |
| endometrium epithelium | UBERON:0004811 | 69.57 | gold quality |
| right adrenal gland | UBERON:0001233 | 68.70 | gold quality |
| ventricular zone | UBERON:0003053 | 68.64 | gold quality |
| frontal cortex | UBERON:0001870 | 68.54 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 68.52 | gold quality |
| ganglionic eminence | UBERON:0004023 | 68.08 | gold quality |
| upper leg skin | UBERON:0004262 | 67.43 | gold quality |
| adrenal gland | UBERON:0002369 | 66.96 | gold quality |
| neocortex | UBERON:0001950 | 66.88 | gold quality |
| left adrenal gland | UBERON:0001234 | 66.55 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 66.49 | silver quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-35 | yes | 92.01 |
| E-MTAB-7606 | no | 3.96 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
97 targeting CDH12, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-574-5P | 100.00 | 66.01 | 989 |
| HSA-MIR-223-3P | 99.99 | 70.14 | 1140 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| HSA-MIR-511-3P | 99.99 | 68.85 | 1467 |
| HSA-MIR-4789-3P | 99.99 | 70.75 | 2484 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-4482-3P | 99.98 | 72.50 | 3147 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-548AA | 99.96 | 70.64 | 3753 |
| HSA-MIR-548AP-3P | 99.96 | 70.64 | 3753 |
| HSA-MIR-548T-3P | 99.96 | 70.64 | 3753 |
| HSA-MIR-3658 | 99.96 | 73.87 | 4379 |
| HSA-MIR-9983-3P | 99.94 | 71.48 | 3631 |
| HSA-MIR-1236-3P | 99.94 | 68.04 | 1695 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-10527-5P | 99.91 | 72.28 | 3754 |
| HSA-MIR-4753-3P | 99.90 | 71.03 | 3786 |
| HSA-MIR-4302 | 99.89 | 67.94 | 1187 |
| HSA-MIR-4697-3P | 99.89 | 67.09 | 1123 |
| HSA-MIR-129-5P | 99.88 | 70.26 | 3273 |
| HSA-MIR-6124 | 99.87 | 69.78 | 3551 |
| HSA-MIR-5010-3P | 99.83 | 70.60 | 2357 |
| HSA-MIR-130B-5P | 99.83 | 68.50 | 1888 |
| HSA-MIR-3681-5P | 99.82 | 66.88 | 387 |
| HSA-MIR-4659A-3P | 99.80 | 72.62 | 4248 |
| HSA-MIR-4659B-3P | 99.80 | 72.62 | 4248 |
Literature-anchored findings (GeneRIF, showing 6)
- E2F4, PHACTR3, PRAME family member and CDH12 most probably play important role in non-small-cell lung cancer geneses (PMID:19473719)
- CDH12 may play an important role in the invasion and metastasis of salivary adenoid cystic carcinoma (PMID:21573496)
- CDH12 may influence CRC cell progression. (PMID:26762412)
- Identification of a CDH12 potential candidate genetic variant for an autosomal dominant form of transgrediens and progrediens palmoplantar keratoderma in a Tunisian family. (PMID:31911611)
- An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer. (PMID:34385456)
- The Role of Cadherin 12 (CDH12) in the Peritoneal Fluid among Patients with Endometriosis and Endometriosis-Related Infertility. (PMID:36141853)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Cdh12 | ENSMUSG00000040452 |
| rattus_norvegicus | Cdh12 | ENSRNOG00000026392 |
Paralogs (33): CDH1 (ENSG00000039068), CDH10 (ENSG00000040731), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDHR5 (ENSG00000099834), CDH20 (ENSG00000101542), PCDH11X (ENSG00000102290), CDH23 (ENSG00000107736), CDH9 (ENSG00000113100), CDH6 (ENSG00000113361), CDH26 (ENSG00000124215), CDHR3 (ENSG00000128536), CDH15 (ENSG00000129910), CDH24 (ENSG00000139880), CDH11 (ENSG00000140937), CDH13 (ENSG00000140945), CDH18 (ENSG00000145526), CDHR1 (ENSG00000148600), CDH22 (ENSG00000149654), CDH8 (ENSG00000150394), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), PCDH9 (ENSG00000184226), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)
Protein
Protein identifiers
Cadherin-12 — P55289 (reviewed: P55289)
Alternative names: Brain cadherin, Neural type cadherin 2
All UniProt accessions (1): P55289
UniProt curated annotations — full annotation on UniProt →
Function. Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.
