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Aliases for SYNGR3 Gene

Aliases for SYNGR3 Gene

  • Synaptogyrin 3 2 3 5
  • Synaptogyrin-3 3

External Ids for SYNGR3 Gene

Previous GeneCards Identifiers for SYNGR3 Gene

  • GC16P002057
  • GC16P002067
  • GC16P001979
  • GC16P002040
  • GC16P001966
  • GC16P002044
  • GC16P002046
  • GC16P002050
  • GC16P002060
  • GC16P002084
  • GC16P002098
  • GC16P002117

Summaries for SYNGR3 Gene

Entrez Gene Summary for SYNGR3 Gene

  • This gene encodes an integral membrane protein. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it is a synaptic vesicle protein that also interacts with the dopamine transporter. The gene product belongs to the synaptogyrin gene family. [provided by RefSeq, Dec 2010]

GeneCards Summary for SYNGR3 Gene

SYNGR3 (Synaptogyrin 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include protein N-terminus binding and SH2 domain binding. An important paralog of this gene is SYNGR1.

UniProtKB/Swiss-Prot for SYNGR3 Gene

  • May play a role in regulated exocytosis. May indirectly regulate the activity of the plasma membrane dopamine transporter SLC6A3 and thereby regulate dopamine transport back from the synaptic cleft into the presynaptic terminal.

Additional gene information for SYNGR3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNGR3 Gene

Genomics for SYNGR3 Gene

GeneHancer (GH) Regulatory Elements for SYNGR3 Gene

Promoters and enhancers for SYNGR3 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
GH16I001989 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 550.8 +2.3 2323 4.4 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 ZNF263 ENSG00000261790 SYNGR3 ENSG00000255513 GFER ZNF598 MAPK8IP3 SPSB3 EME2 ENSG00000260107
GH16I001990 Enhancer 0.7 ENCODE 550.8 -0.2 -195 0 ZIC2 BCL11B HIC1 ZFHX2 GLIS2 ZNF366 PATZ1 SCRT2 ZNF391 ZNF600 ENSG00000261790 SYNGR3 NOXO1
GH16I001962 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 22.8 -25.4 -25438 4.1 HDGF HNRNPUL1 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ENSG00000255513 SNORA64 SNHG9 RPS2 GC16M001962 GC16M001963 GC16M001965 GC16M001966 GC16P001995 GC16P002197
GH16I002032 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 12.2 +48.9 48860 12.8 CLOCK FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A DMAP1 YY1 SLC30A9 SLC9A3R2 PKD1 RAB26 TRAF7 SNORD60 SYNGR3 ENSG00000255513 BRICD5 JPT2 HAGH
GH16I001982 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 5.7 -5.2 -5173 3.3 HNRNPUL1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 GFER NOXO1 ENSG00000255513 ENSG00000261505 SRRM2 LOC105371055 UBE2I ENSG00000260954 TRAF7 ENSG00000260051
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYNGR3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYNGR3 gene promoter:

Genomic Locations for SYNGR3 Gene

Genomic Locations for SYNGR3 Gene
4,616 bases
Plus strand

Genomic View for SYNGR3 Gene

Genes around SYNGR3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNGR3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNGR3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNGR3 Gene

Proteins for SYNGR3 Gene

  • Protein details for SYNGR3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R9S0

    Protein attributes for SYNGR3 Gene

    229 amino acids
    Molecular mass:
    24555 Da
    Quaternary structure:
    • Interacts (via N-terminus) with SLC6A3 (via N-terminus). May interact with VMAT2.

neXtProt entry for SYNGR3 Gene

Post-translational modifications for SYNGR3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYNGR3 Gene

No data available for DME Specific Peptides for SYNGR3 Gene

Domains & Families for SYNGR3 Gene

Gene Families for SYNGR3 Gene

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

Protein Domains for SYNGR3 Gene


Suggested Antigen Peptide Sequences for SYNGR3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the synaptogyrin family.
  • Belongs to the synaptogyrin family.
genes like me logo Genes that share domains with SYNGR3: view

Function for SYNGR3 Gene

Molecular function for SYNGR3 Gene

GENATLAS Biochemistry:
synaptogyrin 3,putative vesicle protein,expressed in brain and placenta
UniProtKB/Swiss-Prot Function:
May play a role in regulated exocytosis. May indirectly regulate the activity of the plasma membrane dopamine transporter SLC6A3 and thereby regulate dopamine transport back from the synaptic cleft into the presynaptic terminal.

Gene Ontology (GO) - Molecular Function for SYNGR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042169 SH2 domain binding IEA --
GO:0047485 protein N-terminus binding IEA --
genes like me logo Genes that share ontologies with SYNGR3: view
genes like me logo Genes that share phenotypes with SYNGR3: view

Animal Model Products

CRISPR Products

miRNA for SYNGR3 Gene

miRTarBase miRNAs that target SYNGR3

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYNGR3 Gene

Localization for SYNGR3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNGR3 Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein. Cell junction, synapse. Note=Found at the neuromuscular synapses. {ECO:0000250 UniProtKB:Q8R191}.

