SYDE1
gene geneOn this page
Also known as 7h3FLJ13511SYD1
Summary
SYDE1 (synapse defective Rho GTPase activating protein 1, HGNC:25824) is a protein-coding gene on chromosome 19p13.12, encoding Rho GTPase-activating protein SYDE1 (Q6ZW31). GTPase activator for the Rho-type GTPases.
The protein encoded by this gene is a Rho GTPase-activating protein highly expressed in placenta. The encoded protein is involved in cytoskeletal remodeling and trophoblast cell migration. Decreased expression of this gene has been associated with intrauterine growth restriction (IUGR).
Source: NCBI Gene 85360 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 129 total
- MANE Select transcript:
NM_033025
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:25824 |
| Approved symbol | SYDE1 |
| Name | synapse defective Rho GTPase activating protein 1 |
| Location | 19p13.12 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | 7h3, FLJ13511, SYD1 |
| Ensembl gene | ENSG00000105137 |
| Ensembl biotype | protein_coding |
| OMIM | 617377 |
| Entrez | 85360 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 9 protein_coding
ENST00000342784, ENST00000597977, ENST00000600252, ENST00000600440, ENST00000602203, ENST00000863343, ENST00000863344, ENST00000863345, ENST00000925189
RefSeq mRNA: 2 — MANE Select: NM_033025
NM_001300910, NM_033025
CCDS: CCDS12324, CCDS74299
Canonical transcript exons
ENST00000342784 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000689545 | 15111313 | 15111439 |
| ENSE00000689546 | 15110521 | 15110735 |
| ENSE00000689549 | 15107401 | 15107521 |
| ENSE00001137355 | 15111632 | 15111792 |
| ENSE00001234392 | 15109704 | 15110348 |
| ENSE00001379114 | 15109056 | 15109397 |
| ENSE00003087216 | 15113560 | 15114974 |
| ENSE00003582784 | 15112346 | 15112571 |
Expression profiles
Bgee: expression breadth ubiquitous, 258 present calls, max score 91.88.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2791 / max 77.1870, expressed in 1296 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 174303 | 8.2791 | 1296 |
Top tissues by expression
280 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| decidua | UBERON:0002450 | 91.88 | gold quality |
| thoracic aorta | UBERON:0001515 | 91.76 | gold quality |
| ascending aorta | UBERON:0001496 | 91.75 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 91.53 | gold quality |
| aorta | UBERON:0000947 | 91.28 | gold quality |
| popliteal artery | UBERON:0002250 | 90.98 | gold quality |
| tibial artery | UBERON:0007610 | 90.97 | gold quality |
| right coronary artery | UBERON:0001625 | 90.88 | gold quality |
| stromal cell of endometrium | CL:0002255 | 90.53 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 90.46 | gold quality |
| placenta | UBERON:0001987 | 90.32 | gold quality |
| coronary artery | UBERON:0001621 | 90.07 | gold quality |
| left coronary artery | UBERON:0001626 | 90.07 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 89.80 | gold quality |
| lower esophagus | UBERON:0013473 | 89.72 | gold quality |
| body of uterus | UBERON:0009853 | 89.17 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 89.16 | gold quality |
| mucosa of stomach | UBERON:0001199 | 88.79 | gold quality |
| apex of heart | UBERON:0002098 | 88.48 | gold quality |
| endocervix | UBERON:0000458 | 88.41 | gold quality |
