CLSTN2
geneOn this page
Also known as CSTN2CS2FLJ39113CDHR13
Summary
CLSTN2 (calsyntenin 2, HGNC:17448) is a protein-coding gene on chromosome 3q23, encoding Calsyntenin-2 (Q9H4D0). Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate synapse formation, and which is involved in learning and memory.
Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Predicted to be located in several cellular components, including Golgi membrane; endoplasmic reticulum membrane; and postsynaptic density. Predicted to be active in cell surface; glutamatergic synapse; and postsynaptic density membrane.
Source: NCBI Gene 64084 — RefSeq curated summary.
At a glance
- GWAS associations: 17
- Clinical variants (ClinVar): 187 total
- MANE Select transcript:
NM_022131
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:17448 |
| Approved symbol | CLSTN2 |
| Name | calsyntenin 2 |
| Location | 3q23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | CSTN2, CS2, FLJ39113, CDHR13 |
| Ensembl gene | ENSG00000158258 |
| Ensembl biotype | protein_coding |
| OMIM | 611323 |
| Entrez | 64084 |
Gene structure
Transcript identifiers
Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron
ENST00000458420, ENST00000511524
RefSeq mRNA: 1 — MANE Select: NM_022131
NM_022131
CCDS: CCDS3112
Canonical transcript exons
ENST00000458420 — 17 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001037980 | 140562811 | 140562956 |
| ENSE00001037981 | 140558640 | 140558857 |
| ENSE00001037982 | 140563080 | 140563203 |
| ENSE00001037986 | 140562138 | 140562308 |
| ENSE00001037995 | 140556513 | 140556661 |
| ENSE00001323069 | 140563961 | 140564145 |
| ENSE00002067943 | 139935185 | 139935483 |
| ENSE00002618362 | 140566053 | 140577397 |
| ENSE00003460827 | 140404558 | 140404766 |
| ENSE00003474379 | 140459521 | 140459769 |
| ENSE00003512187 | 140403629 | 140403824 |
| ENSE00003520080 | 140546515 | 140546681 |
| ENSE00003534288 | 140175951 | 140176073 |
| ENSE00003542073 | 140466610 | 140466731 |
| ENSE00003627637 | 140421125 | 140421274 |
| ENSE00003674166 | 140448519 | 140448704 |
| ENSE00003692488 | 140532324 | 140532486 |
Expression profiles
Bgee: expression breadth ubiquitous, 223 present calls, max score 94.85.
FANTOM5 (CAGE): breadth broad, TPM avg 11.9081 / max 612.0247, expressed in 795 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 38833 | 11.5170 | 779 |
| 38832 | 0.3911 | 177 |
Top tissues by expression
273 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| endothelial cell | CL:0000115 | 94.85 | gold quality |
| pons | UBERON:0000988 | 94.07 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 92.97 | gold quality |
| left ovary | UBERON:0002119 | 91.94 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 91.49 | gold quality |
| postcentral gyrus | UBERON:0002581 | 90.93 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 90.90 | gold quality |
| parietal lobe | UBERON:0001872 | 90.67 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 90.00 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 89.39 | gold quality |
| right ovary | UBERON:0002118 | 88.72 | gold quality |
| entorhinal cortex | UBERON:0002728 | 88.64 | gold quality |
| ovary | UBERON:0000992 | 88.22 | gold quality |
| cortical plate | UBERON:0005343 | 86.24 | gold quality |
| prefrontal cortex | UBERON:0000451 | 84.09 | gold quality |
| primary visual cortex | UBERON:0002436 | 84.04 | gold quality |
| adipose tissue | UBERON:0001013 | 83.93 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 83.93 | gold quality |
| mammary gland | UBERON:0001911 | 83.89 | gold quality |
| mammary duct | UBERON:0001765 | 83.79 | gold quality |
| occipital lobe | UBERON:0002021 | 83.76 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 83.63 | gold quality |
| buccal mucosa cell | CL:0002336 | 83.60 | silver quality |
| vena cava | UBERON:0004087 | 83.36 | silver quality |
| cardiac muscle of right atrium | UBERON:0003379 | 83.24 | silver quality |
| connective tissue | UBERON:0002384 | 82.84 | gold quality |
| frontal cortex | UBERON:0001870 | 82.51 | gold quality |
| cerebral cortex | UBERON:0000956 | 81.60 | gold quality |
| Ammon’s horn | UBERON:0001954 | 81.36 | gold quality |
| neocortex | UBERON:0001950 | 81.30 | gold quality |
