SLITRK2
geneOn this page
Also known as KIAA1854CXorf2
Summary
SLITRK2 (SLIT and NTRK like family member 2, HGNC:13449) is a protein-coding gene on chromosome Xq27.3, encoding SLIT and NTRK-like protein 2 (Q9H156). It is involved in synaptogenesis and promotes excitatory synapse differentiation.
This gene encodes an integral membrane protein that contains two N-terminal leucine-rich repeats domains and contains C-terminal regions similar to neurotrophin receptors. The encoded protein may play a role in modulating neurite activity. Alternatively spliced transcript variants encoding the same protein have been described.
Source: NCBI Gene 84631 — RefSeq curated summary.
At a glance
- Gene–disease (curated): intellectual developmental disorder, X-linked 111 (Strong, GenCC) — +1 more curated relationship
- GWAS associations: 2
- Clinical variants (ClinVar): 143 total — 2 likely-pathogenic
- Phenotypes (HPO): 24
- MANE Select transcript:
NM_032539
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:13449 |
| Approved symbol | SLITRK2 |
| Name | SLIT and NTRK like family member 2 |
| Location | Xq27.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA1854, CXorf2 |
| Ensembl gene | ENSG00000185985 |
| Ensembl biotype | protein_coding |
| OMIM | 300561 |
| Entrez | 84631 |
Gene structure
Transcript identifiers
Ensembl transcripts: 14 — 14 protein_coding
ENST00000335565, ENST00000370490, ENST00000867861, ENST00000867862, ENST00000867863, ENST00000867864, ENST00000867865, ENST00000867866, ENST00000867867, ENST00000867868, ENST00000867869, ENST00000966678, ENST00000966679, ENST00000966680
RefSeq mRNA: 8 — MANE Select: NM_032539
NM_001144003, NM_001144004, NM_001144005, NM_001144006, NM_001144008, NM_001144009, NM_001144010, NM_032539
CCDS: CCDS14680
Canonical transcript exons
ENST00000335565 — 5 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001517261 | 145822005 | 145822153 |
| ENSE00001517265 | 145822383 | 145829856 |
| ENSE00001630476 | 145820474 | 145820536 |
| ENSE00001678002 | 145821348 | 145821884 |
| ENSE00001773254 | 145817829 | 145818026 |
Expression profiles
Bgee: expression breadth ubiquitous, 166 present calls, max score 86.08.
FANTOM5 (CAGE): breadth broad, TPM avg 7.5143 / max 651.2898, expressed in 365 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 197903 | 2.9128 | 153 |
| 197899 | 2.8132 | 319 |
| 197900 | 1.6124 | 245 |
| 197901 | 0.1759 | 85 |
Top tissues by expression
284 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ventricular zone | UBERON:0003053 | 86.08 | gold quality |
| medial globus pallidus | UBERON:0002477 | 83.96 | gold quality |
| caudate nucleus | UBERON:0001873 | 81.54 | gold quality |
| nucleus accumbens | UBERON:0001882 | 81.53 | gold quality |
| ganglionic eminence | UBERON:0004023 | 80.86 | gold quality |
| globus pallidus | UBERON:0001875 | 80.85 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 80.04 | gold quality |
| amygdala | UBERON:0001876 | 79.92 | gold quality |
| right frontal lobe | UBERON:0002810 | 79.51 | gold quality |
| putamen | UBERON:0001874 | 78.97 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 78.91 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 78.30 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 78.22 | gold quality |
| prefrontal cortex | UBERON:0000451 | 78.07 | gold quality |
| cingulate cortex | UBERON:0003027 | 77.98 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 77.71 | gold quality |
| sural nerve | UBERON:0015488 | 77.65 | gold quality |
