SYT9
gene geneOn this page
Summary
SYT9 (synaptotagmin 9, HGNC:19265) is a protein-coding gene on chromosome 11p15.4, encoding Synaptotagmin-9 (Q86SS6). May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.
Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in chemical synaptic transmission; regulation of vesicle-mediated transport; and vesicle-mediated transport. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in hippocampal mossy fiber to CA3 synapse; plasma membrane; and secretory vesicle.
Source: NCBI Gene 143425 — RefSeq curated summary.
At a glance
- GWAS associations: 12
- Clinical variants (ClinVar): 58 total
- MANE Select transcript:
NM_175733
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:19265 |
| Approved symbol | SYT9 |
| Name | synaptotagmin 9 |
| Location | 11p15.4 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000170743 |
| Ensembl biotype | protein_coding |
| OMIM | 613528 |
| Entrez | 143425 |
Gene structure
Transcript identifiers
Ensembl transcripts: 3 — 2 nonsense_mediated_decay, 1 protein_coding
ENST00000318881, ENST00000524820, ENST00000532592
RefSeq mRNA: 1 — MANE Select: NM_175733
NM_175733
CCDS: CCDS7778
Canonical transcript exons
ENST00000318881 — 7 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001126689 | 7313395 | 7313941 |
| ENSE00001291376 | 7251904 | 7252331 |
| ENSE00002166108 | 7466792 | 7469043 |
| ENSE00003486407 | 7303039 | 7303390 |
| ENSE00003538722 | 7416042 | 7416162 |
| ENSE00003554085 | 7420506 | 7420635 |
| ENSE00003626807 | 7417957 | 7418128 |
Expression profiles
Bgee: expression breadth ubiquitous, 153 present calls, max score 91.15.
FANTOM5 (CAGE): breadth broad, TPM avg 1.2631 / max 92.0230, expressed in 262 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 112888 | 0.6337 | 205 |
| 112887 | 0.4017 | 158 |
| 112890 | 0.1176 | 59 |
| 112889 | 0.1101 | 67 |
Top tissues by expression
225 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| medial globus pallidus | UBERON:0002477 | 91.15 | gold quality |
| globus pallidus | UBERON:0001875 | 89.10 | gold quality |
| cerebellar vermis | UBERON:0004720 | 83.25 | silver quality |
| corpus callosum | UBERON:0002336 | 82.93 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 82.92 | silver quality |
| subthalamic nucleus | UBERON:0001906 | 81.58 | silver quality |
| vena cava | UBERON:0004087 | 81.34 | gold quality |
| cerebellum | UBERON:0002037 | 81.26 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 81.25 | gold quality |
| cerebellar cortex | UBERON:0002129 | 81.04 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 80.85 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 80.48 | silver quality |
| lateral globus pallidus | UBERON:0002476 | 80.45 | silver quality |
| cardia of stomach | UBERON:0001162 | 80.43 | gold quality |
| pylorus | UBERON:0001166 | 80.43 | silver quality |
| ventral tegmental area | UBERON:0002691 | 79.98 | silver quality |
| body of tongue | UBERON:0011876 | 79.96 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 79.70 | silver quality |
| substantia nigra pars compacta | UBERON:0001965 | 79.55 | silver quality |
| superior surface of tongue | UBERON:0007371 | 79.51 | gold quality |
| tongue | UBERON:0001723 | 79.47 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 79.44 | gold quality |
| medulla oblongata | UBERON:0001896 | 79.40 | silver quality |
| pericardium | UBERON:0002407 | 79.34 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 79.13 | gold quality |
| pons | UBERON:0000988 | 79.11 | silver quality |
| spinal cord | UBERON:0002240 | 78.83 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 78.82 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 78.82 | gold quality |
