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Aliases for SYN3 Gene

Aliases for SYN3 Gene

  • Synapsin III 2 3 4 5
  • CN28H9.2 (Synapsin III) 3
  • Synapsin-3 3

External Ids for SYN3 Gene

Previous GeneCards Identifiers for SYN3 Gene

  • GC22M029604
  • GC22M031233
  • GC22M032908
  • GC22M015865

Summaries for SYN3 Gene

Entrez Gene Summary for SYN3 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. The protein encoded by this gene shares the synapsin family domain model, with domains A, C, and E exhibiting the highest degree of conservation. The protein contains a unique domain J, located between domains C and E. Based on this gene's localization to 22q12.3, a possible schizophrenia susceptibility locus, and the established neurobiological roles of the synapsins, this family member may represent a candidate gene for schizophrenia. The TIMP3 gene is located within an intron of this gene and is transcribed in the opposite direction. Alternative splicing of this gene results in multiple splice variants that encode different isoforms. [provided by RefSeq, Oct 2008]

GeneCards Summary for SYN3 Gene

SYN3 (Synapsin III) is a Protein Coding gene. Diseases associated with SYN3 include Visual Epilepsy and Seizure Disorder. Among its related pathways are Transmission across Chemical Synapses and Neurotransmitter Release Cycle. An important paralog of this gene is SYN1.

UniProtKB/Swiss-Prot for SYN3 Gene

  • May be involved in the regulation of neurotransmitter release and synaptogenesis.

Gene Wiki entry for SYN3 Gene

Additional gene information for SYN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYN3 Gene

Genomics for SYN3 Gene

GeneHancer (GH) Regulatory Elements for SYN3 Gene

Promoters and enhancers for SYN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I033057 Promoter/Enhancer 1.3 EPDnew ENCODE 550.8 +0.1 78 1 SIN3A DMAP1 ZNF335 GLIS2 EGR1 SCRT2 ZNF143 CREM EGR2 USF2 SYN3 GC22M033050
GH22I032799 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.4 +255.8 255849 5.8 ZSCAN4 ARID4B KLF17 ZNF76 SIN3A DMAP1 YY1 ZNF335 GLIS2 SCRT2 TIMP3 SYN3 GC22M032814
GH22I032796 Enhancer 1.1 Ensembl ENCODE dbSUPER 6.4 +261.3 261322 0.7 CTCF RB1 RAD21 CC2D1A ZFHX2 PATZ1 ZNF143 SMC3 PRDM10 ZNF444 GC22P032796 SYN3 TIMP3
GH22I033018 Enhancer 0.6 ENCODE 11.3 +40.0 39950 0.2 CTCF ZNF654 HLF TRIM22 RAD21 ZSCAN5C SMC3 ZNF143 SMAD4 RUNX3 SYN3 ENSG00000232073 ENSG00000228194 GC22M033050
GH22I032819 Enhancer 0.7 ENCODE dbSUPER 9.6 +238.1 238090 0.9 ZFHX2 POLR2A ZSCAN4 EGR2 ENSG00000229673 SYN3 GC22M032814 TIMP3 GC22P032840 GC22P032841
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYN3 gene promoter:

Genomic Locations for SYN3 Gene

Genomic Locations for SYN3 Gene
550,370 bases
Minus strand

Genomic View for SYN3 Gene

Genes around SYN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYN3 Gene

Proteins for SYN3 Gene

  • Protein details for SYN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B1B1F9

    Protein attributes for SYN3 Gene

    580 amino acids
    Molecular mass:
    63303 Da
    Quaternary structure:
    • Interacts with CAPON.
    • Regulated by calcium. Calcium inhibits ATP binding to the C-domain.

    Three dimensional structures from OCA and Proteopedia for SYN3 Gene

neXtProt entry for SYN3 Gene

Post-translational modifications for SYN3 Gene

  • Phosphorylation at Ser-9 dissociates synapsins from synaptic vesicles.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SYN3 Gene

Domains & Families for SYN3 Gene

Gene Families for SYN3 Gene

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

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 SYN3: view

Function for SYN3 Gene

Molecular function for SYN3 Gene

GENATLAS Biochemistry:
synapsin IIIa,synaptic vesicle-associated phosphoprotein,involved in the regulation of neurotransmitter release,synaptogenesis and synaptic plasticity,with six transcripts (SYN3A to SYN3F),SYN3A,3B,3C deleted in fetal and adult brain,SYN30 only in fetal CNS,SYN3E and 3F non neuronal
UniProtKB/Swiss-Prot Function:
May be involved in the regulation of neurotransmitter release and synaptogenesis.