Single-cell (SCXA)
Detected in 6 experiment(s), a significant marker in 6.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-180759 | yes | 1828.80 |
| E-HCAD-35 | yes | 938.86 |
| E-HCAD-30 | yes | 805.17 |
| E-HCAD-25 | yes | 590.34 |
| E-GEOD-93593 | yes | 7.26 |
| E-ANND-3 | yes | 6.30 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
102 targeting CLSTN2, 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-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-6851-5P | 100.00 | 65.63 | 1294 |
| HSA-MIR-3689D | 100.00 | 66.14 | 1181 |
| HSA-MIR-4533 | 100.00 | 69.48 | 2758 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-513B-5P | 99.99 | 69.96 | 2150 |
| HSA-MIR-27A-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-27B-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-9985 | 99.98 | 72.11 | 2939 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
| HSA-MIR-4731-5P | 99.89 | 67.23 | 2537 |
| HSA-MIR-6124 | 99.87 | 69.78 | 3551 |
| HSA-MIR-5003-3P | 99.85 | 69.29 | 2517 |
| HSA-MIR-576-5P | 99.84 | 70.46 | 2582 |
| HSA-MIR-6515-3P | 99.82 | 68.19 | 1933 |
| HSA-MIR-3913-5P | 99.78 | 67.26 | 968 |
| HSA-MIR-4719 | 99.73 | 72.10 | 3329 |
| HSA-MIR-494-3P | 99.70 | 71.45 | 2795 |
| HSA-MIR-10394-5P | 99.65 | 66.83 | 1852 |
| HSA-MIR-1205 | 99.65 | 66.76 | 1826 |
| HSA-MIR-3158-5P | 99.65 | 67.51 | 1763 |
| HSA-MIR-7156-5P | 99.64 | 68.81 | 1369 |
| HSA-MIR-4666B | 99.64 | 68.69 | 1282 |
| HSA-MIR-298 | 99.63 | 67.56 | 1916 |
| HSA-MIR-425-5P | 99.59 | 67.67 | 900 |
Literature-anchored findings (GeneRIF, showing 8)
- Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation [alcalpha1, alcbeta, alcgamma] (PMID:15037614)
- calsyntenins play an essential role in learning and this role is modulated both by CLSTN2 genotype and, during adolescent development, by exposure to tobacco smoke. (PMID:19058786)
- This study showed that the KIBRA and CLSTN2 genes interactively modulate episodic memory performance. (PMID:19804789)
- No increased risk of any type of late development, and cognitive impairment was associated with CLSTN2 (rs6439886) (PMID:21643791)
- The results of this study supports the view that effects of KIBRA and CLSTN2 polymorphisms genetic polymorphisms on cognitive functioning may be most easily disclosed at suboptimal levels of cognitive ability, such as in old-age depression. (PMID:25080189)
- Study did not find support for an association of KIBRA either alone or in combination with CLSTN2 with memory performance or hippocampal volume, nor did variation in these genes influence longitudinal memory decline or hippocampal atrophy in older adults (PMID:26415670)
- Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake. (PMID:34673103)
- KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study. (PMID:36812656)
Cross-species orthologs
6 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | clstn2a | ENSDARG00000060637 |
| danio_rerio | clstn2b | ENSDARG00000060638 |
| mus_musculus | Clstn2 | ENSMUSG00000032452 |
| rattus_norvegicus | Clstn2 | ENSRNOG00000043085 |
| drosophila_melanogaster | Cals | FBGN0039928 |
| caenorhabditis_elegans | WBGENE00000403 |
Paralogs (2): CLSTN3 (ENSG00000139182), CLSTN1 (ENSG00000171603)
Protein
Protein identifiers
Calsyntenin-2 — Q9H4D0 (reviewed: Q9H4D0)
Alternative names: Alcadein-gamma
All UniProt accessions (1): Q9H4D0
UniProt curated annotations — full annotation on UniProt →
Function. Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate synapse formation, and which is involved in learning and memory. Promotes synapse development by acting as a cell adhesion molecule at the postsynaptic membrane, which associates with neurexin-alpha at the presynaptic membrane.
Subcellular location. Postsynaptic cell membrane. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cell projection. Dendrite.
Tissue specificity. Restricted to the brain.
Post-translational modifications. Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by gamma-secretase within the transmembrane domain releases the beta-Alc-gamma chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with PSEN1.
Domain organisation. Binds synaptic Ca(2+) with its cytoplasmic domain.
Similarity. Belongs to the calsyntenin family.
