GPM6B
gene geneOn this page
Also known as M6BMGC17150MGC54284
Summary
GPM6B (glycoprotein M6B, HGNC:4461) is a protein-coding gene on chromosome Xp22.2, encoding Neuronal membrane glycoprotein M6-b (Q13491). May be involved in neural development.
This gene encodes a membrane glycoprotein that belongs to the proteolipid protein family. Proteolipid protein family members are expressed in most brain regions and are thought to be involved in cellular housekeeping functions such as membrane trafficking and cell-to-cell communication. This protein may also be involved in osteoblast differentiation. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are located on chromosomes Y and 22.
Source: NCBI Gene 2824 — RefSeq curated summary.
At a glance
- GWAS associations: 2
- Clinical variants (ClinVar): 103 total
- MANE Select transcript:
NM_001001995
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:4461 |
| Approved symbol | GPM6B |
| Name | glycoprotein M6B |
| Location | Xp22.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | M6B, MGC17150, MGC54284 |
| Ensembl gene | ENSG00000046653 |
| Ensembl biotype | protein_coding |
| OMIM | 300051 |
| Entrez | 2824 |
Gene structure
Transcript identifiers
Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined
ENST00000316715, ENST00000355135, ENST00000356942, ENST00000398361, ENST00000454189, ENST00000468080, ENST00000472735, ENST00000475307, ENST00000493085, ENST00000493677, ENST00000495211
RefSeq mRNA: 5 — MANE Select: NM_001001995
NM_001001994, NM_001001995, NM_001001996, NM_001318729, NM_005278
CCDS: CCDS14158, CCDS35206, CCDS35207, CCDS48084
Canonical transcript exons
ENST00000316715 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000665456 | 13776238 | 13776303 |
| ENSE00000840448 | 13777352 | 13777425 |
| ENSE00000840449 | 13779818 | 13779989 |
| ENSE00001256001 | 13770939 | 13773030 |
| ENSE00001814264 | 13816844 | 13817093 |
| ENSE00003617141 | 13785622 | 13785808 |
| ENSE00003667413 | 13807650 | 13807769 |
| ENSE00003673184 | 13783365 | 13783521 |
Expression profiles
Bgee: expression breadth ubiquitous, 283 present calls, max score 99.95.
FANTOM5 (CAGE): breadth broad, TPM avg 51.9268 / max 4033.3656, expressed in 680 samples.
FANTOM5 promoters (16 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 198502 | 33.2292 | 647 |
| 198487 | 12.7159 | 321 |
| 198504 | 1.2174 | 290 |
| 198503 | 1.1579 | 296 |
| 198492 | 0.7599 | 125 |
| 198488 | 0.4525 | 118 |
| 198483 | 0.4126 | 125 |
| 198501 | 0.3996 | 158 |
| 198493 | 0.3187 | 113 |
| 198506 | 0.2967 | 189 |
Top tissues by expression
293 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| lateral globus pallidus | UBERON:0002476 | 99.95 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 99.95 | gold quality |
| inferior olivary complex | UBERON:0002127 | 99.94 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 99.94 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 99.92 | gold quality |
| CA1 field of hippocampus | UBERON:0003881 | 99.92 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 99.91 | gold quality |
| medulla oblongata | UBERON:0001896 | 99.90 | gold quality |
| cranial nerve II | UBERON:0000941 | 99.89 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 99.88 | gold quality |
| postcentral gyrus | UBERON:0002581 | 99.88 | gold quality |
| parietal lobe | UBERON:0001872 | 99.86 | gold quality |
| ventral tegmental area | UBERON:0002691 | 99.86 | gold quality |
| pons | UBERON:0000988 | 99.85 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 99.84 | gold quality |
| globus pallidus | UBERON:0001875 | 99.82 | gold quality |
| corpus callosum | UBERON:0002336 | 99.82 | gold quality |
| entorhinal cortex | UBERON:0002728 | 99.80 | gold quality |
| medial globus pallidus | UBERON:0002477 | 99.79 | gold quality |
| lateral nuclear group of thalamus | UBERON:0002736 | 99.79 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 99.74 | gold quality |
| olfactory bulb | UBERON:0002264 | 99.73 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 99.72 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 99.71 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 99.71 | gold quality |
| middle frontal gyrus | UBERON:0002702 | 99.70 | gold quality |