| telencephalon | UBERON:0001893 | 77.64 | gold quality |
| temporal lobe | UBERON:0001871 | 77.27 | gold quality |
| spinal cord | UBERON:0002240 | 77.18 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 77.13 | gold quality |
| neocortex | UBERON:0001950 | 76.88 | gold quality |
| cerebral cortex | UBERON:0000956 | 76.66 | gold quality |
| frontal cortex | UBERON:0001870 | 76.61 | gold quality |
| Ammon’s horn | UBERON:0001954 | 76.38 | gold quality |
| tibial nerve | UBERON:0001323 | 76.28 | gold quality |
| postcentral gyrus | UBERON:0002581 | 76.15 | gold quality |
| primary visual cortex | UBERON:0002436 | 76.06 | gold quality |
| endothelial cell | CL:0000115 | 75.59 | silver quality |
| entorhinal cortex | UBERON:0002728 | 74.47 | gold quality |
Single-cell (SCXA)
Detected in 4 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-6911 | yes | 216.24 |
| E-MTAB-7316 | yes | 28.09 |
| E-GEOD-81383 | no | 536.34 |
| E-ANND-3 | no | 3.72 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
92 targeting SLITRK2, 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-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-188-3P | 100.00 | 68.76 | 1240 |
| HSA-MIR-150-5P | 99.99 | 66.69 | 1976 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-495-3P | 99.96 | 72.81 | 4197 |
| HSA-MIR-5688 | 99.96 | 73.23 | 4504 |
| HSA-MIR-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-651-3P | 99.94 | 73.48 | 5177 |
| HSA-MIR-141-3P | 99.94 | 72.79 | 2421 |
| HSA-MIR-200A-3P | 99.94 | 72.68 | 2420 |
| HSA-MIR-539-5P | 99.93 | 70.30 | 2855 |
| HSA-MIR-1305 | 99.91 | 71.43 | 3443 |
| HSA-MIR-10527-5P | 99.91 | 72.28 | 3754 |
| 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-526B-3P | 99.88 | 74.06 | 2587 |
| HSA-MIR-93-5P | 99.88 | 73.98 | 2606 |
| HSA-MIR-579-3P | 99.86 | 71.66 | 3628 |
| HSA-MIR-4779 | 99.86 | 66.50 | 1583 |
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | slitrk2 | ENSDARG00000006636 |
| mus_musculus | Slitrk2 | ENSMUSG00000036790 |
| rattus_norvegicus | Slitrk2 | ENSRNOG00000011562 |
Paralogs (25): SLITRK3 (ENSG00000121871), 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), LRRC70 (ENSG00000186105), SLIT1 (ENSG00000187122), TLR9 (ENSG00000239732), TPBGL (ENSG00000261594)
Protein
Protein identifiers
SLIT and NTRK-like protein 2 — Q9H156 (reviewed: Q9H156)
All UniProt accessions (2): B3KTY4, Q9H156
UniProt curated annotations — full annotation on UniProt →
Function. It is involved in synaptogenesis and promotes excitatory synapse differentiation. Suppresses neurite outgrowth. Involved in the negative regulation of NTRK2.
Subunit / interactions. Interacts with PTPRD; this interaction is PTPRD splicing-dependent and may induce pre-synaptic differentiation. Interacts with NTRK2.
Subcellular location. Membrane. Cell membrane. Cell projection. Dendrite.
Tissue specificity. Expressed predominantly in the cerebral cortex of the brain but also at low levels in the spinal cord and medulla. Also expressed in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumors.
Disease relevance. Intellectual developmental disorder, X-linked 111 (XLID111) [MIM:301107] A neurodevelopmental disorder characterized by moderate to severe intellectual disability, delayed development, speech delay, and neuropsychiatric and behavioral problems such as anxiety, attention deficit-hyperactivity disorder and autism spectrum disorder. The disease is caused by variants affecting the gene represented in this entry.