| left uterine tube | UBERON:0001303 | 88.25 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 87.92 | gold quality |
| myometrium | UBERON:0001296 | 87.75 | gold quality |
| superficial temporal artery | UBERON:0001614 | 87.71 | silver quality |
| metanephros cortex | UBERON:0010533 | 87.62 | gold quality |
| right ovary | UBERON:0002118 | 87.18 | gold quality |
| vena cava | UBERON:0004087 | 87.07 | silver quality |
| cardia of stomach | UBERON:0001162 | 86.86 | gold quality |
| endothelial cell | CL:0000115 | 86.58 | gold quality |
| tongue squamous epithelium | UBERON:0006919 | 86.38 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-6701 | yes | 77.52 |
| E-ANND-3 | yes | 4.50 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
46 targeting SYDE1, 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-200B-3P | 100.00 | 73.31 | 2693 |
| HSA-MIR-200C-3P | 100.00 | 73.35 | 2685 |
| HSA-MIR-429 | 100.00 | 73.44 | 2698 |
| HSA-MIR-4510 | 100.00 | 66.60 | 2050 |
| HSA-MIR-6127 | 100.00 | 66.76 | 2188 |
| HSA-MIR-6129 | 100.00 | 66.46 | 2080 |
| HSA-MIR-6130 | 100.00 | 66.69 | 2012 |
| HSA-MIR-6133 | 100.00 | 66.48 | 2064 |
| HSA-MIR-8485 | 100.00 | 77.57 | 4731 |
| HSA-MIR-302E | 99.96 | 70.74 | 2669 |
| HSA-MIR-9718 | 99.94 | 68.91 | 918 |
| HSA-MIR-302A-3P | 99.89 | 71.23 | 1777 |
| HSA-MIR-302B-3P | 99.89 | 71.23 | 1777 |
| HSA-MIR-302C-3P | 99.89 | 71.20 | 1778 |
| HSA-MIR-302D-3P | 99.89 | 71.25 | 1777 |
| HSA-MIR-182-5P | 99.87 | 74.03 | 2589 |
| HSA-MIR-6124 | 99.87 | 69.78 | 3551 |
| HSA-MIR-6857-5P | 99.87 | 65.32 | 985 |
| HSA-MIR-373-3P | 99.84 | 70.68 | 1668 |
| HSA-MIR-520E-3P | 99.84 | 70.55 | 1698 |
| HSA-MIR-372-3P | 99.83 | 70.58 | 1691 |
| HSA-MIR-520A-3P | 99.83 | 70.59 | 1687 |
| HSA-MIR-520B-3P | 99.83 | 70.56 | 1699 |
| HSA-MIR-520C-3P | 99.83 | 70.56 | 1699 |
| HSA-MIR-520D-3P | 99.83 | 70.78 | 1676 |
| HSA-MIR-3934-3P | 99.76 | 65.51 | 1351 |
| HSA-MIR-1249-5P | 99.61 | 66.55 | 2049 |
| HSA-MIR-6797-5P | 99.61 | 66.55 | 2084 |
| HSA-MIR-136-5P | 99.50 | 67.26 | 1153 |
| HSA-MIR-3612 | 99.45 | 66.02 | 1333 |
Literature-anchored findings (GeneRIF, showing 1)
- a novel mechanism for GCM1 and SYDE1 in regulation of trophoblast cell migration and invasion during placental development (PMID:27917469)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | SYDE1 | ENSDARG00000077440 |
| mus_musculus | Syde1 | ENSMUSG00000032714 |
| rattus_norvegicus | Syde1 | ENSRNOG00000007307 |
| drosophila_melanogaster | RhoGAP100F | FBGN0039883 |
| caenorhabditis_elegans | WBGENE00006363 |
Paralogs (4): SYDE2 (ENSG00000097096), CHN2 (ENSG00000106069), CHN1 (ENSG00000128656), ARHGAP35 (ENSG00000160007)
Protein
Protein identifiers
Rho GTPase-activating protein SYDE1 — Q6ZW31 (reviewed: Q6ZW31)
Alternative names: Synapse defective protein 1 homolog 1
All UniProt accessions (4): M0QXZ8, M0R101, M0R3D3, Q6ZW31
UniProt curated annotations — full annotation on UniProt →
Function. GTPase activator for the Rho-type GTPases. As a GCM1 downstream effector, it is involved in placental development and positively regulates trophoblast cells migration. It regulates cytoskeletal remodeling by controlling the activity of Rho GTPases including RHOA, CDC42 and RAC1.
Tissue specificity. Expressed in trophoblast cells of placental villi.