Subcellular location. Cell membrane.
Tissue specificity. Brain.
Domain organisation. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| P55289-1 | 1 | yes |
| P55289-2 | 2 |
RefSeq proteins (9): NP_001304156, NP_001304157, NP_001351033, NP_001351034, NP_001351035, NP_001351036, NP_001351037, NP_001351038, NP_004052* (*=MANE)
Domains & families (InterPro)
| 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 (25 total): domain 5, sequence conflict 5, glycosylation site 4, sequence variant 3, topological domain 2, signal peptide 1, propeptide 1, modified residue 1, splice variant 1, chain 1, transmembrane region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P55289-F1 | 77.19 | 0.47 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (1): 787
Glycosylation sites (4): 256, 456, 537, 545
Function
Pathways and Gene Ontology
Reactome pathways
4 pathways
| 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: 100 (showing top):
GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE45365_NK_CELL_VS_CD8_TCELL_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_CALCIUM_DEPENDENT_CELL_CELL_ADHESION, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, MCLACHLAN_DENTAL_CARIES_DN, HOOI_ST7_TARGETS_DN, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_ADHERENS_JUNCTION_ORGANIZATION, GOBP_CELL_CELL_JUNCTION_ASSEMBLY, GOCC_CELL_CELL_JUNCTION, GOCC_MEMBRANE_PROTEIN_COMPLEX, GOCC_ANCHORING_JUNCTION
GO Biological Process (9): cell morphogenesis (GO:0000902), cell-cell junction assembly (GO:0007043), homophilic cell-cell adhesion (GO:0007156), calcium-dependent cell-cell adhesion (GO:0016339), cell migration (GO:0016477), adherens junction organization (GO:0034332), cell-cell adhesion mediated by cadherin (GO:0044331), cell adhesion (GO:0007155), cell-cell adhesion (GO:0098609)
GO Molecular Function (4): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), cadherin binding (GO:0045296), metal ion binding (GO:0046872)
GO Cellular Component (4): plasma membrane (GO:0005886), adherens junction (GO:0005912), catenin complex (GO:0016342), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-3 pathways:
| 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 | 3 |
| cell-cell junction organization | 2 |
| anatomical structure morphogenesis | 1 |
| cell junction assembly | 1 |
| cell motility | 1 |
| cellular process | 1 |
| cell adhesion | 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 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
694 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CDH12 | CDH9 | Q9ULB4 | 540 |
| CDH12 | CDH15 | P55291 | 481 |
| CDH12 | CDH1 | P12830 | 477 |
| CDH12 | CDH2 | P19022 | 475 |
| CDH12 | CDH13 | P55290 | 471 |
| CDH12 | CDH19 | Q9H159 | 459 |
| CDH12 | CDH20 | Q9HBT6 | 446 |
| CDH12 | CDH6 | P55285 | 438 |
| CDH12 | CDH7 | Q9ULB5 | 438 |
| CDH12 | CDH18 | Q13634 | 415 |
| CDH12 | CDH10 | Q9Y6N8 | 413 |
| CDH12 | CRACD | Q6ZU35 | 411 |
| CDH12 | CTNNB1 | P35222 | 401 |
| CDH12 | CDH8 | P55286 | 399 |
| CDH12 | DRC4 | O95995 | 389 |
IntAct
7 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| IGHG1 | PDPK1 | psi-mi:“MI:0914”(association) | 0.350 |
| CTNNA3 | ARVCF | psi-mi:“MI:0914”(association) | 0.350 |
| CDH12 | ARVCF | psi-mi:“MI:0914”(association) | 0.350 |
| CDC20B | DHX16 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (17): CDH12 (Affinity Capture-MS), PKP4 (Affinity Capture-MS), FRMD4A (Affinity Capture-MS), CTNNA1 (Affinity Capture-MS), CTNNB1 (Affinity Capture-MS), CDH12 (Affinity Capture-MS), CTNNA2 (Affinity Capture-MS), ARVCF (Affinity Capture-MS), CDH8 (Affinity Capture-MS), PSEN1 (Affinity Capture-MS), CDH12 (Affinity Capture-MS), CHEK2 (Affinity Capture-MS), CDH24 (Affinity Capture-MS), PCDH1 (Affinity Capture-MS), RBM14-RBM4 (Affinity Capture-MS)
