SNAPC3
gene geneOn this page
Also known as SNAP50PTFbetaMGC33124MGC132011
Summary
SNAPC3 (small nuclear RNA activating complex polypeptide 3, HGNC:11136) is a protein-coding gene on chromosome 9p22.3, encoding snRNA-activating protein complex subunit 3 (Q92966). Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. It is a common-essential gene (DepMap: required in 97.9% of cancer cell lines).
Predicted to enable RNA polymerase III type 3 promoter sequence-specific DNA binding activity and bent DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and core promoter sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nuclear body and nucleolus.
Source: NCBI Gene 6619 — RefSeq curated summary.
At a glance
- Clinical variants (ClinVar): 82 total — 2 pathogenic
- Cancer dependency (DepMap): dependent in 97.9% of screened cell lines (common-essential)
- MANE Select transcript:
NM_001039697
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:11136 |
| Approved symbol | SNAPC3 |
| Name | small nuclear RNA activating complex polypeptide 3 |
| Location | 9p22.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | SNAP50, PTFbeta, MGC33124, MGC132011 |
| Ensembl gene | ENSG00000164975 |
| Ensembl biotype | protein_coding |
| OMIM | 602348 |
| Entrez | 6619 |
Gene structure
Transcript identifiers
Ensembl transcripts: 11 — 8 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined
ENST00000380799, ENST00000380821, ENST00000421710, ENST00000461041, ENST00000467062, ENST00000490969, ENST00000610884, ENST00000892142, ENST00000892143, ENST00000965147, ENST00000965148
RefSeq mRNA: 6 — MANE Select: NM_001039697
NM_001039697, NM_001369647, NM_001369648, NM_001369649, NM_001369650, NM_001369651
CCDS: CCDS6478
Canonical transcript exons
ENST00000380821 — 9 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001089083 | 15433552 | 15433636 |
| ENSE00001089086 | 15444602 | 15444706 |
| ENSE00001089102 | 15451320 | 15451402 |
| ENSE00001089104 | 15447095 | 15447244 |
| ENSE00001486427 | 15459719 | 15461626 |
| ENSE00001732177 | 15457960 | 15458067 |
| ENSE00001887040 | 15422876 | 15423193 |
| ENSE00002716594 | 15453041 | 15453205 |
| ENSE00003556953 | 15423909 | 15423986 |
Expression profiles
Bgee: expression breadth ubiquitous, 288 present calls, max score 93.88.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.9694 / max 270.0191, expressed in 1807 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 96145 | 28.9555 | 1807 |
| 96144 | 0.0139 | 4 |
Top tissues by expression
292 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ganglionic eminence | UBERON:0004023 | 93.88 | gold quality |
| ventricular zone | UBERON:0003053 | 93.75 | gold quality |
| adrenal tissue | UBERON:0018303 | 93.19 | gold quality |
| cortical plate | UBERON:0005343 | 92.58 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 92.40 | gold quality |
| left testis | UBERON:0004533 | 92.20 | gold quality |
| right testis | UBERON:0004534 | 92.18 | gold quality |
| heart right ventricle | UBERON:0002080 | 92.14 | gold quality |
| testis | UBERON:0000473 | 91.35 | gold quality |
| calcaneal tendon | UBERON:0003701 | 90.91 | gold quality |
| embryo | UBERON:0000922 | 90.27 | gold quality |
| biceps brachii | UBERON:0001507 | 90.07 | gold quality |
| sural nerve | UBERON:0015488 | 89.81 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 89.80 | gold quality |