| spinal cord | UBERON:0002240 | 99.65 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 99.64 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 99.63 | gold quality |
| endothelial cell | CL:0000115 | 99.62 | gold quality |
Single-cell (SCXA)
Detected in 26 experiment(s), a significant marker in 24.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-137537 | yes | 3429.53 |
| E-MTAB-8410 | yes | 3362.11 |
| E-CURD-126 | yes | 3154.97 |
| E-GEOD-124263 | yes | 3106.18 |
| E-GEOD-93593 | yes | 3010.74 |
| E-HCAD-5 | yes | 2443.87 |
| E-MTAB-11121 | yes | 1778.69 |
| E-HCAD-11 | yes | 1753.54 |
| E-GEOD-135922 | yes | 1339.19 |
| E-CURD-79 | yes | 809.48 |
| E-MTAB-9154 | yes | 606.14 |
| E-MTAB-7407 | yes | 543.95 |
| E-ANND-5 | yes | 484.95 |
| E-HCAD-35 | yes | 110.35 |
| E-HCAD-25 | yes | 69.17 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
87 targeting GPM6B, 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-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-548N | 99.98 | 71.94 | 4170 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-548AN | 99.97 | 70.91 | 2817 |
| HSA-MIR-590-3P | 99.96 | 74.34 | 6478 |
| HSA-MIR-493-5P | 99.96 | 72.47 | 2382 |
| HSA-MIR-141-3P | 99.94 | 72.79 | 2421 |
| HSA-MIR-200A-3P | 99.94 | 72.68 | 2420 |
| HSA-MIR-652-5P | 99.91 | 67.49 | 505 |
| HSA-MIR-4697-3P | 99.89 | 67.09 | 1123 |
| HSA-MIR-153-5P | 99.89 | 73.86 | 6317 |
| HSA-MIR-579-3P | 99.86 | 71.66 | 3628 |
| HSA-MIR-4728-5P | 99.85 | 69.39 | 4718 |
| HSA-MIR-544A | 99.84 | 68.66 | 1965 |
| HSA-MIR-664B-3P | 99.84 | 71.65 | 3590 |
| HSA-MIR-6785-5P | 99.82 | 68.68 | 4428 |
| HSA-MIR-3121-3P | 99.82 | 71.96 | 3630 |
| HSA-MIR-202-5P | 99.78 | 67.65 | 991 |
| HSA-MIR-1299 | 99.77 | 71.24 | 2389 |
| HSA-MIR-4658 | 99.77 | 64.94 | 514 |
| HSA-MIR-6790-5P | 99.77 | 65.24 | 505 |
| HSA-MIR-4524A-3P | 99.72 | 66.85 | 2406 |
| HSA-MIR-149-3P | 99.72 | 68.22 | 3963 |
| HSA-MIR-1208 | 99.70 | 68.28 | 1533 |
| HSA-MIR-1283 | 99.69 | 72.42 | 3009 |
Literature-anchored findings (GeneRIF, showing 9)
- it is unlikely that mutations in M6B have a role in Pelizaeus-Merzbacher-like syndrome, as examined in eight patients (PMID:15214007)
- Data suggest that M6B regulates serotonin uptake by affecting cellular trafficking of the serotonin transporter. (PMID:18581270)
- Microarray expression analysis of GPM6B-depleted osteogenic human mesenchymal stem cells revealed significant changes in genes involved in cytoskeleton organization and biogenesis. (PMID:21638316)
- Data show the Differences in high resolution melting analysis in promoters of tumor markers neuronal membrane glycoprotein M6-B, melanoma antigen family A12 and immunoglobulin superfamily Fc receptor indicated invasiveness of hepatocellular carcinoma. (PMID:23950870)
- Circulating levels of DR6 and Gpm6B correlate with breast cancer tumor grade. (PMID:24696529)
- Data indicate that neuronal membrane glycoproteins GPM6A and GPM6B may act as novel oncogenes in the development of lymphoid leukemia. (PMID:24916915)
- Increase in the expression levels of mRNA and protein for the Gpm6B is associated with various types of gynaecological malignancy. (PMID:25113253)
- Findings demonstrate that GPM6B plays a crucial role in SMC differentiation and regulates SMC differentiation through the activation of TGF-beta-Smad2/3 signaling via direct interactions with TbetaRI. (PMID:30372567)
- GPM6B Inhibit PCa Proliferation by Blocking Prostate Cancer Cell Serotonin Absorptive Capacity. (PMID:33294057)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | gpm6bb | ENSDARG00000001676 |
| mus_musculus | Gpm6b | ENSMUSG00000031342 |
| rattus_norvegicus | Gpm6b | ENSRNOG00000004613 |
| drosophila_melanogaster | M6 | FBGN0037092 |
| caenorhabditis_elegans | WBGENE00017437 |
Paralogs (2): PLP1 (ENSG00000123560), GPM6A (ENSG00000150625)
Protein
Protein identifiers
Neuronal membrane glycoprotein M6-b — Q13491 (reviewed: Q13491)
All UniProt accessions (6): B7Z248, B7Z613, C9J028, C9J8H8, Q13491, C9JZE8
UniProt curated annotations — full annotation on UniProt →
Function. May be involved in neural development. Involved in regulation of osteoblast function and bone formation. Involved in matrix vesicle release by osteoblasts; this function seems to involve maintenance of the actin cytoskeleton. May be involved in cellular trafficking of SERT and thereby in regulation of serotonin uptake.