ESM2 similar proteins: A0A1S4GGP7, B1Q236, B8V7Q1, B8VIW9, F1QSQ0, F8W3X3, G5EDK5, H2A0L8, O02466, O15943, O44386, O44730, P28827, P34616, P35822, P55289, P70408, Q02763, Q02858, Q03600, Q03763, Q06807, Q09165, Q15262, Q19319, Q24247, Q24298, Q5RJH3, Q60ZN5, Q61495, Q68SP4, Q6W3B0, Q7TMD7, Q7TSF0, Q7TSF1, Q86SJ6, Q86WI1, Q8JHW2, Q8VHN7, Q8WXG9
Diamond homologs: A0A8M2BIB6, B0KW95, B2KI42, B4USZ0, F1PAA9, F1QSQ0, O02840, O35902, O54800, O55075, O55111, O93319, P08641, P09803, P10287, P10288, P12830, P15116, P19022, P19534, P19535, P20310, P22223, P24503, P30944, P32926, P33145, P33146, P33147, P33148, P33150, P33151, P33152, P33545, P39038, P55280, P55283, P55284, P55285, P55286
SIGNOR signaling
2 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| calcium(2+) | “up-regulates activity” | CDH12 | “chemical activation” |
| CDH12 | “up-regulates activity” | CTNNB1 | binding |
Disease & clinical
Clinical variants and AI predictions
ClinVar
166 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 126 |
| Likely benign | 15 |
| Benign | 11 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1809200 | GRCh37/hg19 5p15.33-14.1(chr5:113577-26164852)x1 | Pathogenic |
SpliceAI
5423 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 5:21752232:TATGG:T | acceptor_gain | 1.0000 |
| 5:21752234:TGG:T | acceptor_gain | 1.0000 |
| 5:21752237:C:CC | acceptor_gain | 1.0000 |
| 5:21755665:T:TA | donor_gain | 1.0000 |
| 5:21760556:A:AC | donor_gain | 1.0000 |
| 5:21760557:C:CC | donor_gain | 1.0000 |
| 5:21760557:CTT:C | donor_gain | 1.0000 |
| 5:21783356:A:AC | donor_gain | 1.0000 |
| 5:21783357:C:CC | donor_gain | 1.0000 |
| 5:21783357:CTA:C | donor_gain | 1.0000 |
| 5:21783357:CTAA:C | donor_gain | 1.0000 |
| 5:21816941:ATACC:A | donor_loss | 1.0000 |
| 5:21816942:TACC:T | donor_loss | 1.0000 |
| 5:21816943:A:T | donor_loss | 1.0000 |
| 5:21816944:C:CA | donor_loss | 1.0000 |
| 5:21816964:C:CA | donor_gain | 1.0000 |
| 5:21817143:A:C | acceptor_gain | 1.0000 |
| 5:21842157:ATAC:A | donor_loss | 1.0000 |
| 5:21842158:TA:T | donor_loss | 1.0000 |
| 5:21842159:A:AC | donor_gain | 1.0000 |
| 5:21842159:ACTTT:A | donor_loss | 1.0000 |
| 5:21842160:C:CC | donor_gain | 1.0000 |
| 5:21842160:CT:C | donor_gain | 1.0000 |
| 5:21842160:CTT:C | donor_gain | 1.0000 |
| 5:21842326:CAC:C | acceptor_gain | 1.0000 |
| 5:21842327:ACC:A | acceptor_loss | 1.0000 |
| 5:21842328:CC:C | acceptor_loss | 1.0000 |
| 5:21842329:CTTAA:C | acceptor_loss | 1.0000 |
| 5:21842330:T:C | acceptor_gain | 1.0000 |
| 5:21975090:CCCA:C | donor_gain | 1.0000 |
AlphaMissense
5230 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 5:21975153:T:G | D155A | 1.000 |
| 5:21975162:T:G | D152A | 1.000 |
| 5:21975163:C:G | D152H | 1.000 |
| 5:21975291:C:A | G109V | 1.000 |
| 5:21975291:C:T | G109E | 1.000 |
| 5:21975292:C:A | G109W | 1.000 |
| 5:21975312:A:G | F102S | 1.000 |
| 5:21755609:A:G | C623R | 0.999 |
| 5:21783369:G:T | A461E | 0.999 |
| 5:21802200:G:T | A408D | 0.999 |
| 5:21802206:A:T | V406D | 0.999 |
| 5:21802380:A:T | V348D | 0.999 |
| 5:21842169:A:G | F269S | 0.999 |
| 5:21842175:G:T | P267H | 0.999 |
| 5:21842184:T:G | D264A | 0.999 |
| 5:21842199:A:G | L259P | 0.999 |
| 5:21842211:A:T | V255D | 0.999 |
| 5:21842253:T:G | D241A | 0.999 |
| 5:21842254:C:G | D241H | 0.999 |
| 5:21842259:G:T | A239D | 0.999 |
| 5:21842260:C:G | A239P | 0.999 |
| 5:21842322:A:T | I218N | 0.999 |
| 5:21842328:C:T | G216D | 0.999 |
| 5:21854691:A:G | F209S | 0.999 |
| 5:21854719:A:C | Y200D | 0.999 |
| 5:21854754:T:A | D188V | 0.999 |
| 5:21854754:T:G | D188A | 0.999 |