| midbrain | UBERON:0001891 | 78.81 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 3.72 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
146 targeting SYT9, 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-4510 | 100.00 | 66.60 | 2050 |
| HSA-MIR-6127 | 100.00 | 66.76 | 2188 |
| HSA-MIR-6129 | 100.00 | 66.46 | 2080 |
| HSA-MIR-6130 | 100.00 | 66.69 | 2012 |
| HSA-MIR-6133 | 100.00 | 66.48 | 2064 |
| HSA-MIR-34A-5P | 99.99 | 71.21 | 1784 |
| HSA-MIR-449A | 99.99 | 71.05 | 1776 |
| HSA-MIR-3688-3P | 99.97 | 72.02 | 2834 |
| HSA-MIR-34C-5P | 99.97 | 70.45 | 1577 |
| HSA-MIR-449B-5P | 99.97 | 70.26 | 1580 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-548AT-5P | 99.96 | 70.83 | 2666 |
| HSA-MIR-3605-5P | 99.96 | 67.12 | 932 |
| HSA-MIR-146A-5P | 99.96 | 68.93 | 988 |
| HSA-MIR-146B-5P | 99.96 | 69.13 | 977 |
| HSA-MIR-7153-5P | 99.94 | 68.89 | 1006 |
| HSA-MIR-6508-5P | 99.92 | 70.67 | 2465 |
| HSA-MIR-4493 | 99.90 | 66.48 | 977 |
| HSA-MIR-4753-3P | 99.90 | 71.03 | 3786 |
| HSA-MIR-5682 | 99.89 | 72.56 | 1005 |
| HSA-MIR-4496 | 99.88 | 68.89 | 2236 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-605-3P | 99.88 | 69.22 | 1833 |
| HSA-MIR-8067 | 99.86 | 69.59 | 2260 |
| HSA-MIR-5003-3P | 99.85 | 69.29 | 2517 |
| HSA-MIR-659-3P | 99.85 | 70.69 | 1620 |
| HSA-MIR-6079 | 99.84 | 68.54 | 1170 |
| HSA-MIR-544A | 99.84 | 68.66 | 1965 |
| HSA-MIR-3180-5P | 99.82 | 69.12 | 2422 |
Literature-anchored findings (GeneRIF, showing 3)
- SYT9 expression is significantly downregulated in human masticatory mucosa during wound healing (PMID:28005267)
- The intronic SYT9 variant rs11041321, which exhibits a significant genome-wide association with circulating homocysteine, was associated with the occurrence of congenital cardiac septal defects (CCSDs). This finding helps to characterize the unexpected role of SYT9 in homocysteine metabolism and the development of CCSDs, which further highlighted the interplay of diet, genetics, and human birth defects (PMID:28834160)
- The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein. (PMID:37677740)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | syt9a | ENSDARG00000003994 |
| danio_rerio | syt9b | ENSDARG00000029239 |
| mus_musculus | Syt9 | ENSMUSG00000062542 |
| rattus_norvegicus | Syt9 | ENSRNOG00000019613 |
Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), SYT17 (ENSG00000103528), SYT10 (ENSG00000110975), SYT5 (ENSG00000129990), SYT11 (ENSG00000132718), SYT4 (ENSG00000132872), SYT6 (ENSG00000134207), SYTL2 (ENSG00000137501), SYT16 (ENSG00000139973), SYTL1 (ENSG00000142765), SYT14 (ENSG00000143469), SYT2 (ENSG00000143858), SYTL5 (ENSG00000147041), SYT8 (ENSG00000149043), DOC2A (ENSG00000149927), SYTL3 (ENSG00000164674), TC2N (ENSG00000165929), SYT12 (ENSG00000173227), RPH3AL (ENSG00000181031), C2CD4C (ENSG00000183186), C2CD4A (ENSG00000198535), SYT15 (ENSG00000204176), C2CD4B (ENSG00000205502), SYT3 (ENSG00000213023), C2CD4D (ENSG00000225556), DOC2B (ENSG00000272636), SYT15B (ENSG00000277758)
Protein
Protein identifiers
Synaptotagmin-9 — Q86SS6 (reviewed: Q86SS6)
Alternative names: Synaptotagmin IX
All UniProt accessions (3): Q86SS6, B3KNT7, E9PDN4
UniProt curated annotations — full annotation on UniProt →
Function. May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.
Subunit / interactions. Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT3, SYT6, SYT7 and SYT10.
Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane.
Cofactor. Binds 3 Ca(2+) ions per subunit. The ions are bound to the C2 domains.
Domain organisation. The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.
Similarity. Belongs to the synaptotagmin family.
