MDGA2
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Summary
MDGA2 (MAM domain containing glycosylphosphatidylinositol anchor 2, HGNC:19835) is a protein-coding gene on chromosome 14q21.3, encoding MAM domain-containing glycosylphosphatidylinositol anchor protein 2 (Q7Z553). May be involved in cell-cell interactions.
Predicted to be involved in regulation of synapse organization and spinal cord motor neuron differentiation. Predicted to act upstream of or within several processes, including motor behavior; negative regulation of neuron apoptotic process; and neuron migration. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic density membrane.
Source: NCBI Gene 161357 — RefSeq curated summary.
At a glance
- GWAS associations: 18
- Clinical variants (ClinVar): 62 total — 1 likely-pathogenic
- Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
- MANE Select transcript:
NM_001113498
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:19835 |
| Approved symbol | MDGA2 |
| Name | MAM domain containing glycosylphosphatidylinositol anchor 2 |
| Location | 14q21.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000139915 |
| Ensembl biotype | protein_coding |
| OMIM | 611128 |
| Entrez | 161357 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 4 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined
ENST00000357362, ENST00000399232, ENST00000472499, ENST00000482848, ENST00000486952, ENST00000554762, ENST00000555521, ENST00000557238, ENST00000557516
RefSeq mRNA: 2 — MANE Select: NM_001113498
NM_001113498, NM_182830
CCDS: CCDS41948, CCDS45098
Canonical transcript exons
ENST00000399232 — 17 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001430877 | 47674517 | 47675605 |
| ENSE00001537098 | 46840092 | 46842019 |
| ENSE00003703537 | 46855024 | 46855154 |
| ENSE00003703744 | 47144078 | 47144274 |
| ENSE00003704817 | 47218021 | 47218195 |
| ENSE00003705552 | 47131714 | 47131846 |
| ENSE00003705752 | 46845766 | 46845871 |
| ENSE00003705794 | 46882044 | 46882221 |
| ENSE00003706626 | 46873433 | 46873591 |
| ENSE00003707355 | 46877489 | 46877509 |
| ENSE00003707948 | 47301411 | 47301550 |
| ENSE00003708881 | 47096854 | 47097123 |
| ENSE00003709807 | 46874045 | 46874200 |
| ENSE00003709928 | 46920012 | 46920160 |
| ENSE00003710181 | 47061249 | 47061578 |
| ENSE00003710533 | 47035011 | 47035304 |
| ENSE00003711265 | 46957374 | 46957643 |
Expression profiles
Bgee: expression breadth broad, 85 present calls, max score 84.63.
FANTOM5 (CAGE): breadth broad, TPM avg 3.1512 / max 421.6553, expressed in 387 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 143066 | 2.4759 | 339 |
| 143063 | 0.2683 | 94 |
| 143064 | 0.1798 | 80 |
| 143065 | 0.1733 | 82 |
| 143061 | 0.0539 | 32 |
Top tissues by expression
202 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| cortical plate | UBERON:0005343 | 84.63 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 83.82 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 82.25 | gold quality |
| ventricular zone | UBERON:0003053 | 72.14 | gold quality |
| prefrontal cortex | UBERON:0000451 | 70.56 | gold quality |
| secondary oocyte | CL:0000655 | 68.21 | silver quality |
| corpus callosum | UBERON:0002336 | 67.33 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 65.60 | gold quality |
| ganglionic eminence | UBERON:0004023 | 65.52 | gold quality |
| frontal cortex | UBERON:0001870 | 64.63 | gold quality |
| neocortex | UBERON:0001950 | 64.60 | gold quality |
| spinal cord | UBERON:0002240 | 63.90 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 63.61 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 63.34 | gold quality |
| testis | UBERON:0000473 | 63.32 | gold quality |
| stromal cell of endometrium | CL:0002255 | 62.91 | gold quality |
| primary visual cortex | UBERON:0002436 | 62.65 | gold quality |
| adrenal tissue | UBERON:0018303 | 62.58 | gold quality |
| left testis | UBERON:0004533 | 62.49 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 62.46 | gold quality |
| cerebral cortex | UBERON:0000956 | 62.23 | gold quality |
| right testis | UBERON:0004534 | 60.82 | gold quality |
| hypothalamus | UBERON:0001898 | 60.55 | gold quality |
| right frontal lobe | UBERON:0002810 | 59.48 | gold quality |
| occipital lobe | UBERON:0002021 | 59.38 | gold quality |
| amygdala | UBERON:0001876 | 59.00 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 58.59 | gold quality |
| forebrain | UBERON:0001890 | 57.52 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 56.72 | silver quality |
| Ammon’s horn | UBERON:0001954 | 56.71 | gold quality |
Single-cell (SCXA)
Detected in 5 experiment(s), a significant marker in 5.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-35 | yes | 3136.12 |
| E-GEOD-180759 | yes | 2903.69 |
| E-HCAD-25 | yes | 19.23 |
| E-ANND-3 | yes | 5.83 |
| E-GEOD-93593 | yes | 4.38 |
Regulation
Is transcription factor: yes
Downstream targets (CollecTRI)
2 targets.
