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Aliases for SYN1 Gene

Aliases for SYN1 Gene

  • Synapsin I 2 3 4 5
  • Brain Protein 4.1 3 4
  • Synapsin Ib 3
  • Synapsin-1 3
  • SYN1A 3
  • SYN1b 3
  • SYNI 3

External Ids for SYN1 Gene

Previous GeneCards Identifiers for SYN1 Gene

  • GC0XM046235
  • GC0XM045692
  • GC0XM046478
  • GC0XM046477
  • GC0XM047187
  • GC0XM047316
  • GC0XM047431
  • GC0XM045143

Summaries for SYN1 Gene

Entrez Gene Summary for SYN1 Gene

  • This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for SYN1 Gene

SYN1 (Synapsin I) is a Protein Coding gene. Diseases associated with SYN1 include Epilepsy, X-Linked, With Variable Learning Disabilities And Behavior Disorders and Rett Syndrome. Among its related pathways are Synaptic vesicle cycle and Neurotransmitter Release Cycle. GO annotations related to this gene include protein kinase binding and transporter activity. An important paralog of this gene is SYN2.

UniProtKB/Swiss-Prot for SYN1 Gene

  • Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. The complex formed with NOS1 and CAPON proteins is necessary for specific nitric-oxid functions at a presynaptic level.

Gene Wiki entry for SYN1 Gene

Additional gene information for SYN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYN1 Gene

Genomics for SYN1 Gene

Regulatory Elements for SYN1 Gene

Enhancers for SYN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH047498 0.8 ENCODE dbSUPER 12.3 +121.3 121347 0.2 ZNF217 SMARCE1 CTBP1 GATA3 CEBPB DPF2 SYN1 CFP LINC01560 GC0XP047511 ZNF41
GH0XH047595 0.6 Ensembl ENCODE 13.4 +24.0 24036 1.7 MAFK SYN1 CFP ELK1 UXT-AS1 MIR4769 GC0XM047592
GH0XH047523 1.7 FANTOM5 Ensembl ENCODE dbSUPER 1.8 +96.2 96243 1 ATF1 RB1 ARID4B ZNF2 RAD21 ZNF366 ZNF143 RCOR1 ZNF391 ATF7 ZNF41 LINC01560 CDK16 USP11 ELK1 CFP SYN1 SPACA5 NUS1P1 ARAF
GH0XH048020 1.5 FANTOM5 Ensembl ENCODE 1.6 -401.5 -401483 2 TBP PKNOX1 FOXA2 ZNF76 KLF17 SIN3A RAD21 BRCA1 ZNF2 YY1 ENSG00000204620 INE1 FTSJ1 ZNF81 RBM3 ZNF630 ZNF182 NUS1P1 UBA1 PQBP1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYN1 on UCSC Golden Path with GeneCards custom track

Promoters for SYN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000246430 143 801 ATF1 ARID4B SIN3A ZNF766 GLIS2 ZNF143 ZNF207 ATF7 RUNX3 YY2

Genomic Locations for SYN1 Gene

Genomic Locations for SYN1 Gene
48,046 bases
Minus strand

Genomic View for SYN1 Gene

Genes around SYN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYN1 Gene

Proteins for SYN1 Gene

  • Protein details for SYN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B1AJQ1
    • O75825
    • Q5H9A9

    Protein attributes for SYN1 Gene

    705 amino acids
    Molecular mass:
    74111 Da
    Quaternary structure:
    • Homodimer. Interacts with CAPON. Forms a ternary complex with NOS1. Isoform Ib interacts with PRNP (By similarity).

    Alternative splice isoforms for SYN1 Gene


neXtProt entry for SYN1 Gene

Post-translational modifications for SYN1 Gene

  • Phosphorylation at Ser-9 dissociates synapsins from synaptic vesicles.
  • Substrate of at least four different protein kinases. It is probable that phosphorylation plays a role in the regulation of synapsin-1 in the nerve terminal.
  • Glycosylation at posLast=5555, Thr87, posLast=9696, Ser103, posLast=261261, posLast=432432, Thr526, posLast=564564, and Ser578
  • Modification sites at PhosphoSitePlus

Other Protein References for SYN1 Gene

No data available for DME Specific Peptides for SYN1 Gene

Domains & Families for SYN1 Gene

Gene Families for SYN1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SYN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The A region binds phospholipids with a preference for negatively charged species.
  • Belongs to the synapsin family.
  • The A region binds phospholipids with a preference for negatively charged species.
  • Belongs to the synapsin family.
genes like me logo Genes that share domains with SYN1: view

Function for SYN1 Gene

Molecular function for SYN1 Gene

GENATLAS Biochemistry:
synapsin I,synaptic vesicle associated phosphoprotein,involved in the fine regulation of neurotransmitter release
UniProtKB/Swiss-Prot Function:
Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. The complex formed with NOS1 and CAPON proteins is necessary for specific nitric-oxid functions at a presynaptic level.

