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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SYN1
synapsin I
Chromosome X Β· Xp11.3-p11.23
NCBI Gene: 6853Ensembl: ENSG00000008056.15HGNC: HGNC:11494UniProt: P17600
87PubMed Papers
22Diseases
0Drugs
67Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
presynapsecytoskeletonregulation of synaptic vesicle exocytosisprotein bindingepilepsy, X-linked 1, with variable learning disabilities and behavior disordersX-linked epilepsy - learning disabilities - behavior disordersX-linked non-syndromic intellectual disabilitygenetic disorder
✦AI Summary

SYN1 (synapsin I) is a neuronal phosphoprotein that coats synaptic vesicles and binds to the cytoskeleton, serving as a critical regulator of synaptic vesicle trafficking and neurotransmitter release at presynaptic terminals 1. The protein functions as a cytoskeletal protein-membrane anchor that coordinates synaptic vesicle clustering and exocytosis, thereby controlling chemical synaptic transmission efficiency 2. SYN1 also participates in axon outgrowth and synaptogenesis regulation, with evidence suggesting involvement in nitric oxide signaling through interaction with NOS1 and CAPON proteins at presynaptic sites. Pathogenic SYN1 variants cause X-linked epilepsy characterized by a distinctive electroclinical phenotype, primarily manifesting reflex seizures triggered by cutaneous water contact or defecation, with temporo-perisylvian seizure semiology 3. Affected individuals frequently present developmental delay and behavioral disorders alongside epilepsy 1. Functional connectivity analysis reveals increased temporal lobe connectivity and a shift toward lower-frequency EEG bands in SYN1-related epilepsy 3. Therapeutically, lamotrigine, lacosamide, carbamazepine, and oxcarbazepine demonstrate superior seizure control compared to valproic acid and levetiracetam in this syndrome, with sodium channel blockers emerging as the optimal treatment strategy 4. Additionally, SYN1 expression serves as a synaptic plasticity biomarker, with reduced levels observed in gliomas and depression-associated conditions 56.

Sources cited
1
SYN1 variants are recognized as causing X-linked epilepsy with developmental and behavioral features
PMID: 38612920
2
SYN1-related epilepsy presents distinctive electroclinical pattern with reflex seizures triggered by water contact and temporo-perisylvian semiology
PMID: 39177219
3
SYN1 is a synaptic plasticity biomarker involved in regulating synaptic vesicle exocytosis and neurotransmitter release
PMID: 39089658
4
Lamotrigine, lacosamide, and carbamazepine show superior seizure control in SYN1-related epilepsy compared to valproic acid and levetiracetam
PMID: 40554312
5
SYN1 expression is downregulated in gliomas through REST/CoREST-mediated transcriptional repression
PMID: 27685921
6
SYN1 is a synaptic plasticity biomarker whose expression is restored in depression models following treatment
PMID: 40174476
Disease Associationsβ“˜22
epilepsy, X-linked 1, with variable learning disabilities and behavior disordersOpen Targets
0.77Strong
X-linked epilepsy - learning disabilities - behavior disordersOpen Targets
0.75Strong
X-linked non-syndromic intellectual disabilityOpen Targets
0.69Moderate
genetic disorderOpen Targets
0.45Moderate
X-linked complex neurodevelopmental disorderOpen Targets
0.37Weak
epilepsyOpen Targets
0.35Weak
SeizureOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.31Weak
autism spectrum disorderOpen Targets
0.12Weak
Generalized epilepsy with febrile seizures-plusOpen Targets
0.07Suggestive
generalised epilepsyOpen Targets
0.07Suggestive
acute respiratory distress syndromeOpen Targets
0.06Suggestive
autosomal dominant epilepsy with auditory featuresOpen Targets
0.06Suggestive
Alzheimer diseaseOpen Targets
0.06Suggestive
Benign familial neonatal seizuresOpen Targets
0.06Suggestive
Febrile seizure (within the age range of 3 months to 6 years)Open Targets
0.06Suggestive
temporal lobe epilepsyOpen Targets
0.06Suggestive
juvenile myoclonic epilepsyOpen Targets
0.06Suggestive
neoplasmOpen Targets
0.05Suggestive
benign familial infantile epilepsyOpen Targets
0.05Suggestive