Post-translational modifications. Palmitoylated. Probably palmitoylated by ZDHHC3 and ZDHHC7.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q6ZW31-1 | 1 | yes |
| Q6ZW31-2 | 2 |
RefSeq proteins (2): NP_001287839, NP_149014* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000008 | C2_dom | Domain |
| IPR000198 | RhoGAP_dom | Domain |
| IPR008936 | Rho_GTPase_activation_prot | Homologous_superfamily |
| IPR052118 | Rho-GAP_regulator | Family |
| IPR057459 | SYDE1/2_C2 | Domain |
Pfam: PF00620, PF25336
UniProt features (21 total): modified residue 7, compositionally biased region 5, region of interest 3, domain 2, chain 1, site 1, splice variant 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q6ZW31-F1 | 62.17 | 0.31 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Catalytic / active sites (1): 436 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)
Post-translational modifications (7): 224, 231, 235, 244, 575, 681, 683
Function
Pathways and Gene Ontology
Reactome pathways
10 pathways
| ID | Pathway |
|---|---|
| R-HSA-9013148 | CDC42 GTPase cycle |
| R-HSA-9013404 | RAC2 GTPase cycle |
| R-HSA-9013406 | RHOQ GTPase cycle |
| R-HSA-9013409 | RHOJ GTPase cycle |
| R-HSA-9013423 | RAC3 GTPase cycle |
| R-HSA-9035034 | RHOF GTPase cycle |
| R-HSA-162582 | Signal Transduction |
| R-HSA-194315 | Signaling by Rho GTPases |
| R-HSA-9012999 | RHO GTPase cycle |
| R-HSA-9716542 | Signaling by Rho GTPases, Miro GTPases and RHOBTB3 |
MSigDB gene sets: 126 (showing top):
GOBP_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_ACTIVATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, AATGGAG_MIR136, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION
GO Biological Process (7): signal transduction (GO:0007165), cell migration (GO:0016477), actin cytoskeleton organization (GO:0030036), regulation of Ras protein signal transduction (GO:0046578), regulation of cytoskeleton organization (GO:0051493), activation of GTPase activity (GO:0090630), positive regulation of trophoblast cell migration (GO:1901165)
GO Molecular Function (2): GTPase activator activity (GO:0005096), GTPase regulator activity (GO:0030695)
GO Cellular Component (1): synaptic membrane (GO:0097060)
Reactome top-level categories
Rollup of top-4 pathways:
| Category | Pathways |
|---|---|
| RHO GTPase cycle | 6 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 1 |
| Signaling by Rho GTPases | 1 |
| Signal Transduction | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cytoskeleton organization | 2 |
| GTPase activity | 2 |
| cell communication | 1 |
| cellular process | 1 |
| signaling | 1 |
| regulation of cellular process | 1 |
| cellular response to stimulus | 1 |
| cell motility | 1 |
| actin filament-based process | 1 |
| Ras protein signal transduction | 1 |
| regulation of small GTPase mediated signal transduction | 1 |
| regulation of organelle organization | 1 |
| positive regulation of GTPase activity | 1 |
| positive regulation of cell migration | 1 |
| positive regulation of developmental process | 1 |
| positive regulation of multicellular organismal process | 1 |
| trophoblast cell migration | 1 |
| regulation of trophoblast cell migration | 1 |
| positive regulation of reproductive process | 1 |
| enzyme activator activity | 1 |
| GTPase regulator activity | 1 |
| nucleoside-triphosphatase regulator activity | 1 |
| synapse | 1 |
| plasma membrane region | 1 |
Protein interactions and networks
STRING
848 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SYDE1 | HACL2 | A1L0T0 | 538 |
| SYDE1 | NCAM1 | P13591 | 461 |
| SYDE1 | PAK5 | Q9P286 | 460 |
| SYDE1 | GCM1 | Q9NP62 | 453 |
| SYDE1 | MEIOC | A2RUB1 | 436 |
| SYDE1 | PPP4R3A | Q6IN85 | 418 |
| SYDE1 | CNTROB | Q8N137 | 418 |
| SYDE1 | NLGN2 | Q8NFZ4 | 416 |
| SYDE1 | RHOG | P35238 | 416 |
| SYDE1 | EPHX3 | Q9H6B9 | 410 |
| SYDE1 | PDIK1L | Q8N165 | 406 |
| SYDE1 | RHOB | P01121 | 402 |
| SYDE1 | CBR3 | O75828 | 402 |
| SYDE1 | PACSIN1 | Q9BY11 | 400 |
| SYDE1 | GEN1 | Q17RS7 | 398 |
IntAct
73 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| KBTBD7 | METTL15 | psi-mi:“MI:0914”(association) | 0.730 |
| YWHAG | SHTN1 | psi-mi:“MI:0914”(association) | 0.560 |