| Target | Regulation |
|---|---|
| CDKN1A | Activation |
| TP53 | Activation |
Upstream regulators (CollecTRI, top): KLF6
miRNA regulators (miRDB)
193 targeting MDGA2, 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-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-MIR-4682 | 100.00 | 68.89 | 1258 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-126-5P | 100.00 | 72.71 | 3180 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| HSA-MIR-8068 | 99.98 | 73.85 | 2376 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-507 | 99.97 | 70.11 | 1915 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-557 | 99.96 | 70.01 | 1640 |
| HSA-MIR-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-MIR-4267 | 99.96 | 66.53 | 2368 |
| HSA-MIR-3912-5P | 99.95 | 66.11 | 925 |
| HSA-MIR-651-3P | 99.94 | 73.48 | 5177 |
| HSA-MIR-9983-3P | 99.94 | 71.48 | 3631 |
| HSA-MIR-548AS-5P | 99.94 | 71.22 | 3482 |
| HSA-MIR-218-5P | 99.93 | 72.22 | 2103 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-4760-3P | 99.93 | 70.50 | 2385 |
| HSA-MIR-4778-3P | 99.93 | 70.40 | 1818 |
| HSA-MIR-6835-3P | 99.93 | 70.49 | 2904 |
| HSA-MIR-450B-5P | 99.92 | 71.48 | 3175 |
| HSA-MIR-10523-5P | 99.91 | 69.22 | 2038 |
| HSA-MIR-498-3P | 99.91 | 71.27 | 1114 |
Literature-anchored findings (GeneRIF, showing 7)
- MAMDC1 gene is implicated in neuroticism. (PMID:18762592)
- No association of rs7151262 with neuroticism was found (PMID:19440164)
- A novel uncharacterized gene, MAMDC1 (MAM domain containing glycosylphosphatidylinositol anchor 2, also known as MDGA2, MIM 611128), represents a putative susceptibility gene for systemic lupus erythematosus. (PMID:19997561)
- This finding provides further support for a link between variants in the MDGA2 gene and specific neuroticism-related phenotypes. (PMID:21399569)
- This study demonistrated suggested taht Rostral growth of commissural axons requires the cell adhesion molecule MDGA2 (PMID:21542908)
- Polymorphisms of rs961616 in MAMDC1 gene were associated with rash and photosensitivity, but not disease risk, of systemic lupus erythematosus in Chinese population. (PMID:21660437)
- A novel tumour suppressor gene, MDGA2, which is frequently inactivated by promoter methylation in Gastric cancer was identified. Promoter hypermethylation of MDGA2 represents a prognostic biomarker in patients with early stage Gastric cancer. (PMID:26206665)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | mdga2a | ENSDARG00000024017 |
| ENSDARG00000112111 | ||
| mus_musculus | Mdga2 | ENSMUSG00000034912 |
| rattus_norvegicus | Mdga2 | ENSRNOG00000000618 |
Paralogs (4): MDGA1 (ENSG00000112139), MAMDC2 (ENSG00000165072), MAMDC4 (ENSG00000177943), MALRD1 (ENSG00000204740)
Protein
Protein identifiers
MAM domain-containing glycosylphosphatidylinositol anchor protein 2 — Q7Z553 (reviewed: Q7Z553)
Alternative names: MAM domain-containing protein 1
All UniProt accessions (5): Q7Z553, E9PMG9, G3V5U0, G3V5Z1, H0YJ52
UniProt curated annotations — full annotation on UniProt →
Function. May be involved in cell-cell interactions.
Subunit / interactions. Interacts (through the Ig-like domains) with NLGN2.
Subcellular location. Cell membrane.
Tissue specificity. Detected in Leydig cells, syncytiotrophoblast, duodenal villi epithelial cells and neutrophils from kidney and cutaneous squamous cell carcinoma (at protein level).