RefSeq proteins (1): NP_071414* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002126 | Cadherin-like_dom | Domain |
| IPR013320 | ConA-like_dom_sf | Homologous_superfamily |
| IPR015919 | Cadherin-like_sf | Homologous_superfamily |
| IPR045588 | CLSTN_C | Domain |
Pfam: PF00028, PF19699
UniProt features (23 total): glycosylation site 6, sequence variant 4, compositionally biased region 3, topological domain 2, sequence conflict 2, domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9H4D0-F1 | 79.46 | 0.51 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Glycosylation sites (6): 56, 98, 342, 374, 716, 729
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 160 (showing top):
BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, BENPORATH_ES_WITH_H3K27ME3, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_SYNAPSE_ASSEMBLY, GOBP_ASSOCIATIVE_LEARNING, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, CAGCTG_AP4_Q5, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION
GO Biological Process (6): homophilic cell-cell adhesion (GO:0007156), associative learning (GO:0008306), positive regulation of synaptic transmission (GO:0050806), positive regulation of synapse assembly (GO:0051965), inhibitory synapse assembly (GO:1904862), cell adhesion (GO:0007155)
GO Molecular Function (1): calcium ion binding (GO:0005509)
GO Cellular Component (14): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), cell surface (GO:0009986), dendrite (GO:0030425), postsynaptic membrane (GO:0045211), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), postsynaptic density (GO:0014069), membrane (GO:0016020), cell projection (GO:0042995), synapse (GO:0045202)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| synapse assembly | 2 |
| cytoplasm | 2 |
| endomembrane system | 2 |
| intracellular membrane-bounded organelle | 2 |
| cell-cell adhesion | 1 |
| learning | 1 |
| chemical synaptic transmission | 1 |
| positive regulation of cell communication | 1 |
| positive regulation of signaling | 1 |
| modulation of chemical synaptic transmission | 1 |
| positive regulation of nervous system development | 1 |
| regulation of synapse assembly | 1 |
| positive regulation of cell junction assembly | 1 |
| cellular process | 1 |
| metal ion binding | 1 |
| Golgi apparatus | 1 |
| bounding membrane of organelle | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| neuron projection | 1 |
| dendritic tree | 1 |
| synaptic membrane | 1 |
| postsynapse | 1 |
| postsynaptic density | 1 |
| postsynaptic membrane | 1 |
| postsynaptic specialization membrane | 1 |
| synapse | 1 |
| membrane | 1 |
| cell periphery | 1 |
| asymmetric synapse | 1 |
| postsynaptic specialization | 1 |
| cell junction | 1 |
Protein interactions and networks
STRING
1054 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CLSTN2 | A0A2R8YFG2 | A0A2R8YFG2 | 898 |
| CLSTN2 | GRIP1 | Q9Y3R0 | 669 |
| CLSTN2 | KLC2 | Q9H0B6 | 599 |
| CLSTN2 | CDH17 | Q12864 | 593 |
| CLSTN2 | KLC4 | Q9NSK0 | 589 |
| CLSTN2 | KLC1 | Q07866 | 575 |
| CLSTN2 | KLC3 | Q6P597 | 528 |
| CLSTN2 | NRXN2 | Q9P2S2 | 525 |
| CLSTN2 | SLC12A9 | Q9BXP2 | 477 |
| CLSTN2 | ACAN | P16112 | 447 |
| CLSTN2 | CCN2 | P29279 | 445 |
| CLSTN2 | WWC1 | Q8IX03 | 445 |
| CLSTN2 | FHIT | P49789 | 436 |
| CLSTN2 | FAM227B | Q96M60 | 421 |
| CLSTN2 | VLDLR | P98155 | 407 |
IntAct
2 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CLSTN2 | EXOC3 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (25): CLSTN2 (Proximity Label-MS), CLSTN2 (Affinity Capture-MS), MYCBP2 (Affinity Capture-MS), SPTB (Affinity Capture-MS), RPL23 (Affinity Capture-MS), CUX1 (Affinity Capture-MS), TYK2 (Affinity Capture-MS), NUP37 (Affinity Capture-MS), CLSTN1 (Affinity Capture-MS), NUP160 (Affinity Capture-MS), APBA3 (Affinity Capture-MS), BPIFA1 (Affinity Capture-MS), LMAN1 (Affinity Capture-MS), UTP20 (Affinity Capture-MS), NUP43 (Affinity Capture-MS)