Similarity. Belongs to the SLITRK family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9H156-1 | 1 | yes |
| Q9H156-2 | 2 |
RefSeq proteins (8): NP_001137475, NP_001137476, NP_001137477, NP_001137478, NP_001137480, NP_001137481, NP_001137482, NP_115928* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000372 | LRRNT | Domain |
| 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 (52 total): sequence variant 19, repeat 12, disulfide bond 4, domain 3, topological domain 2, region of interest 2, glycosylation site 2, splice variant 2, signal peptide 1, chain 1, compositionally biased region 1, modified residue 1, transmembrane region 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9H156-F1 | 67.16 | 0.26 |
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): 756
Disulfide bonds (4): 29–35, 33–46, 220–243, 222–263
Glycosylation sites (2): 84, 421
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-388844 | Receptor-type tyrosine-protein phosphatases |
| R-HSA-112316 | Neuronal System |
| R-HSA-6794362 | Protein-protein interactions at synapses |
MSigDB gene sets: 236 (showing top):
WWTAAGGC_UNKNOWN, HNF3ALPHA_Q6, GOBP_SYNAPSE_ASSEMBLY, TTTGTAG_MIR520D, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, FOXD3_01, COUP_01, NKX61_01, GOBP_CELL_CELL_ADHESION
GO Biological Process (5): axonogenesis (GO:0007409), regulation of synapse organization (GO:0050807), positive regulation of synapse assembly (GO:0051965), synaptic membrane adhesion (GO:0099560), regulation of presynapse assembly (GO:1905606)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (7): plasma membrane (GO:0005886), dendrite (GO:0030425), postsynaptic membrane (GO:0045211), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), membrane (GO:0016020), cell projection (GO:0042995)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Protein-protein interactions at synapses | 1 |
| Neuronal System | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| synapse organization | 2 |
| regulation of synapse assembly | 2 |
| synapse | 2 |
| cellular anatomical structure | 2 |
| cell morphogenesis involved in neuron differentiation | 1 |
| neuron projection morphogenesis | 1 |
| axon development | 1 |
| regulation of synapse structure or activity | 1 |
| regulation of cellular component organization | 1 |
| synapse assembly | 1 |
| positive regulation of nervous system development | 1 |
| positive regulation of cell junction assembly | 1 |
| cell-cell adhesion | 1 |
| presynapse assembly | 1 |
| regulation of presynapse organization | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| neuron projection | 1 |
| dendritic tree | 1 |
| synaptic membrane | 1 |
| postsynapse | 1 |
Protein interactions and networks
STRING
1440 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SLITRK2 | NPTX1 | Q15818 | 803 |
| SLITRK2 | PTPRS | Q13332 | 687 |
| SLITRK2 | IL1RAPL1 | Q9NZN1 | 678 |
| SLITRK2 | TBCD | Q9BTW9 | 675 |
| SLITRK2 | HDC | P19113 | 668 |
| SLITRK2 | IMMP2L | Q96T52 | 647 |
| SLITRK2 | PTPRD | P23468 | 589 |
| SLITRK2 | PTPRO | Q16827 | 557 |
| SLITRK2 | FMR1NB | Q8N0W7 | 550 |
| SLITRK2 | SGCE | O43556 | 548 |
| SLITRK2 | FMR1 | Q06787 | 545 |
| SLITRK2 | BAIAP2 | Q9UQB8 | 511 |
| SLITRK2 | CXorf51A | A0A1B0GTR3 | 507 |
| SLITRK2 | NTRK1 | P04629 | 507 |
| SLITRK2 | AFF2 | P51816 | 507 |
IntAct
0 interactions, top by confidence:
BioGRID (2): SLITRK2 (Synthetic Lethality), SLITRK2 (Proximity Label-MS)
ESM2 similar proteins: A1A4H9, A2ARI4, A6NDA9, B0BLW3, B4F7C5, D3ZAL8, D3ZTV3, D4A6D8, D4A7P2, E7FE13, F1MT22, O14498, O43155, O43300, P0DM44, P83286, Q149C3, Q5NVQ6, Q5R6B1, Q5R7M3, Q5RAC4, Q6PFC5, Q6RKD8, Q80WD0, Q80XG9, Q80ZD7, Q80ZD8, Q80ZD9, Q810C0, Q810C1, Q86SJ2, Q86UE6, Q86UN2, Q86VH4, Q86VH5, Q86WK6, Q8BGA3, Q8BLU0, Q8BZ81, Q8C2S7