Subunit / interactions. Interacts with SERT.
Subcellular location. Cell membrane.
Tissue specificity. Neurons and glia; cerebellar Bergmann glia, in glia within white matter tracts of the cerebellum and cerebrum, and in embryonic dorsal root ganglia.
Similarity. Belongs to the myelin proteolipid protein family.
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q13491-1 | 1, A | yes |
| Q13491-2 | 2, B | |
| Q13491-3 | 3 | |
| Q13491-4 | 4 |
RefSeq proteins (5): NP_001001994, NP_001001995, NP_001001996, NP_001305658, NP_005269 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001614 | Myelin_PLP | Family |
| IPR018237 | Myelin_PLP_CS | Conserved_site |
Pfam: PF01275
UniProt features (12 total): transmembrane region 4, splice variant 3, modified residue 2, glycosylation site 2, chain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q13491-F1 | 82.28 | 0.39 |
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 (2): 318, 257
Glycosylation sites (2): 73, 177
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 397 (showing top):
ATF_B, VERHAAK_AML_WITH_NPM1_MUTATED_DN, AGGAAGC_MIR5163P, GCM_MAP4K4, BENPORATH_ES_WITH_H3K27ME3, GOBP_NEUROTRANSMITTER_UPTAKE, ZHAN_MULTIPLE_MYELOMA_MF_UP, TTTGTAG_MIR520D, GOBP_FOCAL_ADHESION_ASSEMBLY, AAGCCAT_MIR135A_MIR135B, GOBP_GLIAL_CELL_DEVELOPMENT, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_EXTRACELLULAR_MATRIX_ASSEMBLY
GO Biological Process (12): ossification (GO:0001503), nervous system development (GO:0007399), protein transport (GO:0015031), central nervous system myelination (GO:0022010), positive regulation of bone mineralization (GO:0030501), regulation of actin cytoskeleton organization (GO:0032956), negative regulation of serotonin uptake (GO:0051612), regulation of focal adhesion assembly (GO:0051893), axon development (GO:0061564), extracellular matrix assembly (GO:0085029), negative regulation of protein localization to cell surface (GO:2000009), cell differentiation (GO:0030154)
GO Molecular Function (2): structural constituent of myelin sheath (GO:0019911), protein binding (GO:0005515)
GO Cellular Component (4): plasma membrane (GO:0005886), myelin sheath (GO:0043209), membrane raft (GO:0045121), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 2 |
| multicellular organismal process | 1 |
| system development | 1 |
| transport | 1 |
| intracellular protein localization | 1 |
| establishment of protein localization | 1 |
| oligodendrocyte development | 1 |
| axon ensheathment in central nervous system | 1 |
| myelination | 1 |
| bone mineralization | 1 |
| regulation of bone mineralization | 1 |
| positive regulation of ossification | 1 |
| positive regulation of biomineral tissue development | 1 |
| actin cytoskeleton organization | 1 |
| regulation of actin filament-based process | 1 |
| regulation of cytoskeleton organization | 1 |
| negative regulation of neurotransmitter uptake | 1 |
| serotonin uptake | 1 |
| regulation of serotonin uptake | 1 |
| regulation of cell-matrix adhesion | 1 |
| focal adhesion assembly | 1 |
| regulation of cell-substrate junction assembly | 1 |
| neuron projection development | 1 |
| cellular component assembly | 1 |
| extracellular matrix organization | 1 |
| protein localization to cell surface | 1 |
| negative regulation of protein localization | 1 |
| regulation of protein localization to cell surface | 1 |
| cellular developmental process | 1 |
| structural molecule activity | 1 |
| myelin sheath | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| membrane microdomain | 1 |
Protein interactions and networks
STRING
1120 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| GPM6B | GDI1 | P31150 | 691 |
| GPM6B | NTNG2 | Q96CW9 | 685 |
| GPM6B | NTNG1 | Q9Y2I2 | 668 |