Phenotypes From GWAS Catalog for SYN3 Gene

Gene Ontology (GO) - Molecular Function for SYN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0005524 ATP binding TAS 15217342
genes like me logo Genes that share ontologies with SYN3: view
genes like me logo Genes that share phenotypes with SYN3: view

Animal Models for SYN3 Gene

MGI Knock Outs for SYN3:

Animal Model Products

CRISPR Products

miRNA for SYN3 Gene

miRTarBase miRNAs that target SYN3

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SYN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYN3 Gene

Localization for SYN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYN3 Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Note=Peripheral membrane protein localized to the cytoplasmic surface of synaptic vesicles.

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 SYN3 gene
Compartment Confidence
cytosol 3
nucleus 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SYN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008021 synaptic vesicle IEA,TAS 9539796
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0030054 cell junction IEA --
GO:0030672 synaptic vesicle membrane IEA --
genes like me logo Genes that share ontologies with SYN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYN3 Gene

Pathways & Interactions for SYN3 Gene

genes like me logo Genes that share pathways with SYN3: view

Pathways by source for SYN3 Gene

SIGNOR curated interactions for SYN3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SYN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007269 neurotransmitter secretion IEA --
GO:0032228 regulation of synaptic transmission, GABAergic TAS 15217342
genes like me logo Genes that share ontologies with SYN3: view

Drugs & Compounds for SYN3 Gene

(1) Drugs for SYN3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with SYN3: view

Transcripts for SYN3 Gene

Unigene Clusters for SYN3 Gene

Synapsin III:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SYN3

Alternative Splicing Database (ASD) splice patterns (SP) for SYN3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b
SP1: - -
SP2: - -

Relevant External Links for SYN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYN3 Gene

mRNA differential expression in normal tissues according to GTEx for SYN3 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.9), Brain - Cortex (x4.8), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for SYN3 Gene

This gene is overexpressed in Frontal cortex (31.7), Brain (25.9), and Fetal Brain (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SYN3 Gene

Protein tissue co-expression partners for SYN3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYN3 Gene:


SOURCE GeneReport for Unigene cluster for SYN3 Gene:


mRNA Expression by UniProt/SwissProt for SYN3 Gene:

Tissue specificity: Neuron specific. Detected predominantly in brain.

Evidence on tissue expression from TISSUES for SYN3 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with SYN3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYN3 Gene

Orthologs for SYN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYN3 33
  • 99.37 (n)
(Canis familiaris)
Mammalia -- 34
  • 93 (a)
SYN3 33
  • 90.2 (n)
-- 34
  • 84 (a)
(Bos Taurus)
Mammalia SYN3 34 33
  • 90.95 (n)
(Mus musculus)
Mammalia Syn3 16 34 33
  • 87.85 (n)
(Rattus norvegicus)
Mammalia Syn3 33
  • 87.33 (n)
(Monodelphis domestica)
Mammalia SYN3 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 73 (a)
-- 34
  • 64 (a)
-- 34
  • 62 (a)
(Gallus gallus)
Aves SYN3 34 33
  • 76.42 (n)
(Anolis carolinensis)
Reptilia SYN3 34
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia syn3 33
  • 70.27 (n)
African clawed frog
(Xenopus laevis)
Amphibia syn3-A 33
(Danio rerio)
Actinopterygii SYN3 34
  • 32 (a)
fruit fly
(Drosophila melanogaster)
Insecta Syn 35 33 34
  • 54.18 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003318 33
(Caenorhabditis elegans)
Secernentea snn-1 33 34
  • 46.46 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 65 (a)
-- 34
  • 46 (a)
Species where no ortholog for SYN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 SYN3 Gene

Gene Tree for SYN3 (if available)
Gene Tree for SYN3 (if available)

Paralogs for SYN3 Gene

Paralogs for SYN3 Gene

(3) SIMAP similar genes for SYN3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SYN3: view

Variants for SYN3 Gene

Sequence variations from dbSNP and Humsavar for SYN3 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1011302671 uncertain-significance, Pseudoinflammatory fundus dystrophy 32,862,859(-) C/T genic_upstream_transcript_variant, intron_variant
rs1031426000 uncertain-significance, Pseudoinflammatory fundus dystrophy 32,862,221(-) C/T genic_upstream_transcript_variant, intron_variant
rs1034054502 uncertain-significance, Pseudoinflammatory fundus dystrophy 32,860,172(-) A/G genic_upstream_transcript_variant, intron_variant
rs1039341802 uncertain-significance, Pseudoinflammatory fundus dystrophy 32,801,672(-) C/G/T genic_upstream_transcript_variant, intron_variant
rs1057519444 pathogenic, Cerebellar vermis atrophy, Generalized hypotonia, Global developmental delay, Seizures, Visual impairment 32,518,208(-) GG/AA coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SYN3 Gene