Isoforms (3)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q7Z553-1 | 1 | yes |
| Q7Z553-2 | 2 | |
| Q7Z553-3 | 3 |
RefSeq proteins (2): NP_001106970, NP_878250 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000998 | MAM_dom | Domain |
| IPR003598 | Ig_sub2 | Domain |
| IPR003599 | Ig_sub | Domain |
| IPR003961 | FN3_dom | Domain |
| IPR007110 | Ig-like_dom | Domain |
| IPR013098 | Ig_I-set | Domain |
| IPR013320 | ConA-like_dom_sf | Homologous_superfamily |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR036116 | FN3_sf | Homologous_superfamily |
| IPR036179 | Ig-like_dom_sf | Homologous_superfamily |
| IPR050958 | Cell_Adh-Cytoskel_Orgn | Family |
Pfam: PF00629, PF07679, PF13927
UniProt features (37 total): domain 8, glycosylation site 8, sequence conflict 8, disulfide bond 6, splice variant 2, signal peptide 1, chain 1, lipid moiety-binding region 1, propeptide 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q7Z553-F1 | 84.96 | 0.56 |
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): 931
Disulfide bonds (6): 62–110, 159–216, 264–310, 359–417, 465–515, 561–611
Glycosylation sites (8): 92, 213, 237, 434, 443, 504, 610, 703
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-163125 | Post-translational modification: synthesis of GPI-anchored proteins |
| R-HSA-392499 | Metabolism of proteins |
| R-HSA-597592 | Post-translational protein modification |
MSigDB gene sets: 162 (showing top):
GOBP_SPINAL_CORD_DEVELOPMENT, GOBP_NEUROGENESIS, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, GOBP_CELL_DIFFERENTIATION_IN_SPINAL_CORD, GOBP_SPINAL_CORD_MOTOR_NEURON_DIFFERENTIATION, AGGCACT_MIR5153P, GOBP_VENTRAL_SPINAL_CORD_DEVELOPMENT, GTGCCTT_MIR506, DAWSON_METHYLATED_IN_LYMPHOMA_TCL1, AAACCAC_MIR140, NF1_Q6_01, IRF1_Q6, CAATGCA_MIR33, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, AAAGACA_MIR511
GO Biological Process (2): nervous system development (GO:0007399), spinal cord motor neuron differentiation (GO:0021522)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (4): extracellular region (GO:0005576), plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Post-translational protein modification | 1 |
| Metabolism of proteins | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| membrane | 2 |
| system development | 1 |
| cell differentiation in spinal cord | 1 |
| ventral spinal cord development | 1 |
| central nervous system neuron differentiation | 1 |
| binding | 1 |
| cell periphery | 1 |
| leaflet of membrane bilayer | 1 |
Protein interactions and networks
STRING
1342 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| MDGA2 | NLGN2 | Q8NFZ4 | 721 |
| MDGA2 | NLGN1 | Q8N2Q7 | 616 |
| MDGA2 | SPPL2C | Q8IUH8 | 576 |
| MDGA2 | PDE4D | Q08499 | 501 |
| MDGA2 | FN1 | P02751 | 469 |
| MDGA2 | SIGLEC15 | Q6ZMC9 | 463 |
| MDGA2 | PRSS35 | Q8N3Z0 | 458 |
| MDGA2 | PTPRM | P28827 | 451 |
| MDGA2 | GALNT13 | Q8IUC8 | 450 |
| MDGA2 | DCLK1 | O15075 | 437 |
| MDGA2 | NLGN3 | Q9NZ94 | 431 |
| MDGA2 | MRTFB | Q9ULH7 | 426 |
| MDGA2 | HS3ST5 | Q8IZT8 | 423 |
| MDGA2 | FBXO33 | Q7Z6M2 | 422 |
| MDGA2 | CCL26 | Q9Y258 | 419 |
IntAct
2 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| MRPL12 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (7): MDGA2 (Affinity Capture-RNA), MDGA2 (Affinity Capture-RNA), MDGA2 (Co-fractionation), MDGA2 (Co-fractionation), NCKAP5L (Co-fractionation), SLC38A7 (Co-fractionation), MDGA2 (Affinity Capture-RNA)
ESM2 similar proteins: A0A8M2B818, A3KPA0, B0JYH6, O55005, O89026, O94898, P0DPA2, P16170, P17790, P36335, P40190, P57087, P57097, P60755, P60756, P85171, Q00560, Q0PMG2, Q0WYX8, Q12866, Q15198, Q15223, Q1WIM2, Q2PFX1, Q52KR2, Q58EG3, Q5BIP2, Q5RJP7, Q60805, Q61490, Q66KX2, Q68FQ2, Q6DJ83, Q6P3A4, Q6PE55, Q6X936, Q7Z553, Q7ZXX1, Q80W68, Q8BLQ9
Diamond homologs: A2AJX4, B3EWZ5, B3EWZ6, B3EX02, C0HL13, O75581, O88572, P35953, P60755, P60756, P85171, P97435, P98072, P98073, P98074, Q0PMG2, Q0WYX8, Q2PC93, Q5VYJ5, Q7Z553, Q8NFP4, Q8QFX6, Q9GMT4, O14786, O35375, P28824, P28825, P79795, P97333, Q16820, Q61847, Q64230, Q9QWJ9, A2ARV4, O14522, O60462, P35822, P98157, P98158, P98164
SIGNOR signaling
4 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| MDGA2 | down-regulates | Proliferation | |
| MDGA2 | “up-regulates quantity by stabilization” | DMAP1 | binding |
| MDGA2 | “up-regulates quantity by expression” | TP53 | “transcriptional regulation” |
| MDGA2 | “up-regulates quantity by expression” | CDKN1A | “transcriptional regulation” |
Disease & clinical
Cancer significance
From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — MEL.