| GPM6B | GRPR | P30550 | 651 |
| GPM6B | GLRA2 | P23416 | 650 |
| GPM6B | GLUD2 | P49448 | 647 |
| GPM6B | HCCS | P53701 | 602 |
| GPM6B | TRAPPC2 | P0DI81 | 582 |
| GPM6B | CDKL5 | O76039 | 552 |
| GPM6B | SLC6A4 | P31645 | 545 |
| GPM6B | PTPRZ1 | P23471 | 515 |
| GPM6B | GLDN | Q6ZMI3 | 505 |
| GPM6B | RAB9A | P51151 | 491 |
| GPM6B | NRCAM | Q92823 | 490 |
| GPM6B | OFD1 | O75665 | 453 |
IntAct
15 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| EGFR | GPM6B | psi-mi:“MI:0915”(physical association) | 0.550 |
| ADGRG5 | KLRG2 | psi-mi:“MI:0914”(association) | 0.530 |
| NUFIP1 | PDE2A | psi-mi:“MI:0914”(association) | 0.530 |
| GPM6B | NME2P1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| MTNR1B | GPM6B | psi-mi:“MI:0915”(physical association) | 0.370 |
| ERBB2 | GPM6B | psi-mi:“MI:0915”(physical association) | 0.370 |
| SLC6A4 | GPM6B | psi-mi:“MI:0915”(physical association) | 0.370 |
| MAPT | SHTN1 | psi-mi:“MI:0914”(association) | 0.350 |
| HAX1 | DNM1L | psi-mi:“MI:0914”(association) | 0.350 |
| GPM6B | TM9SF1 | psi-mi:“MI:0914”(association) | 0.350 |
| SLC44A1 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (35): GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), GPM6B (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), GPM6B (Two-hybrid), STX1A (Two-hybrid), ERGIC3 (Two-hybrid), GPM6B (Two-hybrid), GPM6B (Proximity Label-MS)
ESM2 similar proteins: A0A2R8RY99, A0PK11, A9UL59, B2RVW2, B4L184, B4LC58, B4N5D3, D3ZFW5, O95473, P23290, P35801, P35802, P35803, P36964, P36965, P51674, P56749, P58418, P79826, Q0IIL2, Q0P4G7, Q0VD07, Q11085, Q13491, Q2YDD6, Q53R12, Q5R603, Q5R9K1, Q5R9Q3, Q5R9R3, Q5T9L3, Q5ZLR1, Q6AYR5, Q6CRM6, Q6DID7, Q6P689, Q6UX40, Q754N9, Q7YWX7, Q812E9
Diamond homologs: P04116, P23289, P23290, P23294, P35801, P35802, P35803, P36963, P36964, P36965, P47789, P47790, P51674, P60201, P60202, P60203, P79826, Q0VD07, Q13491, Q5R603, Q5R6E6, Q5R9Q3, Q712P7, Q812E9, Q8HXW7, Q9JJK1
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
103 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 22 |
| Likely benign | 4 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1159 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| X:13776304:C:CC | acceptor_gain | 1.0000 |
| X:13777346:GTTTA:G | donor_loss | 1.0000 |
| X:13777347:TTTAC:T | donor_loss | 1.0000 |
| X:13777348:TTAC:T | donor_loss | 1.0000 |
| X:13777349:TA:T | donor_loss | 1.0000 |
| X:13777350:A:AG | donor_loss | 1.0000 |
| X:13777423:TAC:T | acceptor_gain | 1.0000 |
| X:13777426:C:T | acceptor_loss | 1.0000 |
| X:13777427:T:A | acceptor_loss | 1.0000 |
| X:13779986:CGAA:C | acceptor_gain | 1.0000 |
| X:13783517:GTATC:G | acceptor_gain | 1.0000 |
| X:13783518:TATC:T | acceptor_gain | 1.0000 |
| X:13783520:TC:T | acceptor_gain | 1.0000 |
| X:13783520:TCC:T | acceptor_loss | 1.0000 |
| X:13783521:CC:C | acceptor_gain | 1.0000 |
| X:13783522:C:CC | acceptor_gain | 1.0000 |
| X:13783522:CT:C | acceptor_loss | 1.0000 |
| X:13783523:T:C | acceptor_loss | 1.0000 |
| X:13785619:TA:T | donor_loss | 1.0000 |
| X:13785620:A:AC | donor_gain | 1.0000 |
| X:13785620:AC:A | donor_loss | 1.0000 |
| X:13785620:ACAC:A | donor_gain | 1.0000 |
| X:13785621:C:CG | donor_gain | 1.0000 |
| X:13785621:C:CT | donor_loss | 1.0000 |
| X:13785621:CA:C | donor_gain | 1.0000 |
| X:13785621:CACC:C | donor_gain | 1.0000 |
| X:13785621:CACCT:C | donor_gain | 1.0000 |
| X:13785804:GCAGC:G | acceptor_gain | 1.0000 |
| X:13785805:CAGC:C | acceptor_gain | 1.0000 |
| X:13785805:CAGCC:C | acceptor_gain | 1.0000 |
AlphaMissense
2158 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| X:13785731:C:A | G47W | 1.000 |
| X:13785751:G:T | A40D | 1.000 |
| X:13776239:A:G | L239P | 0.999 |
| X:13776257:C:T | G233D | 0.999 |