| pons | UBERON:0000988 | 89.78 | gold quality |
| tendon | UBERON:0000043 | 88.90 | gold quality |
| medial globus pallidus | UBERON:0002477 | 88.86 | gold quality |
| adult organism | UBERON:0007023 | 88.71 | gold quality |
| right coronary artery | UBERON:0001625 | 88.30 | gold quality |
| rectum | UBERON:0001052 | 88.11 | gold quality |
| endometrium | UBERON:0001295 | 88.10 | gold quality |
| monocyte | CL:0000576 | 87.88 | gold quality |
| popliteal artery | UBERON:0002250 | 87.88 | gold quality |
| tibial artery | UBERON:0007610 | 87.87 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 87.84 | gold quality |
| aorta | UBERON:0000947 | 87.76 | gold quality |
| colonic epithelium | UBERON:0000397 | 87.68 | gold quality |
| thoracic aorta | UBERON:0001515 | 87.66 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 87.60 | gold quality |
| globus pallidus | UBERON:0001875 | 87.58 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.31 |
| E-GEOD-124858 | no | 114.53 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
86 targeting SNAPC3, 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-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-9-3P | 99.96 | 70.88 | 2068 |
| HSA-MIR-144-3P | 99.94 | 73.98 | 2698 |
| HSA-MIR-9983-3P | 99.94 | 71.48 | 3631 |
| HSA-MIR-3143 | 99.93 | 71.96 | 3104 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-1273H-5P | 99.77 | 66.32 | 2471 |
| HSA-MIR-1299 | 99.77 | 71.24 | 2389 |
| HSA-MIR-320A-3P | 99.77 | 69.73 | 2107 |
| HSA-MIR-320B | 99.77 | 69.73 | 2107 |
| HSA-MIR-320C | 99.77 | 69.73 | 2107 |
| HSA-MIR-320D | 99.77 | 69.73 | 2107 |
| HSA-MIR-4429 | 99.77 | 69.62 | 2111 |
| HSA-MIR-6885-3P | 99.75 | 70.36 | 3187 |
| HSA-MIR-4306 | 99.72 | 70.50 | 3630 |
| HSA-MIR-30B-3P | 99.70 | 65.76 | 2325 |
| HSA-MIR-3689A-3P | 99.70 | 65.73 | 2306 |
| HSA-MIR-3689B-3P | 99.70 | 65.71 | 2311 |
| HSA-MIR-3689C | 99.70 | 65.71 | 2311 |
| HSA-MIR-6779-5P | 99.70 | 65.76 | 2363 |
| HSA-MIR-587 | 99.64 | 70.86 | 2611 |
| HSA-MIR-548AV-5P | 99.60 | 70.84 | 2107 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 97.9% of screened cell lines, common-essential.
Literature-anchored findings (GeneRIF, showing 1)
- SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC (PMID:16901896)
Cross-species orthologs
8 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | snapc3 | ENSDARG00000101474 |
| mus_musculus | Snapc3 | ENSMUSG00000028483 |
| rattus_norvegicus | Snapc3 | ENSRNOG00000010825 |
| drosophila_melanogaster | Pbp49 | FBGN0260398 |
| caenorhabditis_elegans | WBGENE00011367 | |
| caenorhabditis_elegans | WBGENE00015098 | |
| caenorhabditis_elegans | snpc-3.2 | WBGENE00021667 |
| caenorhabditis_elegans | Y48G1BL.8 | WBGENE00255594 |
Protein
Protein identifiers
snRNA-activating protein complex subunit 3 — Q92966 (reviewed: Q92966)
Alternative names: Proximal sequence element-binding transcription factor subunit beta, Small nuclear RNA-activating complex polypeptide 3, snRNA-activating protein complex 50 kDa subunit
All UniProt accessions (3): Q92966, Q5T282, Q5T284
UniProt curated annotations — full annotation on UniProt →
Function. Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box.
Subunit / interactions. Part of the SNAPc complex composed of 5 subunits: SNAPC1, SNAPC2, SNAPC3, SNAPC4 and SNAPC5. SNAPC3 interacts with SNAPC1.
Subcellular location. Nucleus.
Similarity. Belongs to the SNAPC3/SRD2 family.