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
143 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 2 |
| Uncertain significance | 88 |
| Likely benign | 14 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (2)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1334906 | NM_032539.5(SLITRK2):c.221T>C (p.Leu74Ser) | Likely pathogenic |
| 1334907 | NM_032539.5(SLITRK2):c.934A>G (p.Thr312Ala) | Likely pathogenic |
SpliceAI
832 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| X:145818413:CAG:C | donor_loss | 0.9900 |
| X:145818414:AG:A | donor_loss | 0.9900 |
| X:145818416:GTAG:G | donor_loss | 0.9900 |
| X:145819523:T:G | donor_gain | 0.9900 |
| X:145829328:T:G | acceptor_gain | 0.9700 |
| X:145818781:G:GT | donor_gain | 0.9600 |
| X:145819213:GAAAT:G | donor_gain | 0.9600 |
| X:145819214:A:T | donor_gain | 0.9600 |
| X:145818373:GCT:G | donor_gain | 0.9500 |
| X:145818501:G:GT | donor_gain | 0.9500 |
| X:145820533:CCAGG:C | donor_loss | 0.9500 |
| X:145820534:CAG:C | donor_loss | 0.9500 |
| X:145820535:AG:A | donor_loss | 0.9500 |
| X:145820536:GG:G | donor_loss | 0.9500 |
| X:145820537:G:GA | donor_loss | 0.9500 |
| X:145820538:T:G | donor_loss | 0.9500 |
| X:145820776:C:CG | donor_gain | 0.9500 |
| X:145822380:AAG:A | acceptor_gain | 0.9400 |
| X:145819031:TCC:T | donor_gain | 0.9300 |
| X:145820472:A:AG | acceptor_gain | 0.9300 |
| X:145820473:G:GG | acceptor_gain | 0.9300 |
| X:145821883:GT:G | donor_gain | 0.9300 |
| X:145822381:A:G | acceptor_gain | 0.9300 |
| X:145829341:A:AG | acceptor_gain | 0.9300 |
| X:145818412:GCAG:G | donor_gain | 0.9200 |
| X:145821704:C:CA | acceptor_gain | 0.9200 |
| X:145818571:C:T | donor_gain | 0.9100 |
| X:145818777:A:T | donor_gain | 0.9100 |
| X:145820468:TTGCA:T | acceptor_loss | 0.9100 |
| X:145820469:TGCA:T | acceptor_loss | 0.9100 |
AlphaMissense
5541 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| X:145822769:T:C | L115P | 1.000 |
| X:145822775:T:C | L117P | 1.000 |
| X:145822841:T:C | L139P | 1.000 |
| X:145822857:T:A | N144K | 1.000 |
| X:145822857:T:G | N144K | 1.000 |
| X:145822904:T:A | L160H | 1.000 |
| X:145822913:T:C | L163P | 1.000 |
| X:145822919:T:C | L165P | 1.000 |
| X:145822922:A:T | N166I | 1.000 |
| X:145822925:A:T | D167V | 1.000 |
| X:145822929:C:A | N168K | 1.000 |
| X:145822929:C:G | N168K | 1.000 |
| X:145822988:T:C | L188P | 1.000 |
| X:145822991:G:T | R189M | 1.000 |
| X:145822998:T:A | N191K | 1.000 |
| X:145822998:T:G | N191K | 1.000 |
| X:145823073:T:A | N216K | 1.000 |
| X:145823073:T:G | N216K | 1.000 |
| X:145823077:T:A | W218R | 1.000 |
| X:145823077:T:C | W218R | 1.000 |
| X:145823079:G:C | W218C | 1.000 |
| X:145823079:G:T | W218C | 1.000 |
| X:145823083:T:A | C220S | 1.000 |
| X:145823083:T:C | C220R | 1.000 |
| X:145823084:G:A | C220Y | 1.000 |
| X:145823084:G:C | C220S | 1.000 |
| X:145823085:C:G | C220W | 1.000 |
| X:145823113:T:A | W230R | 1.000 |
| X:145823113:T:C | W230R | 1.000 |
| X:145823115:G:C | W230C | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1001861008 (X:145824828 C>A,G,T), RS1001870773 (X:145825243 A>G), RS1002479083 (X:145816303 G>A), RS1002869356 (X:145826960 T>C), RS1003076670 (X:145818554 G>C), RS1004732276 (X:145822666 G>A,C), RS1005332798 (X:145825466 C>T), RS1005447188 (X:145816384 G>T), RS1005629705 (X:145825902 G>C,T), RS1005636059 (X:145816105 G>A), RS1006216314 (X:145828376 T>A), RS1006229490 (X:145818218 G>T), RS1006338948 (X:145827729 C>A,T), RS1006613353 (X:145817038 C>T), RS1006855753 (X:145818568 G>A,C)
Disease associations