| X:13776258:C:G | G233R | 0.999 |
| X:13776263:C:T | G231E | 0.999 |
| X:13776264:C:G | G231R | 0.999 |
| X:13776264:C:T | G231R | 0.999 |
| X:13779956:A:G | W147R | 0.999 |
| X:13779956:A:T | W147R | 0.999 |
| X:13783445:C:G | G109R | 0.999 |
| X:13783456:A:G | L105P | 0.999 |
| X:13783466:C:G | G102R | 0.999 |
| X:13783466:C:T | G102R | 0.999 |
| X:13783492:C:T | G93E | 0.999 |
| X:13783493:C:G | G93R | 0.999 |
| X:13783493:C:T | G93R | 0.999 |
| X:13785716:A:G | C52R | 0.999 |
| X:13785730:C:T | G47E | 0.999 |
| X:13785731:C:G | G47R | 0.999 |
| X:13785731:C:T | G47R | 0.999 |
| X:13785757:A:G | L38P | 0.999 |
| X:13785769:G:T | P34H | 0.999 |
| X:13776242:G:T | A238D | 0.998 |
| X:13776284:A:G | L224P | 0.998 |
| X:13777365:C:T | C213Y | 0.998 |
| X:13779940:C:T | G152D | 0.998 |
| X:13779950:C:G | G149R | 0.998 |
| X:13783371:A:C | S133R | 0.998 |
| X:13783371:A:T | S133R | 0.998 |
dbSNP variants (sampled 300 via entrez): RS1000008602 (X:13890139 C>G,T), RS1000014315 (X:13884718 G>A), RS1000018045 (X:13776574 G>A), RS1000067885 (X:13787491 G>A), RS1000094085 (X:13794839 G>A), RS1000105423 (X:13903003 G>A), RS1000141596 (X:13915735 A>G), RS1000157684 (X:13903394 C>G,T), RS1000160465 (X:13829991 G>T), RS1000163493 (X:13793329 A>G), RS1000205980 (X:13807538 A>G), RS1000222772 (X:13939477 A>C,T), RS1000228090 (X:13890556 T>C), RS1000245394 (X:13787886 C>T), RS1000261572 (X:13849089 A>C)
Disease associations
OMIM: gene MIM:300051 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): intellectual disability (MONDO:0001071)
Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST005248_1 | Delayed reward discounting | 1.000000e-08 |
| GCST90011770_87 | Glaucoma (primary open-angle) | 2.000000e-10 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0008476 | delayed reward discounting measurement |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| 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
63 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, affects expression, decreases methylation | 5 |
| trichostatin A | affects cotreatment, increases expression | 3 |
| Benzo(a)pyrene | affects methylation, increases expression, increases methylation | 3 |
| Aflatoxin B1 | affects expression, decreases methylation, increases methylation | 3 |
| mercuric bromide | decreases expression, affects cotreatment | 2 |
| entinostat | affects cotreatment, increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| p-Chloromercuribenzoic Acid | affects cotreatment, decreases expression | 2 |
| testosterone enanthate | affects expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| lead acetate | decreases expression | 1 |
| sulforaphane | decreases expression | 1 |
| sodium arsenite | decreases expression | 1 |
| butyraldehyde | increases expression | 1 |
| chloroquine diphosphate | increases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| potassium chromate(VI) | increases expression | 1 |
| aflatoxin B2 | increases methylation | 1 |
| nickel sulfate | increases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | decreases expression, affects cotreatment | 1 |
| chromium hexavalent ion | increases 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 | affects cotreatment, increases expression, decreases expression | 1 |
| 2,2’,4,4’,5-brominated diphenyl ether | decreases expression | 1 |
| dorsomorphin | increases expression, decreases expression, affects cotreatment | 1 |
| NSC 689534 | affects binding, decreases expression | 1 |
| Temozolomide | increases expression | 1 |
| Decitabine | affects expression | 1 |
| Arsenic Trioxide | decreases expression | 1 |
| Bexarotene | 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
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.