Gene Ontology (GO) - Molecular Function for SYN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0003824 catalytic activity IEA --
GO:0005215 transporter activity TAS 2110562
GO:0005515 protein binding IPI 22163275
GO:0005524 ATP binding TAS 15217342
genes like me logo Genes that share ontologies with SYN1: view
genes like me logo Genes that share phenotypes with SYN1: view

Human Phenotype Ontology for SYN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYN1 Gene

MGI Knock Outs for SYN1:

Animal Model Products

miRNA for SYN1 Gene

miRTarBase miRNAs that target SYN1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for SYN1 Gene

Localization for SYN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYN1 Gene

Cell junction, synapse. Golgi apparatus.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYN1 gene
Compartment Confidence
nucleus 5
cytosol 5
golgi apparatus 3
plasma membrane 2
cytoskeleton 2
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SYN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000795 synaptonemal complex IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005829 cytosol IEA --
GO:0008021 synaptic vesicle IEA,TAS 16141272
GO:0014069 postsynaptic density IEA --
genes like me logo Genes that share ontologies with SYN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYN1 Gene

Pathways & Interactions for SYN1 Gene

genes like me logo Genes that share pathways with SYN1: view

SIGNOR curated interactions for SYN1 Gene

Is activated by:
Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for SYN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007268 chemical synaptic transmission TAS 2110562
GO:0007269 neurotransmitter secretion IEA --
GO:0046928 regulation of neurotransmitter secretion TAS 21563316
GO:0097091 synaptic vesicle clustering IEA --
GO:2000300 regulation of synaptic vesicle exocytosis NAS 10099709
genes like me logo Genes that share ontologies with SYN1: view

Drugs & Compounds for SYN1 Gene

(1) Drugs for SYN1 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine 5'-[γ-thio]triphosphate Experimental Pharma Target 0
genes like me logo Genes that share compounds with SYN1: view

Transcripts for SYN1 Gene

Unigene Clusters for SYN1 Gene

Synapsin I:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYN1 Gene

No ASD Table

Relevant External Links for SYN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYN1 Gene

mRNA differential expression in normal tissues according to GTEx for SYN1 Gene

This gene is overexpressed in Brain - Cortex (x8.6), Brain - Frontal Cortex (BA9) (x7.8), Brain - Anterior cingulate cortex (BA24) (x7.0), and Brain - Hippocampus (x4.3).

Protein differential expression in normal tissues from HIPED for SYN1 Gene

This gene is overexpressed in Brain (42.4) and Frontal cortex (23.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYN1 Gene

Protein tissue co-expression partners for SYN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYN1 Gene:


SOURCE GeneReport for Unigene cluster for SYN1 Gene:


Evidence on tissue expression from TISSUES for SYN1 Gene

  • Nervous system(4.9)
  • Adrenal gland(2)
  • Eye(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SYN1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • head
  • skull
genes like me logo Genes that share expression patterns with SYN1: view

No data available for mRNA Expression by UniProt/SwissProt for SYN1 Gene

Orthologs for SYN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia SYN1 33 34
  • 92.56 (n)
(Bos Taurus)
Mammalia SYN1 33 34
  • 92.53 (n)
(Mus musculus)
Mammalia Syn1 34 16 33
  • 89.93 (n)
(Rattus norvegicus)
Mammalia Syn1 33
  • 89.81 (n)
(Monodelphis domestica)
Mammalia SYN1 34
  • 65 (a)
(Ornithorhynchus anatinus)
Mammalia SYN1 34
  • 52 (a)
(Gallus gallus)
Aves SYN1 34
  • 59 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 82 (a)
-- 34
  • 55 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100158514 33
  • 65.29 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.21531 33
(Danio rerio)
Actinopterygii syn1 34 33
  • 70.69 (n)
fruit fly
(Drosophila melanogaster)
Insecta Syn 35 34
  • 44 (a)
(Caenorhabditis elegans)
Secernentea snn-1 34
  • 24 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
-- 34
  • 46 (a)
Species where no ortholog for SYN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SYN1 Gene

Gene Tree for SYN1 (if available)
Gene Tree for SYN1 (if available)

Paralogs for SYN1 Gene

Paralogs for SYN1 Gene

(3) SIMAP similar genes for SYN1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SYN1: view

Variants for SYN1 Gene

Sequence variations from dbSNP and Humsavar for SYN1 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs137852560 Pathogenic 47,576,222(-) GCTGT(A/G)GGTGG reference, stop-gained
rs200533370 Pathogenic 47,574,285(+) GGATG(C/T)CTGAC reference, missense
rs397514679 Pathogenic 47,574,321(-) CTCCC(C/T)AGCGC reference, stop-gained
rs397514680 Pathogenic 47,574,336(-) CGCCC(A/C/G)CCTCT reference, missense
rs757027813 Pathogenic 47,575,169(+) CTGTC(A/G/T)CTGCC reference, synonymous-codon, stop-gained

Variation tolerance for SYN1 Gene

Gene Damage Index Score: 2.80; 47.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYN1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SYN1 Gene

Disorders for SYN1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SYN1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epilepsy, x-linked, with variable learning disabilities and behavior disorders
  • x-linked epilepsy-learning disabilities-behavior disorders syndrome
rett syndrome
  • rett syndrome, preserved speech variant
- elite association - COSMIC cancer census association via MalaCards
Search SYN1 in MalaCards View complete list of genes associated with diseases


  • Epilepsy X-linked, with variable learning disabilities and behavior disorders (XELBD) [MIM:300491]: A neurologic disorder characterized by variable combinations of epilepsy, learning difficulties, macrocephaly, and aggressive behavior. {ECO:0000269 PubMed:14985377}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SYN1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SYN1: view

No data available for Genatlas for SYN1 Gene

Publications for SYN1 Gene

  1. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60
  2. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 45 60
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 60
  4. Phosphoproteomic analysis of synaptosomes from human cerebral cortex. (PMID: 15822905) DeGiorgis JA … Dosemeci A (Journal of proteome research 2005) 3 4 60
  5. Identification of a mutation in synapsin I, a synaptic vesicle protein, in a family with epilepsy. (PMID: 14985377) Garcia CC … Goodship JA (Journal of medical genetics 2004) 3 4 60

Products for SYN1 Gene

Sources for SYN1 Gene

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