RefSeq proteins (6): NP_001034786, NP_001356576, NP_001356577, NP_001356578, NP_001356579, NP_001356580 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR022042 | snRNA-activating_su3 | Family |
Pfam: PF12251
UniProt features (42 total): strand 21, helix 11, turn 6, region of interest 2, chain 1, sequence variant 1
Structure
Experimental structures (PDB)
18 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 7ZWD | ELECTRON MICROSCOPY | 3 |
| 7ZX8 | ELECTRON MICROSCOPY | 3 |
| 9K3U | ELECTRON MICROSCOPY | 3 |
| 7ZWC | ELECTRON MICROSCOPY | 3.2 |
| 9FSO | ELECTRON MICROSCOPY | 3.28 |
| 9LXN | ELECTRON MICROSCOPY | 3.3 |
| 9FSP | ELECTRON MICROSCOPY | 3.39 |
| 7ZX7 | ELECTRON MICROSCOPY | 3.4 |
| 8IUH | ELECTRON MICROSCOPY | 3.4 |
| 7XUR | ELECTRON MICROSCOPY | 3.49 |
| 7ZXE | ELECTRON MICROSCOPY | 3.5 |
| 9K3V | ELECTRON MICROSCOPY | 3.5 |
| 9FSQ | ELECTRON MICROSCOPY | 3.51 |
| 9FSR | ELECTRON MICROSCOPY | 3.76 |
| 8ITY | ELECTRON MICROSCOPY | 3.9 |
| 8IUE | ELECTRON MICROSCOPY | 4.1 |
| 9FSS | ELECTRON MICROSCOPY | 4.14 |
| 9K3B | ELECTRON MICROSCOPY | 4.8 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q92966-F1 | 85.10 | 0.53 |
Function
Pathways and Gene Ontology
Reactome pathways
7 pathways
| ID | Pathway |
|---|---|
| R-HSA-6807505 | RNA polymerase II transcribes snRNA genes |
| R-HSA-749476 | RNA Polymerase III Abortive And Retractive Initiation |
| R-HSA-76071 | RNA Polymerase III Transcription Initiation From Type 3 Promoter |
| R-HSA-73857 | RNA Polymerase II Transcription |
| R-HSA-74158 | RNA Polymerase III Transcription |
| R-HSA-74160 | Gene expression (Transcription) |
| R-HSA-76046 | RNA Polymerase III Transcription Initiation |
MSigDB gene sets: 144 (showing top):
REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER, GOZGIT_ESR1_TARGETS_DN, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, AACWWCAANK_UNKNOWN, GCM_NF2, BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, DANG_BOUND_BY_MYC, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, PARENT_MTOR_SIGNALING_UP, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX, MARSON_BOUND_BY_FOXP3_STIMULATED, BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP, BENPORATH_MYC_MAX_TARGETS
GO Biological Process (5): transcription by RNA polymerase II (GO:0006366), transcription by RNA polymerase III (GO:0006383), snRNA transcription (GO:0009301), snRNA transcription by RNA polymerase II (GO:0042795), snRNA transcription by RNA polymerase III (GO:0042796)
GO Molecular Function (7): RNA polymerase III general transcription initiation factor activity (GO:0000995), RNA polymerase III type 3 promoter sequence-specific DNA binding (GO:0001006), DNA binding (GO:0003677), bent DNA binding (GO:0003681), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), core promoter sequence-specific DNA binding (GO:0001046), protein binding (GO:0005515)
GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), nuclear body (GO:0016604), snRNA-activating protein complex (GO:0019185)
Reactome top-level categories
Rollup of top-4 pathways:
| Category | Pathways |
|---|---|
| RNA Polymerase III Transcription | 2 |
| Gene expression (Transcription) | 2 |
| RNA Polymerase II Transcription | 1 |
| RNA Polymerase III Transcription Initiation | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| DNA-templated transcription | 3 |
| snRNA transcription | 2 |
| transcription by RNA polymerase III | 2 |
| nuclear lumen | 2 |
| intracellular membraneless organelle | 2 |
| snRNA metabolic process | 1 |
| transcription by RNA polymerase II | 1 |
| general transcription initiation factor activity | 1 |
| RNA polymerase III cis-regulatory region sequence-specific DNA binding | 1 |