ESM2 similar proteins: A0A0R4IKU3, A0A8M9PFP2, A1A5Y0, A2A863, A2VCU8, A5A6L1, B0S5G3, L7VG99, O00622, O08841, O35118, O42493, O93512, P08163, P08833, P16042, P16144, P17668, P18406, Q07663, Q0VCN6, Q13753, Q501P1, Q53RD9, Q5R9Q9, Q61220, Q61592, Q64632, Q6DDW2, Q7T3Q2, Q7ZV46, Q7ZXL5, Q8R4Y4, Q8R553, Q8VDA1, Q91166, Q91167, Q91713, Q99JH7, Q9BQT9
Diamond homologs: A0A8M9PFP2, B0S5G3, F1R520, O02840, O55111, O88278, O94985, P30944, P33151, P55287, P55288, Q0VCN6, Q14517, Q5DRC8, Q5R9Q9, Q63418, Q6Q0N0, Q6URK6, Q6V1P9, Q86UP0, Q8BNA6, Q8R553, Q8VDA1, Q96JQ0, Q99JH7, Q9BQT9, Q9EPL2, Q9ER65, Q9H4D0, Q9HCU4, Q9NYQ6, Q9R0M0, P55289, Q5DRA8, Q5DRE0, Q6V0I7, Q967F4, Q9UN71, Q9V498, Q9VW71
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
187 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 158 |
| Likely benign | 9 |
| Benign | 5 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
5262 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:140012538:G:T | donor_gain | 1.0000 |
| 3:140081310:A:T | donor_gain | 1.0000 |
| 3:140175942:A:AG | acceptor_gain | 1.0000 |
| 3:140175943:T:G | acceptor_gain | 1.0000 |
| 3:140175946:TCTA:T | acceptor_loss | 1.0000 |
| 3:140175948:TA:T | acceptor_loss | 1.0000 |
| 3:140175949:A:AG | acceptor_gain | 1.0000 |
| 3:140175950:G:A | acceptor_loss | 1.0000 |
| 3:140175950:G:GC | acceptor_gain | 1.0000 |
| 3:140175950:GT:G | acceptor_gain | 1.0000 |
| 3:140175950:GTC:G | acceptor_gain | 1.0000 |
| 3:140175950:GTCA:G | acceptor_gain | 1.0000 |
| 3:140175950:GTCAA:G | acceptor_gain | 1.0000 |
| 3:140176069:TGCAG:T | donor_loss | 1.0000 |
| 3:140176070:GCAGG:G | donor_loss | 1.0000 |
| 3:140176071:CAG:C | donor_loss | 1.0000 |
| 3:140176072:AGGTG:A | donor_loss | 1.0000 |
| 3:140176073:GG:G | donor_loss | 1.0000 |
| 3:140176074:G:GC | donor_loss | 1.0000 |
| 3:140176075:T:A | donor_loss | 1.0000 |
| 3:140403624:T:A | acceptor_gain | 1.0000 |
| 3:140403626:CAGG:C | acceptor_loss | 1.0000 |
| 3:140403627:A:AG | acceptor_gain | 1.0000 |
| 3:140403627:AG:A | acceptor_gain | 1.0000 |
| 3:140403627:AGG:A | acceptor_gain | 1.0000 |
| 3:140403627:AGGG:A | acceptor_gain | 1.0000 |
| 3:140403628:G:GA | acceptor_gain | 1.0000 |
| 3:140403628:GG:G | acceptor_gain | 1.0000 |
| 3:140403628:GGG:G | acceptor_gain | 1.0000 |
| 3:140403628:GGGG:G | acceptor_gain | 1.0000 |
AlphaMissense
6353 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:140175966:C:A | P42Q | 1.000 |
| 3:140175983:T:G | Y48D | 1.000 |
| 3:140175990:G:A | G50E | 1.000 |
| 3:140176017:T:A | V59D | 1.000 |
| 3:140176041:C:A | A67D | 1.000 |
| 3:140403644:T:C | F83S | 1.000 |
| 3:140403644:T:G | F83C | 1.000 |
| 3:140403767:T:A | I124N | 1.000 |
| 3:140404566:T:A | V146D | 1.000 |
| 3:140404572:T:A | I148K | 1.000 |
| 3:140421125:G:A | G213D | 1.000 |
| 3:140421125:G:T | G213V | 1.000 |
| 3:140459753:C:G | C402W | 1.000 |
| 3:140466717:T:A | W444R | 1.000 |
| 3:140466717:T:C | W444R | 1.000 |
| 3:140532341:G:C | W454C | 1.000 |
| 3:140532341:G:T | W454C | 1.000 |
| 3:140175965:C:T | P42S | 0.999 |
| 3:140175970:G:C | W43C | 0.999 |
| 3:140175970:G:T | W43C | 0.999 |
| 3:140175983:T:C | Y48H | 0.999 |
| 3:140175989:G:A | G50R | 0.999 |
| 3:140175989:G:C | G50R | 0.999 |
| 3:140176023:T:C | L61S | 0.999 |
| 3:140176035:T:A | L65Q | 0.999 |
| 3:140176035:T:C | L65P | 0.999 |
| 3:140176046:G:C | D69H | 0.999 |
| 3:140176047:A:C | D69A | 0.999 |
| 3:140176047:A:T | D69V | 0.999 |
