SLITRK3
geneOn this page
Also known as KIAA0848
Summary
SLITRK3 (SLIT and NTRK like family member 3, HGNC:23501) is a protein-coding gene on chromosome 3q26.1, encoding SLIT and NTRK-like protein 3 (O94933). Suppresses neurite outgrowth.
This gene encodes a member of the Slitrk family of structurally related transmembrane proteins that are involved in controlling neurite outgrowth. The encoded protein contains two leucine-rich repeat (LRR) domains and a C-terminal domain that is partially similar to Trk neurotrophin receptor protein. Enhanced expression of this gene was found in tissue from several different types of tumors. Alternative splicing results in multiple transcript variants, all encoding the same protein.
Source: NCBI Gene 22865 — RefSeq curated summary.
At a glance
- Gene–disease (curated): epilepsy (Limited, GenCC) — +1 more curated relationship
- GWAS associations: 3
- Clinical variants (ClinVar): 113 total — 1 pathogenic
- MANE Select transcript:
NM_001318810
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:23501 |
| Approved symbol | SLITRK3 |
| Name | SLIT and NTRK like family member 3 |
| Location | 3q26.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA0848 |
| Ensembl gene | ENSG00000121871 |
| Ensembl biotype | protein_coding |
| OMIM | 609679 |
| Entrez | 22865 |
Gene structure
Transcript identifiers
Ensembl transcripts: 7 — 7 protein_coding
ENST00000241274, ENST00000475390, ENST00000497724, ENST00000925264, ENST00000925265, ENST00000925266, ENST00000925267
RefSeq mRNA: 3 — MANE Select: NM_001318810
NM_001318810, NM_001318811, NM_014926
CCDS: CCDS3197
Canonical transcript exons
ENST00000475390 — 2 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001837903 | 165186720 | 165190851 |
| ENSE00001953036 | 165195580 | 165196384 |
Expression profiles
Bgee: expression breadth ubiquitous, 151 present calls, max score 83.56.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.1191 / max 133.7300, expressed in 171 samples.
FANTOM5 promoters (10 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 45431 | 0.3267 | 94 |
| 45432 | 0.1667 | 70 |
| 45430 | 0.1544 | 72 |
| 45428 | 0.0930 | 52 |
| 45433 | 0.0889 | 57 |
| 45425 | 0.0841 | 41 |
| 203012 | 0.0580 | 42 |
| 45426 | 0.0551 | 30 |
| 45427 | 0.0512 | 32 |
| 45429 | 0.0411 | 28 |
Top tissues by expression
277 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| left uterine tube | UBERON:0001303 | 83.56 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 82.75 | gold quality |
| prefrontal cortex | UBERON:0000451 | 78.70 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 78.30 | gold quality |
| primary visual cortex | UBERON:0002436 | 77.77 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 77.70 | gold quality |
| lower esophagus | UBERON:0013473 | 77.62 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 76.90 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 74.84 | gold quality |
| frontal cortex | UBERON:0001870 | 74.74 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 74.62 | gold quality |
| postcentral gyrus | UBERON:0002581 | 74.61 | gold quality |
| neocortex | UBERON:0001950 | 74.20 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 74.07 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 74.01 | gold quality |
| cerebral cortex | UBERON:0000956 | 73.49 | gold quality |
| right frontal lobe | UBERON:0002810 | 72.92 | gold quality |
| occipital lobe | UBERON:0002021 | 72.73 | gold quality |
| caudate nucleus | UBERON:0001873 | 72.50 | gold quality |
