SYDE1

gene
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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

FieldValue
HGNC IDHGNC:25824
Approved symbolSYDE1
Namesynapse defective Rho GTPase activating protein 1
Location19p13.12
Locus typegene with protein product
StatusApproved
Aliases7h3, FLJ13511, SYD1
Ensembl geneENSG00000105137
Ensembl biotypeprotein_coding
OMIM617377
Entrez85360

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

ExonStartEnd
ENSE000006895451511131315111439
ENSE000006895461511052115110735
ENSE000006895491510740115107521
ENSE000011373551511163215111792
ENSE000012343921510970415110348
ENSE000013791141510905615109397
ENSE000030872161511356015114974
ENSE000035827841511234615112571

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 IDTPM avgSamples expressed
1743038.27911296

Top tissues by expression

280 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
deciduaUBERON:000245091.88gold quality
thoracic aortaUBERON:000151591.76gold quality
ascending aortaUBERON:000149691.75gold quality
descending thoracic aortaUBERON:000234591.53gold quality
aortaUBERON:000094791.28gold quality
popliteal arteryUBERON:000225090.98gold quality
tibial arteryUBERON:000761090.97gold quality
right coronary arteryUBERON:000162590.88gold quality
stromal cell of endometriumCL:000225590.53gold quality
tendon of biceps brachiiUBERON:000818890.46gold quality
placentaUBERON:000198790.32gold quality
coronary arteryUBERON:000162190.07gold quality
left coronary arteryUBERON:000162690.07gold quality
lower esophagus muscularis layerUBERON:003583389.80gold quality
lower esophagusUBERON:001347389.72gold quality
body of uterusUBERON:000985389.17gold quality
esophagogastric junction muscularis propriaUBERON:003584189.16gold quality
mucosa of stomachUBERON:000119988.79gold quality
apex of heartUBERON:000209888.48gold quality
endocervixUBERON:000045888.41gold quality
left uterine tubeUBERON:000130388.25gold quality
muscle layer of sigmoid colonUBERON:003580587.92gold quality
myometriumUBERON:000129687.75gold quality
superficial temporal arteryUBERON:000161487.71silver quality
metanephros cortexUBERON:001053387.62gold quality
right ovaryUBERON:000211887.18gold quality
vena cavaUBERON:000408787.07silver quality
cardia of stomachUBERON:000116286.86gold quality
endothelial cellCL:000011586.58gold quality
tongue squamous epitheliumUBERON:000691986.38gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-6701yes77.52
E-ANND-3yes4.50

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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-8485100.0077.574731
HSA-MIR-302E99.9670.742669
HSA-MIR-971899.9468.91918
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-182-5P99.8774.032589
HSA-MIR-612499.8769.783551
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-373-3P99.8470.681668
HSA-MIR-520E-3P99.8470.551698
HSA-MIR-372-3P99.8370.581691
HSA-MIR-520A-3P99.8370.591687
HSA-MIR-520B-3P99.8370.561699
HSA-MIR-520C-3P99.8370.561699
HSA-MIR-520D-3P99.8370.781676
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-136-5P99.5067.261153
HSA-MIR-361299.4566.021333

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

OrganismSymbolGene ID
danio_rerioSYDE1ENSDARG00000077440
mus_musculusSyde1ENSMUSG00000032714
rattus_norvegicusSyde1ENSRNOG00000007307
drosophila_melanogasterRhoGAP100FFBGN0039883
caenorhabditis_elegansWBGENE00006363

Paralogs (4): SYDE2 (ENSG00000097096), CHN2 (ENSG00000106069), CHN1 (ENSG00000128656), ARHGAP35 (ENSG00000160007)

Protein

Protein identifiers

Rho GTPase-activating protein SYDE1Q6ZW31 (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 IDNamesCanonical?
Q6ZW31-11yes
Q6ZW31-22

RefSeq proteins (2): NP_001287839, NP_149014* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR000198RhoGAP_domDomain
IPR008936Rho_GTPase_activation_protHomologous_superfamily
IPR052118Rho-GAP_regulatorFamily
IPR057459SYDE1/2_C2Domain

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)