RefSeq proteins (1): NP_783860* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000008 | C2_dom | Domain |
| IPR001565 | Synaptotagmin | Domain |
| IPR035892 | C2_domain_sf | Homologous_superfamily |
Pfam: PF00168
UniProt features (28 total): binding site 16, sequence variant 4, topological domain 2, domain 2, chain 1, transmembrane region 1, modified residue 1, region of interest 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q86SS6-F1 | 75.27 | 0.48 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (16): 309; 309; 310; 311; 311; 311; 314; 317; 317; 383; 389; 443 …
Post-translational modifications (1): 177
Function
Pathways and Gene Ontology
Reactome pathways
7 pathways
| ID | Pathway |
|---|---|
| R-HSA-6794361 | Neurexins and neuroligins |
| R-HSA-8856825 | Cargo recognition for clathrin-mediated endocytosis |
| R-HSA-8856828 | Clathrin-mediated endocytosis |
| R-HSA-112316 | Neuronal System |
| R-HSA-199991 | Membrane Trafficking |
| R-HSA-5653656 | Vesicle-mediated transport |
| R-HSA-6794362 | Protein-protein interactions at synapses |
MSigDB gene sets: 165 (showing top):
GOBP_REGULATION_OF_VESICLE_FUSION, ACTACCT_MIR196A_MIR196B, NKX25_02, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_NEUROTRANSMITTER_TRANSPORT, RACCACAR_AML_Q6, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, SP1_Q2_01, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT
GO Biological Process (5): chemical synaptic transmission (GO:0007268), vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), positive regulation of vesicle fusion (GO:0031340), calcium-dependent activation of synaptic vesicle fusion (GO:0099502)
GO Molecular Function (8): SNARE binding (GO:0000149), phosphatidylserine binding (GO:0001786), calcium-dependent phospholipid binding (GO:0005544), phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), identical protein binding (GO:0042802), metal ion binding (GO:0046872), calcium ion sensor activity (GO:0061891), protein binding (GO:0005515)
GO Cellular Component (9): plasma membrane (GO:0005886), clathrin-coated endocytic vesicle membrane (GO:0030669), synaptic vesicle membrane (GO:0030672), dense core granule (GO:0031045), exocytic vesicle (GO:0070382), hippocampal mossy fiber to CA3 synapse (GO:0098686), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202)
Reactome top-level categories
Rollup of top-5 pathways:
| Category | Pathways |
|---|---|
| Protein-protein interactions at synapses | 1 |
| Clathrin-mediated endocytosis | 1 |
| Membrane Trafficking | 1 |
| Vesicle-mediated transport | 1 |
| Neuronal System | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| protein binding | 2 |
| phospholipid binding | 2 |
| anterograde trans-synaptic signaling | 1 |
| transport | 1 |
| cellular process | 1 |
| calcium-ion regulated exocytosis | 1 |
| regulation of regulated secretory pathway | 1 |
| vesicle fusion | 1 |
| positive regulation of organelle organization | 1 |
| regulation of vesicle fusion | 1 |
| positive regulation of transport | 1 |
| synaptic vesicle exocytosis | 1 |
| positive regulation of synaptic vesicle fusion to presynaptic active zone membrane | 1 |
| anion binding | 1 |
| modified amino acid binding | 1 |
| phosphatidylinositol phosphate binding | 1 |
| phosphatidylinositol bisphosphate binding | 1 |
| cation binding | 1 |
| calcium ion binding | 1 |
| metal ion sensor activity | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| clathrin-coated vesicle membrane | 1 |
| endocytic vesicle membrane | 1 |
| clathrin-coated endocytic vesicle | 1 |
| synaptic vesicle | 1 |
| exocytic vesicle membrane | 1 |
| secretory granule | 1 |
| transport vesicle | 1 |
| secretory vesicle | 1 |
| thorny excrescence | 1 |
| neuron to neuron synapse | 1 |
| hippocampal mossy fiber expansion | 1 |
| cellular anatomical structure | 1 |
| cytoplasm | 1 |
| intracellular vesicle | 1 |
| cell junction | 1 |
Protein interactions and networks
STRING