| cingulate cortex | UBERON:0003027 | 72.50 | gold quality |
| telencephalon | UBERON:0001893 | 72.42 | gold quality |
| nucleus accumbens | UBERON:0001882 | 72.35 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 72.31 | gold quality |
| Ammon’s horn | UBERON:0001954 | 72.18 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 72.11 | gold quality |
| parietal lobe | UBERON:0001872 | 71.67 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 71.62 | gold quality |
| cerebellar cortex | UBERON:0002129 | 71.61 | gold quality |
| entorhinal cortex | UBERON:0002728 | 71.50 | gold quality |
| endothelial cell | CL:0000115 | 71.47 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 3.43 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
102 targeting SLITRK3, 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-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-190A-3P | 100.00 | 80.35 | 5520 |
| HSA-MIR-3134 | 100.00 | 66.43 | 777 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-574-5P | 100.00 | 66.01 | 989 |
| HSA-MIR-511-3P | 99.99 | 68.85 | 1467 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-MIR-6835-3P | 99.93 | 70.49 | 2904 |
| HSA-MIR-515-5P | 99.92 | 69.82 | 2343 |
| HSA-MIR-519E-5P | 99.92 | 69.62 | 2358 |
| HSA-MIR-10523-5P | 99.91 | 69.22 | 2038 |
| HSA-MIR-106A-5P | 99.90 | 73.94 | 2683 |
| HSA-MIR-548E-5P | 99.89 | 72.73 | 4486 |
| HSA-MIR-17-5P | 99.89 | 73.83 | 2665 |
| HSA-MIR-106B-5P | 99.88 | 74.72 | 2795 |
| HSA-MIR-20A-5P | 99.88 | 74.76 | 2769 |
| HSA-MIR-20B-5P | 99.88 | 74.01 | 2621 |
| HSA-MIR-519D-3P | 99.88 | 73.97 | 2607 |
| HSA-MIR-93-5P | 99.88 | 73.98 | 2606 |
| HSA-MIR-30A-3P | 99.87 | 69.74 | 2928 |
| HSA-MIR-30D-3P | 99.87 | 69.92 | 2917 |
| HSA-MIR-30E-3P | 99.87 | 69.68 | 2942 |
| HSA-MIR-548AZ-5P | 99.83 | 69.94 | 3230 |
| HSA-MIR-548T-5P | 99.83 | 69.91 | 3220 |
| HSA-MIR-1323 | 99.83 | 69.89 | 2471 |
| HSA-MIR-4420 | 99.82 | 70.08 | 1624 |
| HSA-MIR-4307 | 99.82 | 70.45 | 3374 |
Literature-anchored findings (GeneRIF, showing 2)
- SLITRK3 expression is a highly significant predictor of gastrointestinal stromal tumor recurrence and metastasis. (PMID:26217092)
- SLITRK2, an X-linked modifier of the age at onset in C9orf72 frontotemporal lobar degeneration. (PMID:34687211)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | slitrk3a | ENSDARG00000078123 |
| mus_musculus | Slitrk3 | ENSMUSG00000048304 |
| rattus_norvegicus | Slitrk3 | ENSRNOG00000009821 |
Paralogs (25): LRFN3 (ENSG00000126243), LRFN1 (ENSG00000128011), SLIT2 (ENSG00000145147), LRFN2 (ENSG00000156564), LRRC38 (ENSG00000162494), SLITRK5 (ENSG00000165300), LRFN5 (ENSG00000165379), LRTM2 (ENSG00000166159), LINGO1 (ENSG00000169783), LRRN2 (ENSG00000170382), LRRN3 (ENSG00000173114), LRFN4 (ENSG00000173621), LINGO2 (ENSG00000174482), LRRN1 (ENSG00000175928), SLITRK1 (ENSG00000178235), GP5 (ENSG00000178732), SLITRK4 (ENSG00000179542), LRRC55 (ENSG00000183908), SLIT3 (ENSG00000184347), SLITRK6 (ENSG00000184564), SLITRK2 (ENSG00000185985), LRRC70 (ENSG00000186105), SLIT1 (ENSG00000187122), TLR9 (ENSG00000239732), TPBGL (ENSG00000261594)
Protein
Protein identifiers
SLIT and NTRK-like protein 3 — O94933 (reviewed: O94933)
All UniProt accessions (2): C9K0R4, O94933
UniProt curated annotations — full annotation on UniProt →
Function. Suppresses neurite outgrowth.
Subcellular location. Membrane.
Tissue specificity. Expressed in the occipital lobe of the cerebral cortex of the brain. Expressed at higher levels in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumors.
Similarity. Belongs to the SLITRK family.