| YWHAB | SHTN1 | psi-mi:“MI:0914”(association) | 0.530 |
| YWHAE | SHTN1 | psi-mi:“MI:0914”(association) | 0.530 |
| Xpo1 | IFT56 | psi-mi:“MI:0914”(association) | 0.350 |
| SYDE1 | Coq10b | psi-mi:“MI:0914”(association) | 0.350 |
| SYDE1 | Ppfibp1 | psi-mi:“MI:0914”(association) | 0.350 |
| Arhgap28 | EZR | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAH | SHTN1 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAQ | SHTN1 | psi-mi:“MI:0914”(association) | 0.350 |
| CALM1 | MYO1C | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAE | DEPDC5 | psi-mi:“MI:0914”(association) | 0.350 |
| LURAP1 | CIBAR1 | psi-mi:“MI:0914”(association) | 0.350 |
| SYDE1 | POLR2D | psi-mi:“MI:0914”(association) | 0.350 |
| APBB1 | HERC2 | psi-mi:“MI:0914”(association) | 0.350 |
| SYDE1 | APBB1 | psi-mi:“MI:0914”(association) | 0.350 |
| AFG2B | MMP24OS | psi-mi:“MI:0914”(association) | 0.350 |
| CTNNA1 | EFCAB5 | psi-mi:“MI:0914”(association) | 0.350 |
| DCLK1 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SIPA1L1 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| KIF1C | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| MAST3 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| EIF4E2 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| SRGAP2 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| GIGYF1 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| NADK | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| NF1 | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| CDC25B | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| CDC25C | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
| AFDN | SYDE1 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (132): SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), POLR2D (Affinity Capture-MS), KLHDC2 (Affinity Capture-MS), TYW3 (Affinity Capture-MS), POLR2A (Affinity Capture-MS), POLR2J (Affinity Capture-MS), RPAP2 (Affinity Capture-MS), POLR2I (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS), SYDE1 (Affinity Capture-MS)
ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7
Diamond homologs: A0A0G2JTR4, A1A4S6, A2AB59, A2RUV4, A4IF90, A4II46, A6QNS3, A6X8Z5, A7KAX9, A7YY57, A8WRJ2, D3ZFJ3, E7EZG2, E7F3F0, F1LXF1, O14559, O94466, P11274, P15882, P30337, P34288, P38339, P46941, P52757, P55194, P81128, P97393, Q03070, Q08DP6, Q10164, Q12979, Q13017, Q15311, Q17QN0, Q20498, Q2M1Z3, Q3TBD2, Q3UIA2, Q52LW3, Q53QZ3
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 80 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | 6 | 80.6× | 3e-08 |
| Activation of BAD and translocation to mitochondria | 5 | 76.1× | 5e-07 |
| SARS-CoV-1 targets host intracellular signalling and regulatory pathways | 5 | 67.2× | 8e-07 |
| Activation of BH3-only proteins | 5 | 49.6× | 2e-06 |
| RHO GTPases activate PKNs | 6 | 38.1× | 8e-07 |
| Intrinsic Pathway for Apoptosis | 5 | 29.3× | 2e-05 |
| Translocation of SLC2A4 (GLUT4) to the plasma membrane | 7 | 21.6× | 2e-06 |
| SARS-CoV-1-host interactions | 5 | 17.6× | 2e-04 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| protein targeting | 5 | 25.8× | 3e-04 |
| substantia nigra development | 5 | 25.8× | 3e-04 |
| intracellular protein localization | 7 | 10.3× | 8e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
129 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 121 |
| Likely benign | 4 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
942 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 19:15107517:GCGCG:G | donor_gain | 1.0000 |
| 19:15107519:GCG:G | donor_gain | 1.0000 |
| 19:15107520:CG:C | donor_gain | 1.0000 |
| 19:15107520:CGG:C | donor_loss | 1.0000 |
| 19:15107521:GG:G | donor_gain | 1.0000 |
| 19:15107522:G:GG | donor_gain | 1.0000 |
| 19:15107522:GTA:G | donor_loss | 1.0000 |
| 19:15107523:T:G | donor_loss | 1.0000 |
| 19:15110516:CTCA:C | acceptor_loss | 1.0000 |
| 19:15110519:A:AG | acceptor_gain | 1.0000 |
| 19:15110519:AG:A | acceptor_gain | 1.0000 |
| 19:15110520:G:GG | acceptor_gain | 1.0000 |
| 19:15110520:GG:G | acceptor_gain | 1.0000 |
| 19:15110520:GGGT:G | acceptor_gain | 1.0000 |
| 19:15110732:GCGG:G | donor_gain | 1.0000 |