| 5:21854755:C:G | D188H | 0.999 |
| 5:21854761:C:G | D186H | 0.999 |
| 5:21975137:A:C | F160L | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000001454 (5:22834207 G>C), RS1000005121 (5:22744349 A>G), RS1000005366 (5:22316733 A>G), RS1000009781 (5:21750554 G>C,T), RS1000010667 (5:22717500 A>G), RS1000014089 (5:22598430 G>A), RS1000018705 (5:22597664 A>G), RS1000022651 (5:22143821 A>G), RS1000025179 (5:22377516 A>G), RS1000025225 (5:22522017 G>A), RS1000025419 (5:21949013 C>T), RS1000031537 (5:22476158 C>A,G,T), RS1000032561 (5:22390413 A>C,G,T), RS1000033243 (5:21843328 C>T), RS1000035371 (5:21805212 A>C)
Disease associations
OMIM: gene MIM:600562 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
11 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000427_5 | Waist circumference | 2.000000e-06 |
| GCST004558_85 | Body mass index (joint analysis main effects and physical activity interaction) | 7.000000e-07 |
| GCST004568_1 | Body mass index (physical activity interaction) | 3.000000e-08 |
| GCST004568_2 | Body mass index (physical activity interaction) | 3.000000e-07 |
| GCST004863_143 | Mosquito bite size | 9.000000e-06 |
| GCST005578_4 | Low white blood cell count (conditioned on rs2814778) | 4.000000e-07 |
| GCST005578_5 | Low white blood cell count (conditioned on rs2814778) | 2.000000e-07 |
| GCST005760_5 | Dimensional psychopathology (Cognitive) | 4.000000e-07 |
| GCST007603_35 | Smoking initiation | 5.000000e-08 |
| GCST007678_2 | Brooding (response to stress) | 5.000000e-07 |
| GCST008810_93 | Smoking initiation (ever regular vs never regular) | 1.000000e-08 |
EFO canonical traits (7, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004340 | body mass index |
| EFO:0008002 | physical activity measurement |
| EFO:0003940 | physical activity |
| EFO:0008378 | mosquito bite reaction size measurement |
| EFO:0009098 | cognitive domain measurement |
| EFO:0005670 | smoking initiation |
| EFO:0009858 | brooding stress response |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
28 total (human), top 28 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Aflatoxin B1 | decreases methylation, increases methylation, affects expression, decreases expression | 4 |
| sodium arsenite | affects methylation, decreases expression, increases reaction, decreases methylation | 2 |
| Resveratrol | affects cotreatment, decreases expression, increases expression | 2 |
| Copper | affects cotreatment, decreases expression, affects binding | 2 |
| Valproic Acid | decreases expression | 2 |
| methyleugenol | decreases expression | 1 |
| bisphenol A | affects methylation | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | affects cotreatment, increases expression | 1 |
| aflatoxin B2 | decreases methylation | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects cotreatment, increases expression | 1 |
| glycidamide | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| entinostat | decreases expression | 1 |
| NSC 689534 | affects binding, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Coumestrol | affects cotreatment, increases expression | 1 |
| Lead | affects methylation | 1 |
| Lipopolysaccharides | increases expression, affects cotreatment | 1 |
| Niclosamide | decreases reaction, increases expression | 1 |
| Silicon Dioxide | increases expression | 1 |
| Tetrachlorodibenzodioxin | increases expression | 1 |
| Tretinoin | increases expression | 1 |
| Triclosan | increases expression | 1 |
| Cyclosporine | decreases expression | 1 |
| Silver Compounds | increases expression | 1 |
| Cadmium Chloride | increases expression | 1 |
| Acrylamide | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.