RefSeq proteins (3): NP_001305739, NP_001305740, NP_055741 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000483 | Cys-rich_flank_reg_C | Domain |
| IPR001611 | Leu-rich_rpt | Repeat |
| IPR003591 | Leu-rich_rpt_typical-subtyp | Repeat |
| IPR032675 | LRR_dom_sf | Homologous_superfamily |
Pfam: PF13855
UniProt features (29 total): repeat 12, domain 3, region of interest 3, topological domain 2, compositionally biased region 2, glycosylation site 2, signal peptide 1, chain 1, sequence variant 1, sequence conflict 1, transmembrane region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O94933-F1 | 64.70 | 0.24 |
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 (2): 68, 596
Function
Pathways and Gene Ontology
Reactome pathways
8 pathways
| ID | Pathway |
|---|---|
| R-HSA-388844 | Receptor-type tyrosine-protein phosphatases |
| R-HSA-9013423 | RAC3 GTPase cycle |
| R-HSA-112316 | Neuronal System |
| R-HSA-162582 | Signal Transduction |
| R-HSA-194315 | Signaling by Rho GTPases |
| R-HSA-6794362 | Protein-protein interactions at synapses |
| R-HSA-9012999 | RHO GTPase cycle |
| R-HSA-9716542 | Signaling by Rho GTPases, Miro GTPases and RHOBTB3 |
MSigDB gene sets: 181 (showing top):
AGGAAGC_MIR5163P, BENPORATH_ES_WITH_H3K27ME3, GOBP_SYNAPSE_ASSEMBLY, TGCACTT_MIR519C_MIR519B_MIR519A, TTTGTAG_MIR520D, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOCC_CELL_SURFACE, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, ATGCAGT_MIR217, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, chr3q26
GO Biological Process (9): axonogenesis (GO:0007409), synaptic transmission, GABAergic (GO:0051932), positive regulation of synapse assembly (GO:0051965), terminal button organization (GO:0072553), neurotransmitter-gated ion channel clustering (GO:0072578), gephyrin clustering involved in postsynaptic density assembly (GO:0097116), synaptic membrane adhesion (GO:0099560), regulation of presynapse assembly (GO:1905606), postsynaptic density assembly (GO:0097107)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (7): plasma membrane (GO:0005886), cell surface (GO:0009986), postsynaptic density membrane (GO:0098839), GABA-ergic synapse (GO:0098982), postsynaptic specialization membrane (GO:0099634), membrane (GO:0016020), postsynaptic membrane (GO:0045211)
Reactome top-level categories
Rollup of top-6 pathways:
| Category | Pathways |
|---|---|
| Protein-protein interactions at synapses | 1 |
| RHO GTPase cycle | 1 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 1 |
| Neuronal System | 1 |
| Signaling by Rho GTPases | 1 |
| Signal Transduction | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| regulation of synapse assembly | 2 |
| synapse organization | 2 |
| cellular anatomical structure | 2 |
| postsynaptic membrane | 2 |
| synaptic membrane | 2 |
| cell morphogenesis involved in neuron differentiation | 1 |
| neuron projection morphogenesis | 1 |
| axon development | 1 |
| chemical synaptic transmission | 1 |
| synapse assembly | 1 |
| positive regulation of nervous system development | 1 |
| positive regulation of cell junction assembly | 1 |
| presynapse organization | 1 |
| receptor clustering | 1 |
| protein localization to synapse | 1 |
| postsynaptic density assembly | 1 |
| cell-cell adhesion | 1 |
| presynapse assembly | 1 |
| regulation of presynapse organization | 1 |
| postsynaptic density organization | 1 |
| postsynaptic specialization assembly | 1 |