Variant ID Type Subtype PubMed ID
dgv1313e212 CNV loss 25503493
dgv20e194 CNV deletion 18987734
dgv2454n106 CNV deletion 24896259
dgv4561n100 CNV gain 25217958
esv1085289 CNV insertion 17803354
esv1328555 CNV insertion 17803354
esv1395557 CNV insertion 17803354
esv1664547 CNV deletion 17803354
esv23339 CNV gain 19812545
esv2476031 CNV deletion 19546169
esv2529621 CNV insertion 19546169
esv2638943 CNV deletion 19546169
esv2666744 CNV deletion 23128226
esv2724149 CNV deletion 23290073
esv2724150 CNV deletion 23290073
esv2724152 CNV deletion 23290073
esv2724153 CNV deletion 23290073
esv2724154 CNV deletion 23290073
esv2724155 CNV deletion 23290073
esv2742642 CNV deletion 23290073
esv2762119 CNV gain 21179565
esv3032679 CNV deletion 24192839
esv3356573 CNV duplication 20981092
esv3558080 CNV deletion 23714750
esv3558081 CNV deletion 23714750
esv3568368 CNV loss 25503493
esv3568369 CNV loss 25503493
esv3647609 CNV loss 21293372
esv3647611 CNV loss 21293372
esv3917 CNV loss 18987735
esv6171 CNV loss 19470904
esv998207 CNV deletion 20482838
nsv1056220 CNV gain 25217958
nsv1059368 CNV loss 25217958
nsv1061384 CNV loss 25217958
nsv1064719 CNV loss 25217958
nsv1071789 CNV deletion 25765185
nsv1071790 CNV deletion 25765185
nsv1071791 CNV deletion 25765185
nsv1111234 CNV tandem duplication 24896259
nsv1116956 CNV deletion 24896259
nsv1118950 CNV deletion 24896259
nsv1125230 CNV insertion 24896259
nsv1125755 CNV tandem duplication 24896259
nsv1129230 CNV insertion 24896259
nsv1131657 CNV deletion 24896259
nsv1136670 CNV deletion 24896259
nsv1152679 CNV insertion 26484159
nsv1160750 CNV duplication 26073780
nsv191235 CNV deletion 16902084
nsv191249 CNV insertion 16902084
nsv3599 CNV deletion 18451855
nsv3600 CNV insertion 18451855
nsv459875 CNV gain 19166990
nsv472826 CNV novel sequence insertion 20440878
nsv473313 CNV novel sequence insertion 20440878
nsv507934 OTHER sequence alteration 20534489
nsv588896 CNV gain 21841781
nsv588897 CNV loss 21841781
nsv953073 CNV deletion 24416366
nsv955479 CNV deletion 24416366
nsv955482 CNV deletion 24416366
nsv964625 CNV duplication 23825009

Variation tolerance for SYN3 Gene

Residual Variation Intolerance Score: 45.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.61; 72.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYN3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYN3 Gene

Disorders for SYN3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SYN3 Gene - From: ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
visual epilepsy
  • epilepsy, visual
seizure disorder
  • epilepsy
  • sczd
attention deficit-hyperactivity disorder
  • adhd
- elite association - COSMIC cancer census association via MalaCards
Search SYN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SYN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYN3 Gene

Publications for SYN3 Gene

  1. Association between synapsin III gene promoter SNPs and multiple sclerosis in Basque patients. (PMID: 18755822) Otaegui D … Lopez de Munain A (Multiple sclerosis (Houndmills, Basingstoke, England) 2009) 3 22 44 58
  2. Association and expression study of synapsin III and schizophrenia. (PMID: 19766700) Chen Q … Chen X (Neuroscience letters 2009) 3 22 44 58
  3. A third member of the synapsin gene family. (PMID: 9539796) Kao HT … Greengard P (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 58
  4. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PMID: 21998595) N'Diaye A … Haiman CA (PLoS genetics 2011) 3 44 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for SYN3 Gene

  • Addgene plasmids for SYN3

Sources for SYN3 Gene

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