| 3:140176052:G:C | D71H | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000001013 (3:140004114 G>A), RS1000015825 (3:140520684 A>G), RS1000021689 (3:140440683 C>T), RS1000024043 (3:140316765 G>A), RS1000027679 (3:140027126 A>G,T), RS1000029026 (3:140271321 T>A), RS1000030162 (3:140199873 A>G), RS1000039650 (3:140130426 C>T), RS1000041169 (3:140036543 A>G), RS1000053491 (3:140003910 G>C), RS1000054250 (3:140247499 C>A), RS1000056927 (3:139976701 C>T), RS1000058431 (3:139936148 T>C), RS1000060430 (3:139958776 G>C,T), RS1000065710 (3:140045687 A>G)
Disease associations
OMIM: gene MIM:611323 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
17 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST001104_4 | Sudden cardiac arrest | 2.000000e-06 |
| GCST001523_21 | Visceral adipose tissue adjusted for BMI | 7.000000e-06 |
| GCST001712_42 | Myopia (pathological) | 4.000000e-07 |
| GCST001891_1 | Multiple sclerosis (OCB status) | 8.000000e-07 |
| GCST002248_5 | Fasting insulin (dietary factor interaction) | 3.000000e-06 |
| GCST002253_7 | Homeostasis model assessment of insulin resistance (dietary factor interaction) | 4.000000e-06 |
| GCST002480_1 | Hodgkin’s lymphoma | 8.000000e-07 |
| GCST002592_16 | Neuritic plaque | 6.000000e-06 |
| GCST002685_7 | Refractive astigmatism | 5.000000e-06 |
| GCST003262_626 | Post bronchodilator FEV1 | 1.000000e-06 |
| GCST003264_772 | Post bronchodilator FEV1/FVC ratio | 3.000000e-07 |
| GCST003831_27 | Asthma | 2.000000e-06 |
| GCST004748_36 | Lung cancer | 7.000000e-06 |
| GCST007741_25 | Iris color (b* coordinate) | 3.000000e-06 |
| GCST008755_7 | Phenylephrine infusion rate during anesthesia | 2.000000e-06 |
| GCST009311_6 | Letter-number span reordering | 6.000000e-06 |
| GCST010292_5 | Response to lamotrigine and valproic acid in genetic generalized epilepsy | 4.000000e-06 |
EFO canonical traits (10, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004278 | sudden cardiac arrest |
| EFO:0004340 | body mass index |
| EFO:0004207 | pathological myopia |
| EFO:0008111 | diet measurement |
| EFO:0004501 | HOMA-IR |
| EFO:0006798 | neuritic plaque measurement |
| EFO:0004314 | forced expiratory volume |
| EFO:0004713 | FEV/FVC ratio |
| EFO:0009764 | eye colour measurement |
| EFO:0004874 | memory performance |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
37 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, affects expression | 6 |
| trichostatin A | affects cotreatment, increases expression | 2 |
| sodium arsenite | increases expression, affects methylation | 2 |
| Panobinostat | affects cotreatment, increases expression | 2 |
| Aflatoxin B1 | decreases methylation, increases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| methylmercuric chloride | increases expression | 1 |
| bisphenol A | affects cotreatment, increases expression | 1 |
| terbufos | increases methylation | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | increases expression, affects cotreatment | 1 |
| 2,2’,4,4’,5-brominated diphenyl ether | increases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| incobotulinumtoxinA | decreases expression | 1 |
| Arsenic Trioxide | affects cotreatment, decreases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Dexamethasone | affects cotreatment, increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Fonofos | increases methylation | 1 |
| Formaldehyde | increases expression | 1 |
| Indomethacin | affects cotreatment, increases expression | 1 |
| Lead | affects expression | 1 |
| Methapyrilene | increases methylation | 1 |
| Nickel | decreases expression | 1 |
| Parathion | increases methylation | 1 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Hodgkins lymphoma