| excitatory synapse assembly | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| postsynaptic density | 1 |
| postsynaptic specialization membrane | 1 |
| synapse | 1 |
| postsynaptic specialization | 1 |
| postsynapse | 1 |
Protein interactions and networks
STRING
1858 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SLITRK3 | PTPRD | P23468 | 858 |
| SLITRK3 | NLGN2 | Q8NFZ4 | 805 |
| SLITRK3 | IL1RAPL1 | Q9NZN1 | 715 |
| SLITRK3 | PTPRS | Q13332 | 660 |
| SLITRK3 | NTRK1 | P04629 | 588 |
| SLITRK3 | NLGN1 | Q8N2Q7 | 546 |
| SLITRK3 | NTRK3 | Q16288 | 527 |
| SLITRK3 | GPHN | Q9NQX3 | 501 |
| SLITRK3 | NRXN2 | Q9P2S2 | 497 |
| SLITRK3 | LRR1 | Q96L50 | 492 |
| SLITRK3 | NRXN1 | Q9ULB1 | 468 |
| SLITRK3 | PTPRF | P10586 | 466 |
| SLITRK3 | UNC5D | Q6UXZ4 | 454 |
| SLITRK3 | NLGN3 | Q9NZ94 | 450 |
| SLITRK3 | BOC | Q9BWV1 | 423 |
IntAct
16 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SLITRK3 | WFS1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| EGFR | NDUFA4 | psi-mi:“MI:0914”(association) | 0.530 |
| SLITRK3 | H2BC9 | psi-mi:“MI:0915”(physical association) | 0.400 |
| SLITRK3 | H1-2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| SLITRK3 | H3C13 | psi-mi:“MI:0915”(physical association) | 0.400 |
| SLITRK3 | RHBDF2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| SBSN | SLITRK3 | psi-mi:“MI:0915”(physical association) | 0.400 |
| CACNA1C | DISP2 | psi-mi:“MI:0914”(association) | 0.350 |
| HCN1 | POTEF | psi-mi:“MI:0914”(association) | 0.350 |
| SLITRK3 | TCAF2 | psi-mi:“MI:0914”(association) | 0.350 |
| KCNE3 | PIK3R2 | psi-mi:“MI:0914”(association) | 0.350 |
| PCDHGA7 | SDCBP | psi-mi:“MI:0914”(association) | 0.350 |
| TRIM54 | SLITRK3 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (22): SLITRK3 (Affinity Capture-MS), SLITRK3 (Affinity Capture-RNA), SLITRK3 (Proximity Label-MS), SLITRK3 (Synthetic Lethality), HIST1H1C (Proximity Label-MS), SLITRK3 (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), SLITRK3 (Two-hybrid), ERBB2 (Affinity Capture-MS), SLITRK3 (Affinity Capture-MS), KCNT2 (Affinity Capture-MS), FAM115C (Affinity Capture-MS), ACVR2A (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), ATE1 (Affinity Capture-MS)
ESM2 similar proteins: A1XQX3, A1XQY0, A1XQY3, A2ALI5, A6QLD2, B5X216, D0PRN4, E9PUN2, O35181, O75151, O94933, O94991, P0C7U0, P15379, P23470, P49415, P56975, P58401, P80560, Q05909, Q3SXY7, Q3UH99, Q3V1G4, Q4W8E7, Q58EG3, Q5EGE1, Q5R3F8, Q5R5B8, Q63376, Q63475, Q68BL8, Q68FM6, Q6QD51, Q6ZSJ9, Q76KF0, Q80Z10, Q810B7, Q810B9, Q8AXP2, Q8C8T7
Diamond homologs: E9Q7T7, G5EFX6, O02678, O15335, O46390, O46403, O55226, O70210, O94933, O94991, P14770, P21809, P21810, P28653, P47853, P83503, Q27972, Q5RAC4, Q6NUI6, Q6RKD8, Q7Z2Q7, Q810B7, Q810B9, Q810C0, Q810C1, Q8C031, Q8C110, Q91009, Q96PX8, Q9GKQ6, Q9H156, Q9HCJ2, Q9NZU1, B1H234, Q5R6T0, Q8BGT1, Q9NZU0, Q7M6Z0, Q80WD1, Q810B8
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
113 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 106 |
| Likely benign | 3 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 930212 | NM_001318810.2(SLITRK3):c.1816G>T (p.Glu606Ter) | Pathogenic |
SpliceAI
287 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:165190847:CAAAA:C | acceptor_gain | 1.0000 |
| 3:165190852:C:CC | acceptor_gain | 0.9900 |
| 3:165192715:TGAG:T | donor_gain | 0.9900 |
| 3:165190848:AAAA:A | acceptor_gain | 0.9800 |
| 3:165190849:AAA:A | acceptor_gain | 0.9800 |
| 3:165190850:AA:A | acceptor_gain | 0.9800 |