ModelpLDDTFraction very-high
AF-Q6ZW31-F162.170.31

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

IDPathway
R-HSA-9013148CDC42 GTPase cycle
R-HSA-9013404RAC2 GTPase cycle
R-HSA-9013406RHOQ GTPase cycle
R-HSA-9013409RHOJ GTPase cycle
R-HSA-9013423RAC3 GTPase cycle
R-HSA-9035034RHOF GTPase cycle
R-HSA-162582Signal Transduction
R-HSA-194315Signaling by Rho GTPases
R-HSA-9012999RHO GTPase cycle
R-HSA-9716542Signaling 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:

CategoryPathways
RHO GTPase cycle6
Signaling by Rho GTPases, Miro GTPases and RHOBTB31
Signaling by Rho GTPases1
Signal Transduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoskeleton organization2
GTPase activity2
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cell motility1
actin filament-based process1
Ras protein signal transduction1
regulation of small GTPase mediated signal transduction1
regulation of organelle organization1
positive regulation of GTPase activity1
positive regulation of cell migration1
positive regulation of developmental process1
positive regulation of multicellular organismal process1
trophoblast cell migration1
regulation of trophoblast cell migration1
positive regulation of reproductive process1
enzyme activator activity1
GTPase regulator activity1
nucleoside-triphosphatase regulator activity1
synapse1
plasma membrane region1

Protein interactions and networks

STRING

848 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYDE1HACL2A1L0T0538
SYDE1NCAM1P13591461
SYDE1PAK5Q9P286460
SYDE1GCM1Q9NP62453
SYDE1MEIOCA2RUB1436
SYDE1PPP4R3AQ6IN85418
SYDE1CNTROBQ8N137418
SYDE1NLGN2Q8NFZ4416
SYDE1RHOGP35238416
SYDE1EPHX3Q9H6B9410
SYDE1PDIK1LQ8N165406
SYDE1RHOBP01121402
SYDE1CBR3O75828402
SYDE1PACSIN1Q9BY11400
SYDE1GEN1Q17RS7398

IntAct

73 interactions, top by confidence:

ABTypeScore
KBTBD7METTL15psi-mi:“MI:0914”(association)0.730
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
YWHABSHTN1psi-mi:“MI:0914”(association)0.530
YWHAESHTN1psi-mi:“MI:0914”(association)0.530
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
SYDE1Coq10bpsi-mi:“MI:0914”(association)0.350
SYDE1Ppfibp1psi-mi:“MI:0914”(association)0.350
Arhgap28EZRpsi-mi:“MI:0914”(association)0.350
YWHAHSHTN1psi-mi:“MI:0914”(association)0.350
YWHAQSHTN1psi-mi:“MI:0914”(association)0.350
CALM1MYO1Cpsi-mi:“MI:0914”(association)0.350
YWHAEDEPDC5psi-mi:“MI:0914”(association)0.350
LURAP1CIBAR1psi-mi:“MI:0914”(association)0.350
SYDE1POLR2Dpsi-mi:“MI:0914”(association)0.350
APBB1HERC2psi-mi:“MI:0914”(association)0.350
SYDE1APBB1psi-mi:“MI:0914”(association)0.350
AFG2BMMP24OSpsi-mi:“MI:0914”(association)0.350
CTNNA1EFCAB5psi-mi:“MI:0914”(association)0.350
DCLK1SYDE1psi-mi:“MI:0915”(physical association)0.000
SIPA1L1SYDE1psi-mi:“MI:0915”(physical association)0.000
KIF1CSYDE1psi-mi:“MI:0915”(physical association)0.000
MAST3SYDE1psi-mi:“MI:0915”(physical association)0.000
EIF4E2SYDE1psi-mi:“MI:0915”(physical association)0.000
SRGAP2SYDE1psi-mi:“MI:0915”(physical association)0.000
GIGYF1SYDE1psi-mi:“MI:0915”(physical association)0.000
NADKSYDE1psi-mi:“MI:0915”(physical association)0.000
NF1SYDE1psi-mi:“MI:0915”(physical association)0.000
CDC25BSYDE1psi-mi:“MI:0915”(physical association)0.000
CDC25CSYDE1psi-mi:“MI:0915”(physical association)0.000
AFDNSYDE1psi-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:

PathwayPartnersFoldFDR
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex680.6×3e-08
Activation of BAD and translocation to mitochondria576.1×5e-07
SARS-CoV-1 targets host intracellular signalling and regulatory pathways567.2×8e-07
Activation of BH3-only proteins549.6×2e-06
RHO GTPases activate PKNs638.1×8e-07
Intrinsic Pathway for Apoptosis529.3×2e-05
Translocation of SLC2A4 (GLUT4) to the plasma membrane721.6×2e-06
SARS-CoV-1-host interactions517.6×2e-04