Epilepsy, X-linked 1, with variable learning disabilities and behavior disordersUniProt
Intellectual developmental disorder, X-linked 50UniProt
Pathogenic Variants67
NM_006950.3(SYN1):c.1258dup (p.Arg420fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|SYN1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 420
NM_006950.3(SYN1):c.1259G>A (p.Arg420Gln)Likely pathogenic
Intellectual disability, X-linked 50|not provided|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 420
NM_006950.3(SYN1):c.361G>T (p.Glu121Ter)Pathogenic
not provided|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2024β†’ Residue 121
NM_006950.3(SYN1):c.838-2A>GLikely pathogenic
not provided|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|SYN1-related disorder
β˜…β˜…β˜†β˜†2023
NM_006950.3(SYN1):c.528-2A>TPathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|not provided
β˜…β˜…β˜†β˜†2022
NM_006950.3(SYN1):c.2del (p.Met1fs)Pathogenic
not provided|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2022β†’ Residue 1
NM_006950.3(SYN1):c.1264C>T (p.Arg422Ter)Pathogenic
not provided|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2022β†’ Residue 422
NM_006950.3(SYN1):c.1439dup (p.Leu481fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2022β†’ Residue 481
NM_006950.3(SYN1):c.1001del (p.Asn334fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2022β†’ Residue 334
NM_006950.3(SYN1):c.1447C>T (p.Gln483Ter)Pathogenic
Seizure|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜…β˜†β˜†2022β†’ Residue 483
NM_006950.3(SYN1):c.745C>T (p.Gln249Ter)Pathogenic
Intellectual disability|Intellectual disability, X-linked 50
β˜…β˜…β˜†β˜†2022β†’ Residue 249
NM_006950.3(SYN1):c.700C>T (p.Arg234Ter)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|not provided|Intellectual disability, X-linked 50
β˜…β˜…β˜†β˜†2022β†’ Residue 234
NM_006950.3(SYN1):c.1131del (p.Lys378fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2025β†’ Residue 378
NM_006950.3(SYN1):c.685-2A>GLikely pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2025
NM_006950.3(SYN1):c.1144del (p.Asp382fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2025β†’ Residue 382
NM_006950.3(SYN1):c.1158+1G>ALikely pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2025
NM_006950.3(SYN1):c.1321del (p.Ala441fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 441
NM_006950.3(SYN1):c.1258_1261dup (p.Gln421fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2024β†’ Residue 421
NM_006950.3(SYN1):c.1166dup (p.Ser390fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|Epilepsy
β˜…β˜†β˜†β˜†2024β†’ Residue 390
NM_006950.3(SYN1):c.57_63del (p.Asn19fs)Pathogenic
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
β˜…β˜†β˜†β˜†2024β†’ Residue 19
View on ClinVar β†—
Related Genes
CAMK2AProtein interaction100%SLC17A7Protein interaction100%CALML4Protein interaction100%CALML5Protein interaction100%CALML3Protein interaction100%CALML6Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Heart
10%
Bone Marrow
3%
Ovary
2%
Liver
1%
Lung
1%
Gene Interaction Network
Click a node to explore
SYN1CAMK2ASLC17A7CALML4CALML5CALML3CALML6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P17600
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.32Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.18 [0.11–0.32]
RankingsWhere SYN1 stands among ~20K protein-coding genes
  • #5,519of 20,598
    Most Researched87
  • #1,086of 5,498
    Most Pathogenic Variants67 Β· top quartile
  • #1,318of 17,882
    Most Constrained (LOEUF)0.32 Β· top 10%
Genes detectedSYN1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
X-Linked Epilepsies: A Narrative Review.
PMID: 38612920
Int J Mol Sci Β· 2024
1.00
2
Cooperative CAR targeting to selectively eliminate AML and minimize escape.
PMID: 37802054
Cancer Cell Β· 2023
0.90
3
Buyang huanwu decoction improves synaptic plasticity of ischemic stroke by regulating the cAMP/PKA/CREB pathway.
PMID: 39089658
J Ethnopharmacol Β· 2024
0.80
4
Electro-Clinical Features and Functional Connectivity Analysis in SYN1-Related Epilepsy.
PMID: 39177219
Ann Neurol Β· 2024
0.70
5
A novel human endogenous retroviral protein inhibits cell-cell fusion.
PMID: 23492904
Sci Rep Β· 2013
0.60