762 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SYT9 | TUBB2A | Q13885 | 711 |
| SYT9 | TRPV1 | Q8NER1 | 690 |
| SYT9 | TUBB | P05218 | 670 |
| SYT9 | ZNF614 | Q8N883 | 540 |
| SYT9 | VAMP8 | Q9BV40 | 509 |
| SYT9 | STON2 | Q8WXE9 | 462 |
| SYT9 | VAMP3 | Q15836 | 450 |
| SYT9 | STX1A | Q16623 | 427 |
| SYT9 | SNAPIN | O95295 | 425 |
| SYT9 | SLC18A2 | Q05940 | 421 |
| SYT9 | DLGAP3 | O95886 | 412 |
| SYT9 | VAMP2 | P19065 | 412 |
| SYT9 | NLGN4X | Q8N0W4 | 385 |
| SYT9 | SLC18A3 | Q16572 | 384 |
| SYT9 | ZNF793 | Q6ZN11 | 375 |
IntAct
12 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SLC39A5 | FAM171A2 | psi-mi:“MI:0914”(association) | 0.640 |
| TMBIM6 | SYT9 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TMEM50A | SYT9 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UPK1B | SYT9 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SYT9 | LRP6 | psi-mi:“MI:0914”(association) | 0.350 |
| UPK1B | SYT9 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (26): SYT9 (Two-hybrid), SYT9 (Affinity Capture-MS), SYT9 (Reconstituted Complex), SYT9 (Affinity Capture-Western), TUBB (Reconstituted Complex), TUBB (Affinity Capture-Western), DNAJC5 (FRET), SYT9 (Two-hybrid), SYT9 (Two-hybrid), TMEM50A (Two-hybrid), SYT9 (Co-purification), SYT9 (Proximity Label-MS), SYT9 (Proximity Label-MS), SYT9 (Proximity Label-MS), SYNCRIP (Reconstituted Complex)
ESM2 similar proteins: A0A8I3NFE2, A0FGR8, A0FGR9, A2AP18, A4IJ05, O08625, O08874, O15357, O75038, P51432, P70218, P70268, Q01970, Q12851, Q3TZZ7, Q3U7R1, Q4VX76, Q5DTI8, Q5FWL4, Q5M7N9, Q5R8Q5, Q5RAG2, Q5RCK6, Q5RJH2, Q61161, Q62807, Q63433, Q6DN12, Q6XYQ8, Q7ZWU7, Q812E4, Q86SS6, Q8K394, Q8TDW5, Q920M7, Q925C0, Q92918, Q99JE6, Q99N48, Q9BSJ8
Diamond homologs: A0A075F932, A0FGR8, A4IJ05, K8FE10, O00445, O00750, O08625, O08835, O35681, O43581, P04409, P05128, P05129, P05130, P05696, P10102, P10829, P13677, P17252, P20444, P21521, P21579, P21707, P24505, P24506, P24507, P29101, P34693, P40748, P40749, P41823, P41885, P46096, P46097, P47191, P47708, P47709, P47861, P48018, P50232
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
58 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 49 |
| Likely benign | 2 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2134 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 11:7252332:G:GA | donor_loss | 1.0000 |
| 11:7252332:G:GG | donor_gain | 1.0000 |
| 11:7252333:T:A | donor_loss | 1.0000 |
| 11:7303035:GCA:G | acceptor_loss | 1.0000 |
| 11:7303036:CAGAT:C | acceptor_loss | 1.0000 |
| 11:7303037:A:AG | acceptor_gain | 1.0000 |
| 11:7303037:A:C | acceptor_loss | 1.0000 |
| 11:7303038:G:GA | acceptor_loss | 1.0000 |
| 11:7303038:G:GG | acceptor_gain | 1.0000 |
| 11:7313942:G:GG | donor_gain | 1.0000 |
| 11:7417945:T:TA | acceptor_gain | 1.0000 |
| 11:7252330:AG:A | donor_gain | 0.9900 |
| 11:7252331:GG:G | donor_gain | 0.9900 |
| 11:7303038:GA:G | acceptor_gain | 0.9900 |
| 11:7303038:GAT:G | acceptor_gain | 0.9900 |
| 11:7303038:GATA:G | acceptor_gain | 0.9900 |
| 11:7303038:GATAT:G | acceptor_gain | 0.9900 |
| 11:7303228:G:GG | donor_gain | 0.9900 |
| 11:7303395:G:GG | donor_gain | 0.9900 |
| 11:7313392:AAG:A | acceptor_gain | 0.9900 |
| 11:7313393:A:G | acceptor_gain | 0.9900 |
| 11:7313902:G:GT | donor_gain | 0.9900 |
| 11:7313937:CCAAT:C | donor_gain | 0.9900 |
| 11:7313940:AT:A | donor_gain | 0.9900 |
| 11:7313941:TGT:T | donor_loss | 0.9900 |
| 11:7313943:TG:T | donor_loss | 0.9900 |
| 11:7313944:G:GC | donor_loss | 0.9900 |
| 11:7313945:A:AC | donor_loss | 0.9900 |
| 11:7313946:G:T | donor_loss | 0.9900 |
| 11:7321395:G:T | donor_gain | 0.9900 |
AlphaMissense
3241 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 11:7313562:G:A | G222E | 1.000 |
| 11:7313568:T:C | L224P | 1.000 |
| 11:7313607:T:C | L237P | 1.000 |
| 11:7313627:G:C | A244P | 1.000 |
| 11:7313637:T:C | L247S | 1.000 |
| 11:7313637:T:G | L247W | 1.000 |
| 11:7313648:G:C | D251H | 1.000 |
| 11:7313649:A:C | D251A | 1.000 |
| 11:7313667:A:G | D257G | 1.000 |