GO biological processes:

GO termPartnersFoldFDR
protein targeting525.8×3e-04
substantia nigra development525.8×3e-04
intracellular protein localization710.3×8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

129 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance121
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

942 predictions. Top by Δscore:

VariantEffectΔscore
19:15107517:GCGCG:Gdonor_gain1.0000
19:15107519:GCG:Gdonor_gain1.0000
19:15107520:CG:Cdonor_gain1.0000
19:15107520:CGG:Cdonor_loss1.0000
19:15107521:GG:Gdonor_gain1.0000
19:15107522:G:GGdonor_gain1.0000
19:15107522:GTA:Gdonor_loss1.0000
19:15107523:T:Gdonor_loss1.0000
19:15110516:CTCA:Cacceptor_loss1.0000
19:15110519:A:AGacceptor_gain1.0000
19:15110519:AG:Aacceptor_gain1.0000
19:15110520:G:GGacceptor_gain1.0000
19:15110520:GG:Gacceptor_gain1.0000
19:15110520:GGGT:Gacceptor_gain1.0000
19:15110732:GCGG:Gdonor_gain1.0000
19:15110734:GG:Gdonor_gain1.0000
19:15110735:GG:Gdonor_gain1.0000
19:15110735:GGTG:Gdonor_loss1.0000
19:15110736:G:GGdonor_gain1.0000
19:15111310:CA:Cacceptor_loss1.0000
19:15111311:A:ACacceptor_loss1.0000
19:15111312:GGTA:Gacceptor_gain1.0000
19:15111409:G:GTdonor_gain1.0000
19:15111436:ACTGG:Adonor_loss1.0000
19:15111438:TGGTC:Tdonor_loss1.0000
19:15111439:GGTC:Gdonor_loss1.0000
19:15111440:G:GGdonor_gain1.0000
19:15111440:GT:Gdonor_loss1.0000
19:15111441:T:Gdonor_loss1.0000
19:15111789:AAGGG:Adonor_loss1.0000

AlphaMissense

4631 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:15111642:G:CK476N1.000
19:15111642:G:TK476N1.000
19:15111319:G:AG433R0.999
19:15111319:G:CG433R0.999
19:15111320:G:AG433E0.999
19:15111328:C:AR436S0.999
19:15111354:G:CK444N0.999
19:15111354:G:TK444N0.999
19:15111362:T:AL447H0.999
19:15111362:T:CL447P0.999
19:15111638:T:CL475P0.999
19:15111650:T:CL479P0.999
19:15112374:T:CL536P0.999
19:15112405:C:AN546K0.999
19:15112405:C:GN546K0.999
19:15112410:T:CM548T0.999
19:15112428:C:AA554D0.999
19:15112435:C:GC556W0.999
19:15112440:G:AG558E0.999
19:15110229:T:CF319S0.998
19:15110631:T:CF396L0.998
19:15110633:T:AF396L0.998
19:15110633:T:GF396L0.998
19:15110728:G:AG428E0.998
19:15111325:T:CY435H0.998
19:15111332:T:CL437P0.998
19:15111335:G:AC438Y0.998
19:15111338:G:AG439D0.998
19:15111374:T:CF451S0.998
19:15111429:T:AN469K0.998

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):

StudyTraitp-value
GCST003771_20Loneliness8.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007865loneliness 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.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, increases methylation5
Benzo(a)pyrenedecreases methylation, increases expression, increases methylation2
Doxorubicindecreases expression, affects response to substance2
GSK-J4increases expression1
FR900359affects phosphorylation1
sodium arsenateincreases abundance, increases expression1
terbufosincreases methylation1
sodium arseniteincreases expression1
sulindac sulfideincreases expression1
cupric chlorideincreases expression1
coumarindecreases phosphorylation1
muconaldehydedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Temozolomideincreases expression1
Leflunomidedecreases expression1
Acetaminophendecreases expression1
Arbutindecreases expression1
Arsenicincreases abundance, increases expression1
Calcitriolincreases expression1
Cisplatindecreases expression1
Fonofosincreases methylation1
Estradiolincreases expression, affects cotreatment1
Lipopolysaccharidesincreases expression, affects response to substance1
Parathionincreases methylation1
Silicon Dioxidedecreases methylation, increases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.