| 3:165190851:ACTG:A | acceptor_loss | 0.9800 |
| 3:165190852:C:CA | acceptor_loss | 0.9800 |
| 3:165190853:T:G | acceptor_loss | 0.9800 |
| 3:165192723:G:A | donor_gain | 0.9600 |
| 3:165192566:CG:C | acceptor_gain | 0.9500 |
| 3:165193555:TGG:T | donor_gain | 0.9400 |
| 3:165190859:A:T | acceptor_gain | 0.9200 |
| 3:165192567:G:C | acceptor_gain | 0.9200 |
| 3:165190854:G:C | acceptor_loss | 0.9100 |
| 3:165195264:TTC:T | donor_gain | 0.9000 |
| 3:165195265:TCT:T | donor_gain | 0.9000 |
| 3:165195681:AG:A | donor_gain | 0.9000 |
| 3:165195577:TA:T | donor_loss | 0.8900 |
| 3:165195578:ACC:A | donor_loss | 0.8900 |
| 3:165195579:C:A | donor_loss | 0.8900 |
| 3:165190858:C:CT | acceptor_gain | 0.8800 |
| 3:165195582:A:AC | donor_gain | 0.8700 |
| 3:165192712:G:C | donor_gain | 0.8600 |
| 3:165195580:C:G | donor_loss | 0.8600 |
| 3:165195676:A:AC | donor_gain | 0.8400 |
| 3:165195677:C:CC | donor_gain | 0.8400 |
| 3:165195527:A:AC | donor_gain | 0.8300 |
| 3:165195528:C:CC | donor_gain | 0.8300 |
| 3:165195760:C:CT | donor_gain | 0.8300 |
AlphaMissense
6394 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:165189139:C:A | W564C | 1.000 |
| 3:165189139:C:G | W564C | 1.000 |
| 3:165189141:A:G | W564R | 1.000 |
| 3:165189141:A:T | W564R | 1.000 |
| 3:165189220:G:C | N537K | 1.000 |
| 3:165189220:G:T | N537K | 1.000 |
| 3:165189289:G:C | N514K | 1.000 |
| 3:165189289:G:T | N514K | 1.000 |
| 3:165189433:G:C | N466K | 1.000 |
| 3:165189433:G:T | N466K | 1.000 |
| 3:165189449:A:G | L461P | 1.000 |
| 3:165189505:A:C | N442K | 1.000 |
| 3:165189505:A:T | N442K | 1.000 |
| 3:165189530:A:C | L434W | 1.000 |
| 3:165189577:A:C | N418K | 1.000 |
| 3:165189577:A:T | N418K | 1.000 |
| 3:165189593:A:G | L413P | 1.000 |
| 3:165189655:G:C | C392W | 1.000 |
| 3:165189656:C:G | C392S | 1.000 |
| 3:165189656:C:T | C392Y | 1.000 |
| 3:165189657:A:G | C392R | 1.000 |
| 3:165189657:A:T | C392S | 1.000 |
| 3:165189662:A:T | V390D | 1.000 |
| 3:165189694:A:C | C379W | 1.000 |
| 3:165189695:C:T | C379Y | 1.000 |
| 3:165189696:A:G | C379R | 1.000 |
| 3:165189700:A:C | C377W | 1.000 |
| 3:165189702:A:G | C377R | 1.000 |
| 3:165189712:G:C | C373W | 1.000 |
| 3:165189713:C:T | C373Y | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000180315 (3:165198040 T>G), RS1000283363 (3:165192235 T>A), RS1000592840 (3:165186225 T>G), RS1000752452 (3:165192607 T>G), RS1001206038 (3:165192333 G>C), RS1001296487 (3:165191012 T>C), RS1001643123 (3:165191282 G>T), RS1002067358 (3:165197482 A>G,T), RS1002140772 (3:165197286 G>A), RS1002173973 (3:165189685 G>A), RS1002229992 (3:165195627 A>G,T), RS1002374531 (3:165192084 T>A), RS1002970955 (3:165190873 A>C,G), RS1003034814 (3:165194024 A>C), RS1003127667 (3:165196114 C>A,T)
Disease associations
OMIM: gene MIM:609679 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| epilepsy | Limited | Autosomal dominant |
| complex neurodevelopmental disorder | Limited | Autosomal recessive |
Mondo (3): intellectual disability (MONDO:0001071), epilepsy (MONDO:0005027), complex neurodevelopmental disorder (MONDO:0100038)
Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
3 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST006585_987 | Blood protein levels | 4.000000e-19 |
| GCST009391_1199 | Metabolite levels | 2.000000e-07 |
| GCST009391_46 | Metabolite levels | 6.000000e-06 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0010456 | allantoin measurement |
| EFO:0010114 | citrate measurement |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D004827 | Epilepsy | C10.228.140.490 |