| nucleic acid binding | 1 |
| DNA binding | 1 |
| RNA polymerase II transcription regulatory region sequence-specific DNA binding | 1 |
| cis-regulatory region sequence-specific DNA binding | 1 |
| transcription cis-regulatory region binding | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
| nucleoplasm | 1 |
| transcription regulator complex | 1 |
Protein interactions and networks
STRING
1244 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SNAPC3 | SNAPC1 | Q16533 | 999 |
| SNAPC3 | SNAPC2 | Q13487 | 999 |
| SNAPC3 | SNAPC4 | Q5SXM2 | 997 |
| SNAPC3 | SNAPC5 | O75971 | 983 |
| SNAPC3 | TBP | P20226 | 806 |
| SNAPC3 | TAF1A | Q15573 | 681 |
| SNAPC3 | POLI | Q9UNA4 | 597 |
| SNAPC3 | ZNF488 | Q96MN9 | 548 |
| SNAPC3 | LSM8 | O95777 | 537 |
| SNAPC3 | CCDC171 | Q6TFL3 | 475 |
| SNAPC3 | ASXL1 | Q8IXJ9 | 473 |
| SNAPC3 | TAF1D | Q9H5J8 | 465 |
| SNAPC3 | MNMIP1 | A4FU49 | 451 |
| SNAPC3 | TNPO3 | Q9Y5L0 | 449 |
| SNAPC3 | SHISA4 | Q96DD7 | 448 |
IntAct
80 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SNAPC1 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.850 |
| SNAPC1 | SNAPC3 | psi-mi:“MI:0914”(association) | 0.850 |
| SNAPC4 | SNAPC1 | psi-mi:“MI:0914”(association) | 0.790 |
| SNAPC1 | SNAPC5 | psi-mi:“MI:0914”(association) | 0.740 |
| SNAPC1 | SNAPC5 | psi-mi:“MI:0915”(physical association) | 0.740 |
| HSD17B14 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.670 |
| SNAPC3 | HSD17B14 | psi-mi:“MI:0915”(physical association) | 0.670 |
| CEP57L1 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC3 | CEP57L1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TTC4 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NFKBID | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| UBE3A | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ZNF620 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC3 | KATNBL1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNRNP35 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| SNAPC3 | HSPB1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NEFL | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC3 | WFS1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC3 | KIF1B | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (64): HSD17B14 (Two-hybrid), CEP57L1 (Two-hybrid), SNAPC3 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), SNAPC3 (Two-hybrid), SNAPC3 (Two-hybrid), SNAPC3 (Two-hybrid), NFKBID (Two-hybrid), ZNF620 (Two-hybrid), SNRNP35 (Two-hybrid), TTC4 (Two-hybrid), SNAPC3 (Two-hybrid)
ESM2 similar proteins: A0A087WRI3, A2AIP0, A4IFQ0, A8MTA8, H3BNL1, O70373, O95983, P21580, P55199, Q0VB26, Q1JQA1, Q1RMS8, Q2TA11, Q2TBR5, Q3B7L5, Q3ZK22, Q4R6Y6, Q4R8W3, Q4VA36, Q5RFL7, Q5XI52, Q60769, Q62522, Q68FX7, Q69Z89, Q6ZQR2, Q702N8, Q76JQ2, Q7Z6J9, Q86UT8, Q8CEG5, Q8CHQ0, Q8IW40, Q8N1D5, Q8N6G2, Q8N801, Q8NFG4, Q8QZS3, Q91Z62, Q91ZP9
Diamond homologs: Q4R6Y6, Q5BK68, Q5E9M5, Q8L627, Q92966, Q9D2C9
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| SNAPC3 | “form complex” | SNAPC | binding |
Disease & clinical
Clinical variants and AI predictions
ClinVar
82 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 2 |
| Likely pathogenic | 0 |
| Uncertain significance | 67 |
| Likely benign | 3 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (2)
| Variant ID | HGVS | Classification |
|---|---|---|
| 562130 | GRCh37/hg19 9p23-22.2(chr9:14178768-16619009)x1 | Pathogenic |
| 59101 | GRCh38/hg38 9p23-22.2(chr9:11818291-17963882)x1 | Pathogenic |
SpliceAI
1797 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 9:15423907:A:AG | acceptor_gain | 1.0000 |
| 9:15423908:G:GG | acceptor_gain | 1.0000 |