OMIM: gene MIM:300561 | disease phenotypes: MIM:301107, MIM:233100
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| intellectual developmental disorder, X-linked 111 | Strong | X-linked |
ClinGen Gene-Disease Validity (1)
Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.
| Disease | Classification | Inheritance |
|---|---|---|
| X-linked complex neurodevelopmental disorder | Limited | XL |
Mondo (3): intellectual disability (MONDO:0001071), intellectual developmental disorder, X-linked 111 (MONDO:0957203), familial renal glucosuria (MONDO:0009297)
Orphanet (2): Familial renal glucosuria (Orphanet:69076), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)
HPO phenotypes
24 total (24 of 24 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000718 | Aggressive behavior |
| HP:0000722 | Compulsive behaviors |
| HP:0000729 | Autistic behavior |
| HP:0000739 | Anxiety |
| HP:0000750 | Delayed speech and language development |
| HP:0000752 | Hyperactivity |
| HP:0001249 | Intellectual disability |
| HP:0001250 | Seizure |
| HP:0001257 | Spasticity |
| HP:0001263 | Global developmental delay |
| HP:0001332 | Dystonia |
| HP:0001344 | Absent speech |
| HP:0001417 | X-linked inheritance |
| HP:0002119 | Ventriculomegaly |
| HP:0002317 | Unsteady gait |
| HP:0002751 | Kyphoscoliosis |
| HP:0003593 | Infantile onset |
| HP:0007371 | Corpus callosum atrophy |
| HP:0011968 | Feeding difficulties |
| HP:0033725 | Thin corpus callosum |
| HP:0034295 | Reduced cerebral white matter volume |
| HP:0100021 | Cerebral palsy |
| HP:0100035 | Phonic tics |
| HP:0410170 | Hippocampal atrophy |
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST009391_1318 | Metabolite levels | 5.000000e-06 |
| GCST009391_1320 | Metabolite levels | 7.000000e-06 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0010519 | pantothenic acid measurement |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D006030 | Glycosuria, Renal | C12.050.351.968.419.815.532; C12.050.351.968.934.363.450; C12.200.777.419.815.532; C12.200.777.934.363.450; C12.950.419.815.532; C12.950.934.363.450; C16.320.831.532; C18.452.394.937.450 |
| 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
13 total (human), top 13 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | increases expression, increases methylation | 2 |
| arsenite | decreases methylation | 1 |
| sodium arsenite | decreases expression | 1 |
| zinc chromate | increases expression, increases abundance | 1 |
| chromium hexavalent ion | increases abundance, increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| Gemcitabine | increases expression | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Folic Acid | increases expression | 1 |
| Lead | affects expression | 1 |
| Cadmium Chloride | increases abundance, increases expression | 1 |
| Copper Sulfate | increases expression | 1 |
Clinical trials (associated diseases)
197 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT05657860 | PHASE4 | COMPLETED | Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome |
| NCT05744479 | PHASE4 | RECRUITING | Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability |
| NCT06107829 | PHASE4 | WITHDRAWN | Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities |
| NCT06997198 | PHASE4 | NOT_YET_RECRUITING | Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities |
| NCT02270736 | PHASE3 | COMPLETED | Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability |
| NCT02304302 | PHASE2 | COMPLETED | Down Syndrome Memantine Follow-up Study |
| NCT03862950 | PHASE2 | COMPLETED | A Trial of Metformin in Individuals With Fragile X Syndrome (Met) |
| NCT04529226 | PHASE2 | UNKNOWN | Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis |
| NCT04821856 | PHASE2 | COMPLETED | Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability |
| NCT05273320 | PHASE1 | COMPLETED | Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities |
| NCT05301361 | PHASE1 | ENROLLING_BY_INVITATION | Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities |
| NCT06016764 | PHASE1 | COMPLETED | Use of MRI and cTBS for Catatonia in Autism |
| NCT06586827 | PHASE1 | COMPLETED | Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD |
| NCT07531940 | PHASE1 | NOT_YET_RECRUITING | Escalating Doses of Memantine in Down Syndrome (MEDS-123) |
| NCT03479476 | PHASE2/PHASE3 | COMPLETED | A Trial of Metformin in Individuals With Fragile X Syndrome |
| NCT02616796 | PHASE1/PHASE2 | COMPLETED | Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome |
| NCT06860672 | EARLY_PHASE1 | RECRUITING | Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation |
| NCT00597948 | Not specified | COMPLETED | Healthy Lifestyles for People With Intellectual Disabilities |
| NCT01087320 | Not specified | RECRUITING | Genome Medical Sequencing for Gene Discovery |
| NCT01652963 | Not specified | UNKNOWN | Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills |
| NCT01695395 | Not specified | COMPLETED | Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder |
| NCT01867554 | Not specified | COMPLETED | Research and Characterization of New Genes Involved in Intellectual Disability |
| NCT01915381 | Not specified | COMPLETED | Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities |
| NCT01988623 | Not specified | COMPLETED | Pivotal Response Treatment for Individuals With Intellectual Disabilities |
| NCT02099773 | Not specified | COMPLETED | Support Staff-client Interactions With Augmentative and Alternative Communication |
| NCT02136849 | Not specified | COMPLETED | Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic |
| NCT02225041 | Not specified | COMPLETED | Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood |
| NCT02414438 | Not specified | COMPLETED | Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study |
| NCT02451761 | Not specified | COMPLETED | Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability |
| NCT02461420 | Not specified | ACTIVE_NOT_RECRUITING | Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome |
| NCT02461459 | Not specified | ACTIVE_NOT_RECRUITING | Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC) |
| NCT02486081 | Not specified | COMPLETED | Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population |
| NCT02504502 | Not specified | COMPLETED | Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients |
| NCT02513277 | Not specified | COMPLETED | Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study |
| NCT02561754 | Not specified | COMPLETED | Weight Management for Adolescents With IDD |
| NCT02591446 | Not specified | COMPLETED | Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders |
| NCT02714868 | Not specified | COMPLETED | Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications) |
| NCT02721394 | Not specified | UNKNOWN | FCT With Young Children With ID in the UK: A Feasibility Project V.1 |
| NCT02746614 | Not specified | COMPLETED | Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability |
| NCT02836405 | Not specified | COMPLETED | TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders |
Related Atlas pages
- Associated diseases: intellectual developmental disorder, X-linked 111, X-linked complex neurodevelopmental disorder
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): familial renal glucosuria, intellectual developmental disorder, X-linked 111