| D008607 | Intellectual Disability | C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
25 total (human), top 25 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | increases expression, affects expression, affects cotreatment | 4 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| sotorasib | affects cotreatment, increases expression | 1 |
| ethyl-p-hydroxybenzoate | increases expression | 1 |
| terbufos | increases methylation | 1 |
| arsenite | increases methylation | 1 |
| ferrous chloride | decreases expression | 1 |
| aflatoxin B2 | increases methylation | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| trametinib | affects cotreatment, increases expression | 1 |
| NVP-BKM120 | increases expression, affects cotreatment | 1 |
| Sunitinib | increases expression | 1 |
| Amiodarone | increases expression | 1 |
| Benzo(a)pyrene | affects methylation, decreases methylation, increases methylation | 1 |
| Calcitriol | decreases expression, affects cotreatment | 1 |
| Cytarabine | decreases expression | 1 |
| Fonofos | increases methylation | 1 |
| Parathion | increases methylation | 1 |
| Rotenone | decreases expression | 1 |
| Testosterone | decreases expression, affects cotreatment | 1 |
| Asbestos, Serpentine | decreases methylation | 1 |
| Asbestos, Crocidolite | increases methylation | 1 |
| Antirheumatic Agents | increases expression | 1 |
| Okadaic Acid | decreases expression | 1 |
Clinical trials (associated diseases)
497 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00004637 | PHASE4 | COMPLETED | Double-Blind, Placebo-Controlled Trial of Vitamin E as Add-on Therapy for Children With Epilepsy |
| NCT00043914 | PHASE4 | COMPLETED | Measurement Of Serum Levels Of Two Antiepileptic Drugs During Conversion In Patients With Epilepsy |
| NCT00132223 | PHASE4 | UNKNOWN | Effects on the Diagnostic Accuracy of Magnetic Imaging Angiographies of the Supra-Aortic Vessels by Three Different Magnetic Resonance Contrast Agents in Patients |
| NCT00133081 | PHASE4 | UNKNOWN | Study to Improve the Treatment of Epilepsy (SITE) |
| NCT00137709 | PHASE4 | UNKNOWN | Hormone Profiles in Adults With Newly Diagnosed Epilepsy |
| NCT00154076 | PHASE4 | COMPLETED | A Multicenter Comparative Trial of Zonisamide and Topiramate as Initial Monotherapy in Untreated Epilepsies |
| NCT00165828 | PHASE4 | TERMINATED | Efficacy and Safety of an add-on Treatment With Zonisamide in Adults With Focal Epileptic Seizures With or Without Secondary Generalization |
| NCT00181116 | PHASE4 | COMPLETED | Levetiracetam for Benign Rolandic Epilepsy |
| NCT00207935 | PHASE4 | COMPLETED | Use of Sustained Release Antiepileptic Medication (Depakote® ER) for Pediatric Epilepsy in a Mental Retardation/Developmental Disorder Population |
| NCT00215592 | PHASE4 | COMPLETED | Open Label, Zonegran (Zonisamide) In Partial Onset Seizures |
| NCT00266604 | PHASE4 | COMPLETED | A Study to Evaluate the Dosing, Effectiveness and Safety of Topiramate for the Treatment of Epilepsy |
| NCT00288639 | PHASE4 | COMPLETED | Lyrica (Pregabalin) Administered as an Add-on Therapy for Partial Seizures (LEADER). |
| NCT00312676 | PHASE4 | UNKNOWN | Compare Tolerability of an Overnight Switch to Gradual Switch Between Two Different Forms of Depakote |
| NCT00323947 | PHASE4 | COMPLETED | Methylphenidate for Treating Attention Deficit Hyperactivity Disorder in Children With Both ADHD and Epilepsy |