| 9:15423908:GCCTT:G | acceptor_gain | 1.0000 |
| 9:15423987:G:GA | donor_loss | 1.0000 |
| 9:15433540:C:G | acceptor_gain | 1.0000 |
| 9:15433547:AACAG:A | acceptor_gain | 1.0000 |
| 9:15433550:AG:A | acceptor_gain | 1.0000 |
| 9:15433551:GG:G | acceptor_gain | 1.0000 |
| 9:15433633:GATG:G | donor_gain | 1.0000 |
| 9:15444597:TTCAG:T | acceptor_loss | 1.0000 |
| 9:15444598:TCAG:T | acceptor_loss | 1.0000 |
| 9:15444598:TCAGG:T | acceptor_gain | 1.0000 |
| 9:15444599:CAGG:C | acceptor_gain | 1.0000 |
| 9:15444600:A:AG | acceptor_gain | 1.0000 |
| 9:15444600:A:C | acceptor_loss | 1.0000 |
| 9:15444600:AG:A | acceptor_gain | 1.0000 |
| 9:15444600:AGGA:A | acceptor_gain | 1.0000 |
| 9:15444601:G:A | acceptor_gain | 1.0000 |
| 9:15444601:G:GA | acceptor_gain | 1.0000 |
| 9:15444601:G:T | acceptor_loss | 1.0000 |
| 9:15444601:GGA:G | acceptor_gain | 1.0000 |
| 9:15444601:GGAG:G | acceptor_gain | 1.0000 |
| 9:15444601:GGAGT:G | acceptor_gain | 1.0000 |
| 9:15444702:ATAAG:A | donor_gain | 1.0000 |
| 9:15444703:TAAG:T | donor_gain | 1.0000 |
| 9:15444704:AAG:A | donor_gain | 1.0000 |
| 9:15444705:AG:A | donor_gain | 1.0000 |
| 9:15444705:AGG:A | donor_loss | 1.0000 |
| 9:15444706:GG:G | donor_gain | 1.0000 |
| 9:15444707:G:GG | donor_gain | 1.0000 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000037035 (9:15443854 A>G), RS1000141949 (9:15439421 C>G,T), RS1000184641 (9:15432547 T>C), RS1000221548 (9:15435155 C>A,T), RS1000257620 (9:15430899 A>G), RS1000302981 (9:15464403 A>G,T), RS1000362100 (9:15426068 G>C,T), RS1000382412 (9:15448963 T>C), RS1000394004 (9:15422327 C>G,T), RS1000416291 (9:15426237 C>G,T), RS1000502696 (9:15445506 A>G,T), RS1000539947 (9:15441390 T>TTTC), RS1000664276 (9:15440571 G>A,T), RS1000673489 (9:15436662 T>C), RS1000721926 (9:15435444 C>T)
Disease associations
OMIM: gene MIM:602348 | 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
0 associations (top):
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
33 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, decreases expression, increases expression | 5 |
| sodium arsenite | affects cotreatment, increases abundance, increases expression, affects expression | 2 |
| entinostat | decreases expression, affects cotreatment | 2 |
| Aflatoxin B1 | decreases methylation, increases expression, increases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| bisphenol F | affects cotreatment, decreases expression | 1 |
| methylmercuric chloride | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| titanium dioxide | decreases expression | 1 |
| manganese chloride | increases expression, affects cotreatment, increases abundance | 1 |
| K 7174 | 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 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| Temozolomide | increases expression | 1 |
| Sunitinib | increases expression | 1 |
| Air Pollutants, Occupational | decreases expression | 1 |
| Arsenic | affects cotreatment, increases abundance, increases expression | 1 |
| Atrazine | decreases expression | 1 |
| Benzo(a)pyrene | decreases methylation | 1 |
| Carmustine | increases expression | 1 |
| Cisplatin | increases response to substance | 1 |
| Coumestrol | decreases expression | 1 |
| Dexamethasone | affects cotreatment, decreases expression | 1 |
| Dimethyl Sulfoxide | increases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Hydrogen Peroxide | increases expression | 1 |
| Indomethacin | affects cotreatment, decreases expression | 1 |
| Manganese | affects cotreatment, increases abundance, increases expression | 1 |
| Nickel | decreases expression | 1 |
| Nicotine | 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.