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 SYNGR3 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYNGR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008021 synaptic vesicle ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS,IEA 9760194
GO:0030054 cell junction IEA --
GO:0030672 synaptic vesicle membrane IBA --
genes like me logo Genes that share ontologies with SYNGR3: view

Pathways & Interactions for SYNGR3 Gene

SuperPathways for SYNGR3 Gene

No Data Available

Interacting Proteins for SYNGR3 Gene

Gene Ontology (GO) - Biological Process for SYNGR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0021762 substantia nigra development IEP,HEP 22926577
GO:0032411 positive regulation of transporter activity IEA,ISS --
GO:0045055 regulated exocytosis IEA,ISS --
genes like me logo Genes that share ontologies with SYNGR3: view

No data available for Pathways by source and SIGNOR curated interactions for SYNGR3 Gene

Drugs & Compounds for SYNGR3 Gene

No Compound Related Data Available

Transcripts for SYNGR3 Gene

Unigene Clusters for SYNGR3 Gene

Synaptogyrin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNGR3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c
SP1: - - - - - -
SP2: - - -
SP3: - - - -
SP4: -
SP5: -

Relevant External Links for SYNGR3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYNGR3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYNGR3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNGR3 Gene

This gene is overexpressed in Brain - Cortex (x6.7), Brain - Hypothalamus (x6.2), Brain - Anterior cingulate cortex (BA24) (x6.1), and Brain - Frontal Cortex (BA9) (x5.9).

Protein differential expression in normal tissues from HIPED for SYNGR3 Gene

This gene is overexpressed in Frontal cortex (48.5) and Brain (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYNGR3 Gene

Protein tissue co-expression partners for SYNGR3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYNGR3 Gene:


SOURCE GeneReport for Unigene cluster for SYNGR3 Gene:


mRNA Expression by UniProt/SwissProt for SYNGR3 Gene:

Tissue specificity: Expressed in brain and placenta.

Evidence on tissue expression from TISSUES for SYNGR3 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with SYNGR3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNGR3 Gene

Orthologs for SYNGR3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYNGR3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYNGR3 34
  • 94 (a)
(Bos Taurus)
Mammalia SYNGR3 33 34
  • 90.98 (n)
(Canis familiaris)
Mammalia SYNGR3 33
  • 90.88 (n)
(Mus musculus)
Mammalia Syngr3 33 16 34
  • 86.17 (n)
(Rattus norvegicus)
Mammalia Syngr3 33
  • 85.46 (n)
(Monodelphis domestica)
Mammalia SYNGR3 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia SYNGR3 34
  • 72 (a)
(Gallus gallus)
Aves SYNGR3 33 34
  • 71.32 (n)
(Anolis carolinensis)
Reptilia SYNGR3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia syngr3 33
  • 64.9 (n)
(Danio rerio)
Actinopterygii syngr3a 33 34
  • 63.86 (n)
syngr3b 34
  • 58 (a)
fruit fly
(Drosophila melanogaster)
Insecta synaptogyrin 35 34
  • 38 (a)
(Caenorhabditis elegans)
Secernentea sng-1 34
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
Species where no ortholog for SYNGR3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 SYNGR3 Gene

Gene Tree for SYNGR3 (if available)
Gene Tree for SYNGR3 (if available)

Paralogs for SYNGR3 Gene

Paralogs for SYNGR3 Gene

(3) SIMAP similar genes for SYNGR3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SYNGR3: view

Variants for SYNGR3 Gene

Sequence variations from dbSNP and Humsavar for SYNGR3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000711983 -- 1,992,324(+) G/T intron_variant
rs1000976998 -- 1,992,833(+) G/A/T intron_variant
rs1001374114 -- 1,994,493(+) TTTTT/TTTTTTTT downstream_transcript_variant
rs1001532463 -- 1,989,601(+) G/A upstream_transcript_variant
rs1001661328 -- 1,994,773(+) C/T downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SYNGR3 Gene

Variant ID Type Subtype PubMed ID
dgv336n27 CNV loss 19166990
dgv455n67 CNV gain 20364138
dgv4858n54 CNV loss 21841781
dgv4859n54 CNV loss 21841781
esv2422427 CNV duplication 17116639
nsv1136206 CNV deletion 24896259
nsv1160329 CNV deletion 26073780
nsv471070 CNV gain 18288195
nsv471072 CNV loss 18288195
nsv521569 CNV loss 19592680
nsv523037 CNV loss 19592680
nsv571179 CNV loss 21841781
nsv827501 CNV loss 20364138
nsv952901 CNV deletion 24416366

Variation tolerance for SYNGR3 Gene

Gene Damage Index Score: 2.01; 37.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNGR3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNGR3 Gene

Disorders for SYNGR3 Gene

Additional Disease Information for SYNGR3

No disorders were found for SYNGR3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYNGR3 Gene

Publications for SYNGR3 Gene

  1. Characterization of the human synaptogyrin gene family. (PMID: 9760194) Kedra D … Dumanski JP (Human genetics 1998) 2 3 4 22 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X … Chen J (Molecular systems biology 2015) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for SYNGR3 Gene

Sources for SYNGR3 Gene

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