| NCT00385411 | PHASE4 | COMPLETED | Study of Valproate in Young Patients Suffering From Epilepsy |
| NCT00522418 | PHASE4 | TERMINATED | Study Comparing Best Medical Practice With or Without VNS Therapy in Pharmacoresistant Partial Epilepsy Patients |
| NCT00537940 | PHASE4 | COMPLETED | Comparative Study Of Pregabalin And Gabapentin As Adjunctive Therapy In Subjects With Partial Seizures |
| NCT00552526 | PHASE4 | UNKNOWN | Ketogenic Diet vs.Antiepileptic Drug Treatment in Drug Resistant Epilepsy |
| NCT00564915 | PHASE4 | COMPLETED | RCT of the Efficacy of the Ketogenic Diet in the Treatment of Epilepsy |
| NCT00571155 | PHASE4 | COMPLETED | Trial of Levetiracetam in Patients With Primary Brain Tumors and Symptomatic Seizures Who Undergo Surgery |
| NCT00572195 | PHASE4 | COMPLETED | RNS® System LTT Study |
| NCT00610532 | PHASE4 | TERMINATED | Evaluating the Transporter Protein Inhibitor Probenecid In Patients With Epilepsy |
| NCT00630357 | PHASE4 | COMPLETED | Trial to Evaluate the Safety and Efficacy of Keppra After Conversion to Mono-therapy in Subjects With Partial Epilepsy |
| NCT00630630 | PHASE4 | COMPLETED | Study on Safety and Efficacy of Levetiracetam in the Adjunctive Treatment of Female Subjects With C1 Catamenial Epilepsy |
| NCT00630968 | PHASE4 | COMPLETED | S.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy |
| NCT00631150 | PHASE4 | COMPLETED | A Phase IV-Pharmacovigilance Study of Keppra Greece - S.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy |
| NCT00659958 | PHASE4 | COMPLETED | ZAGAL Study: Evaluating Effectiveness and Tolerability of Zonisamide as Adjunctive Therapy in Patients With Partial Onset Seizures Treated With Two Antiepileptic Drugs |
| NCT00713622 | PHASE4 | COMPLETED | Comparing The Effect On Cognition Of Adjunctive Therapy With Zonisamide Versus Sodium Valproate |
| NCT00807989 | PHASE4 | COMPLETED | The Efficacy and Safety of Low Dose Combination of LTG and VPA Compared to CBZ Monotherapy |
| NCT00832884 | PHASE4 | COMPLETED | The Safety of Intravenous Lacosamide |
| NCT00869622 | PHASE4 | COMPLETED | Antiepileptic Drugs and Osteoporotic Prevention Trial |
| NCT00896987 | PHASE4 | COMPLETED | Lamotrigine Cognitive Function Study in Adult Untreated Epilepsies |
| NCT00952081 | PHASE4 | COMPLETED | A Pilot Study to Evaluate Efficacy and Safety of Clevidipine in Neurosurgical Patients |
| NCT01118455 | PHASE4 | TERMINATED | Trial to Assess Vagus Nerve Stimulation Therapy vs. Anti-Epileptic Drug (AED) Treatment in Children With Refractory Seizures |
| NCT01127165 | PHASE4 | COMPLETED | Low and High Dose Zonisamide in Children as Monotherapy |
| NCT01127256 | PHASE4 | COMPLETED | Comparative Study of Zonisamide and Carbamazepine as an Initial Monotherapy: Efficacy and Safety Evaluation |
| NCT01140867 | PHASE4 | COMPLETED | Open-label, Multi-center Trial of Zonisamide as Adjunctive Therapy in Patients With Uncontrolled Partial Epilepsy |
| NCT01175954 | PHASE4 | COMPLETED | Cognitive and Behavioral Effects of Lacosamide |
| NCT01229735 | PHASE4 | COMPLETED | Levetiracetam Versus Topiramate as Adjunctive Therapy to Evaluate Efficacy and Safety in Subjects With Refractory Partial Onset Seizures |
| NCT01244724 | PHASE4 | TERMINATED | Lexapro for Major Depression in Patients With Epilepsy |
Related Atlas pages
- Associated diseases: epilepsy, complex neurodevelopmental disorder
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): complex neurodevelopmental disorder, epilepsy