| 11:7313670:C:A | P258H | 1.000 |
| 11:7313670:C:G | P258R | 1.000 |
| 11:7313672:T:G | Y259D | 1.000 |
| 11:7313676:T:A | V260D | 1.000 |
| 11:7313718:C:T | T274I | 1.000 |
| 11:7313724:T:A | V276D | 1.000 |
| 11:7313731:A:C | R278S | 1.000 |
| 11:7313731:A:T | R278S | 1.000 |
| 11:7313745:C:A | P283H | 1.000 |
| 11:7313750:T:C | F285L | 1.000 |
| 11:7313752:T:A | F285L | 1.000 |
| 11:7313752:T:G | F285L | 1.000 |
| 11:7313805:T:A | L303H | 1.000 |
| 11:7313805:T:C | L303P | 1.000 |
| 11:7313823:A:C | D309A | 1.000 |
| 11:7313823:A:T | D309V | 1.000 |
| 11:7313825:T:C | F310L | 1.000 |
| 11:7313827:T:A | F310L | 1.000 |
| 11:7313827:T:G | F310L | 1.000 |
| 11:7313829:A:C | D311A | 1.000 |
| 11:7313829:A:T | D311V | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000001245 (11:7270100 T>A,C), RS1000051028 (11:7262916 G>A,C), RS1000053869 (11:7401668 T>A), RS1000063979 (11:7237845 A>T), RS1000071053 (11:7328460 G>A), RS1000091370 (11:7445957 C>A), RS1000126131 (11:7378426 G>T), RS1000136516 (11:7269327 C>T), RS1000139862 (11:7394458 A>G), RS1000140365 (11:7415239 G>C), RS1000146497 (11:7368941 A>G), RS1000159323 (11:7247285 T>C), RS1000162638 (11:7430735 C>G,T), RS1000163569 (11:7349641 C>G), RS1000179528 (11:7263980 G>A,T)
Disease associations
OMIM: gene MIM:613528 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
12 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST001414_22 | Phospholipid levels (plasma) | 3.000000e-08 |
| GCST002284_9 | QRS duration in Tripanosoma cruzi seropositivity | 2.000000e-07 |
| GCST002285_14 | Chagas cardiomyopathy in Tripanosoma cruzi seropositivity | 6.000000e-06 |
| GCST002935_9 | Lead levels | 1.000000e-06 |
| GCST006035_10 | Breast cancer and/or colorectal cancer | 2.000000e-06 |
| GCST006086_19 | Familial lung cancer | 8.000000e-06 |
| GCST006998_6 | Cerebrospinal fluid p-tau levels in mild cognitive impairment | 4.000000e-07 |
| GCST007676_6 | 3-month functional outcome in ischaemic stroke (modified Rankin score) | 4.000000e-06 |
| GCST010600_4 | Dietary fat liking | 1.000000e-06 |
| GCST010725_20 | Malaria | 4.000000e-69 |
| GCST010725_33 | Malaria | 2.000000e-67 |
| GCST010725_51 | Malaria | 1.000000e-55 |
EFO canonical traits (4, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0006953 | family history of lung cancer |
| EFO:0004760 | t-tau measurement |
| EFO:0009603 | stroke outcome severity measurement |
| EFO:0010816 | dietary fat liking measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
29 total (human), top 29 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Aflatoxin B1 | affects expression, decreases methylation | 3 |
| mercuric bromide | decreases expression, affects cotreatment | 2 |
| Benzo(a)pyrene | decreases expression, increases methylation | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| Valproic Acid | increases expression | 2 |
| p-Chloromercuribenzoic Acid | affects cotreatment, decreases expression | 2 |
| methylmercuric chloride | decreases expression | 1 |
| methyleugenol | decreases expression | 1 |
| propionaldehyde | increases expression | 1 |
| bisphenol A | affects cotreatment, increases methylation, decreases methylation | 1 |
| ethyl-p-hydroxybenzoate | decreases expression | 1 |
| trichostatin A | decreases expression, increases expression | 1 |
| butyraldehyde | increases expression | 1 |
| pentanal | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| entinostat | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Fulvestrant | affects cotreatment, increases methylation | 1 |
| Aldehydes | increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Niclosamide | decreases expression | 1 |
| Tretinoin | increases expression | 1 |
| Triclosan | decreases expression | 1 |
| 8-Bromo Cyclic Adenosine Monophosphate | increases expression | 1 |
| Cyclosporine | decreases expression | 1 |
| Okadaic Acid | increases 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): Chagas cardiomyopathy