Clinical variants and AI predictions
ClinVar
62 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 1 |
| Uncertain significance | 46 |
| Likely benign | 2 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1708469 | NM_001113498.3(MDGA2):c.278_279dup (p.Ala94fs) | Likely pathogenic |
SpliceAI
4551 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 14:46845757:GATAC:G | donor_loss | 1.0000 |
| 14:46845758:ATACT:A | donor_loss | 1.0000 |
| 14:46845759:TACTT:T | donor_loss | 1.0000 |
| 14:46845760:ACT:A | donor_loss | 1.0000 |
| 14:46845761:CT:C | donor_loss | 1.0000 |
| 14:46845762:TT:T | donor_loss | 1.0000 |
| 14:46845763:TA:T | donor_loss | 1.0000 |
| 14:46845764:A:AC | donor_gain | 1.0000 |
| 14:46845764:ACT:A | donor_gain | 1.0000 |
| 14:46845764:ACTC:A | donor_loss | 1.0000 |
| 14:46845765:C:CC | donor_gain | 1.0000 |
| 14:46845765:C:G | donor_loss | 1.0000 |
| 14:46845765:CT:C | donor_gain | 1.0000 |
| 14:46845765:CTC:C | donor_gain | 1.0000 |
| 14:46845765:CTCTT:C | donor_gain | 1.0000 |
| 14:46845868:TGAG:T | acceptor_gain | 1.0000 |
| 14:46873593:T:C | acceptor_gain | 1.0000 |
| 14:46874040:CATA:C | donor_loss | 1.0000 |
| 14:46874043:A:C | donor_loss | 1.0000 |
| 14:46874044:CC:C | donor_loss | 1.0000 |
| 14:46874044:CCTT:C | donor_gain | 1.0000 |
| 14:46874047:T:A | donor_gain | 1.0000 |
| 14:46874198:CTC:C | acceptor_gain | 1.0000 |
| 14:46874201:C:CC | acceptor_gain | 1.0000 |
| 14:46877487:A:AC | donor_gain | 1.0000 |
| 14:46877488:C:CC | donor_gain | 1.0000 |
| 14:46882040:TTA:T | donor_loss | 1.0000 |
| 14:46882041:TACC:T | donor_gain | 1.0000 |
| 14:46882042:A:AC | donor_gain | 1.0000 |
| 14:46882042:AC:A | donor_gain | 1.0000 |
AlphaMissense
6647 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 14:46855066:C:A | W878C | 1.000 |
| 14:46855066:C:G | W878C | 1.000 |
| 14:46855068:A:G | W878R | 1.000 |
| 14:46855068:A:T | W878R | 1.000 |
| 14:46874127:C:A | W768C | 1.000 |
| 14:46874127:C:G | W768C | 1.000 |
| 14:46874129:A:G | W768R | 1.000 |
| 14:46874129:A:T | W768R | 1.000 |
| 14:46882103:A:G | L717P | 1.000 |
| 14:46920074:A:G | W657R | 1.000 |
| 14:46920074:A:T | W657R | 1.000 |
| 14:46957530:A:G | W576R | 1.000 |
| 14:46957530:A:T | W576R | 1.000 |
| 14:47035016:A:T | V536D | 1.000 |
| 14:47035078:A:C | C515W | 1.000 |
| 14:47035080:A:G | C515R | 1.000 |
| 14:47035086:A:C | Y513D | 1.000 |
| 14:47035192:C:A | W477C | 1.000 |
| 14:47035192:C:G | W477C | 1.000 |
| 14:47035194:A:G | W477R | 1.000 |
| 14:47035194:A:T | W477R | 1.000 |
| 14:47035230:A:G | C465R | 1.000 |
| 14:47061316:A:C | C417W | 1.000 |
| 14:47061317:C:T | C417Y | 1.000 |
| 14:47061318:A:G | C417R | 1.000 |
| 14:47061324:A:C | Y415D | 1.000 |
| 14:47061329:C:T | G413E | 1.000 |
| 14:47061330:C:A | G413W | 1.000 |
| 14:47061335:T:A | D411V | 1.000 |
| 14:47061335:T:C | D411G | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000010745 (14:46866629 T>C), RS1000014846 (14:47399765 TA>T,TAA), RS1000015536 (14:47417935 A>G), RS1000016283 (14:47127534 G>C,T), RS1000018385 (14:47406676 C>A,T), RS1000018405 (14:47586541 C>T), RS1000021031 (14:47531162 G>A), RS1000028480 (14:47135871 C>G,T), RS1000029684 (14:47625581 T>C), RS1000037307 (14:47252001 G>A,T), RS1000040421 (14:47088577 A>G,T), RS1000041444 (14:47009571 C>T), RS1000044300 (14:47199663 T>C), RS1000045762 (14:46910741 C>T), RS1000048935 (14:47080831 A>G)
Disease associations