| 19:15110734:GG:G | donor_gain | 1.0000 |
| 19:15110735:GG:G | donor_gain | 1.0000 |
| 19:15110735:GGTG:G | donor_loss | 1.0000 |
| 19:15110736:G:GG | donor_gain | 1.0000 |
| 19:15111310:CA:C | acceptor_loss | 1.0000 |
| 19:15111311:A:AC | acceptor_loss | 1.0000 |
| 19:15111312:GGTA:G | acceptor_gain | 1.0000 |
| 19:15111409:G:GT | donor_gain | 1.0000 |
| 19:15111436:ACTGG:A | donor_loss | 1.0000 |
| 19:15111438:TGGTC:T | donor_loss | 1.0000 |
| 19:15111439:GGTC:G | donor_loss | 1.0000 |
| 19:15111440:G:GG | donor_gain | 1.0000 |
| 19:15111440:GT:G | donor_loss | 1.0000 |
| 19:15111441:T:G | donor_loss | 1.0000 |
| 19:15111789:AAGGG:A | donor_loss | 1.0000 |
AlphaMissense
4631 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 19:15111642:G:C | K476N | 1.000 |
| 19:15111642:G:T | K476N | 1.000 |
| 19:15111319:G:A | G433R | 0.999 |
| 19:15111319:G:C | G433R | 0.999 |
| 19:15111320:G:A | G433E | 0.999 |
| 19:15111328:C:A | R436S | 0.999 |
| 19:15111354:G:C | K444N | 0.999 |
| 19:15111354:G:T | K444N | 0.999 |
| 19:15111362:T:A | L447H | 0.999 |
| 19:15111362:T:C | L447P | 0.999 |
| 19:15111638:T:C | L475P | 0.999 |
| 19:15111650:T:C | L479P | 0.999 |
| 19:15112374:T:C | L536P | 0.999 |
| 19:15112405:C:A | N546K | 0.999 |
| 19:15112405:C:G | N546K | 0.999 |
| 19:15112410:T:C | M548T | 0.999 |
| 19:15112428:C:A | A554D | 0.999 |
| 19:15112435:C:G | C556W | 0.999 |
| 19:15112440:G:A | G558E | 0.999 |
| 19:15110229:T:C | F319S | 0.998 |
| 19:15110631:T:C | F396L | 0.998 |
| 19:15110633:T:A | F396L | 0.998 |
| 19:15110633:T:G | F396L | 0.998 |
| 19:15110728:G:A | G428E | 0.998 |
| 19:15111325:T:C | Y435H | 0.998 |
| 19:15111332:T:C | L437P | 0.998 |
| 19:15111335:G:A | C438Y | 0.998 |
| 19:15111338:G:A | G439D | 0.998 |
| 19:15111374:T:C | F451S | 0.998 |
| 19:15111429:T:A | N469K | 0.998 |
dbSNP variants (sampled 300 via entrez): RS1000107815 (19:15106561 A>G), RS1000113488 (19:15114456 G>A), RS1000297336 (19:15105723 T>C), RS1000351539 (19:15113092 C>T), RS1001292350 (19:15111867 G>C), RS1001376220 (19:15107883 G>A,T), RS1001474827 (19:15108528 G>A), RS1001767823 (19:15111081 G>A,C), RS1002180242 (19:15113056 C>T), RS1002326123 (19:15114621 C>A,G,T), RS1002843131 (19:15110056 G>A,T), RS1002959192 (19:15110346 G>A,C,T), RS1003119591 (19:15110387 C>A,T), RS1003150564 (19:15110071 C>T), RS1003889313 (19:15107611 G>A)
Disease associations
OMIM: gene MIM:617377 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003771_20 | Loneliness | 8.000000e-07 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0007865 | loneliness measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
39 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, decreases expression, affects expression, increases methylation | 5 |
| Benzo(a)pyrene | decreases methylation, increases expression, increases methylation | 2 |
| Doxorubicin | decreases expression, affects response to substance | 2 |
| GSK-J4 | increases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| sodium arsenate | increases abundance, increases expression | 1 |
| terbufos | increases methylation | 1 |
| sodium arsenite | increases expression | 1 |
| sulindac sulfide | increases expression | 1 |
| cupric chloride | increases expression | 1 |
| coumarin | decreases phosphorylation | 1 |
| muconaldehyde | decreases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, 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 |
| abrine | decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| 4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid | decreases expression | 1 |
| Temozolomide | increases expression | 1 |
| Leflunomide | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Arbutin | decreases expression | 1 |
| Arsenic | increases abundance, increases expression | 1 |
| Calcitriol | increases expression | 1 |
| Cisplatin | decreases expression | 1 |
| Fonofos | increases methylation | 1 |
| Estradiol | increases expression, affects cotreatment | 1 |
| Lipopolysaccharides | increases expression, affects response to substance | 1 |
| Parathion | increases methylation | 1 |
| Silicon Dioxide | decreases methylation, increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.