OMIM: gene MIM:611128 | disease phenotypes: MIM:615873
GenCC curated gene-disease
Mondo (2): intellectual disability (MONDO:0001071), ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder (MONDO:0014379)
Orphanet (2): Helsmoortel-Van der Aa syndrome (Orphanet:404448), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
18 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000080_13 | Hemostatic factors and hematological phenotypes | 2.000000e-07 |
| GCST000226_1 | Neuroticism | 7.000000e-07 |
| GCST001453_1 | Sexual dysfunction (SSRI/SNRI-related) | 3.000000e-07 |
| GCST001476_13 | Response to tocilizumab in rheumatoid arthritis | 2.000000e-07 |
| GCST001762_141 | Obesity-related traits | 3.000000e-07 |
| GCST001974_2 | Idiopathic pulmonary fibrosis | 4.000000e-06 |
| GCST003059_18 | Parkinson’s disease | 1.000000e-06 |
| GCST003262_530 | Post bronchodilator FEV1 | 3.000000e-06 |
| GCST003264_1369 | Post bronchodilator FEV1/FVC ratio | 8.000000e-08 |
| GCST003784_14 | Multiple system atrophy | 4.000000e-06 |
| GCST004744_4 | Lung adenocarcinoma | 3.000000e-06 |
| GCST005566_20 | Insomnia | 3.000000e-07 |
| GCST006427_32 | Depression in smokers | 4.000000e-06 |
| GCST006460_11 | Bronchopulmonary dysplasia in preterm infants | 3.000000e-06 |
| GCST007001_7 | Cerebrospinal AB1-42 levels in normal cognition | 5.000000e-07 |
| GCST008476_11 | Emphysema annual change measurement in smokers (percent low attenuation area) | 8.000000e-06 |
| GCST010988_537 | Adult body size | 9.000000e-14 |
| GCST90000047_248 | Age at first sexual intercourse | 2.000000e-12 |
EFO canonical traits (8, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004714 | sexual dysfunction |
| EFO:0004810 | interleukin-6 measurement |
| EFO:0000768 | idiopathic pulmonary fibrosis |
| EFO:0004314 | forced expiratory volume |
| EFO:0004713 | FEV/FVC ratio |
| EFO:0004670 | beta-amyloid 1-42 measurement |
| EFO:0007626 | emphysema imaging measurement |
| EFO:0009749 | age at first sexual intercourse 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)
PharmGKB clinical annotations
1 annotations.
| Variant | Type | Level | Drugs | Phenotypes |
|---|---|---|---|---|
| rs1160351 | Toxicity | 3 | fluvoxamine;milnacipran;paroxetine | Major Depressive Disorder |
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs1160351 | MDGA2 | 3 | 0.00 | 1 | fluvoxamine;milnacipran;paroxetine |
CTD chemical–gene interactions
14 total (human), top 14 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | affects splicing, decreases expression | 2 |
| Aflatoxin B1 | decreases expression, decreases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| methyleugenol | decreases expression | 1 |
| trichostatin A | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| bisphenol S | decreases methylation | 1 |
| Resveratrol | decreases expression, affects cotreatment | 1 |
| Sunitinib | increases expression | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Lead | affects expression | 1 |
| Plant Extracts | affects cotreatment, decreases expression | 1 |
| Triclosan | decreases expression | 1 |
| Valproic Acid | increases expression | 1 |
Clinical trials (associated diseases)
199 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
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder, bronchopulmonary dysplasia, insomnia, multiple system atrophy, neurotic disorder