SYNGR3 Gene

Name	synaptogyrin 3
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSynaptogyrin‐3 (SYNGR3) is a synaptic vesicular membrane protein that plays a critical role in dopaminergic neurotransmission. It directly interacts with the dopamine transporter (DAT) through the cytoplasmic N termini of both proteins, forming a complex that also includes the vesicular monoamine transporter‐2 (VMAT2). This complex appears to couple dopamine re‐uptake with vesicular storage, thus contributing to efficient dopamine turnover at presynaptic terminals."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn the neuronal context, SYNGR3 is selectively distributed in discrete regions of the brain. Detailed subcellular analyses have shown that synaptogyrin-3 localizes to synaptic vesicles and can co-reside on the same vesicle with synaptogyrin-1, suggesting that distinct synaptogyrin isoforms may underlie functionally diverse populations of synapses."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAt the transcriptional level, the promoter of the SYNGR3 gene lacks classic TATA or CAAT boxes but contains an XCPE1 motif, SP1-binding sites, and several non-canonical NGFI-B response elements. These latter elements are bound by the nuclear-receptor NURR1, a factor critical for dopaminergic neuron differentiation and maintenance, and activation of NURR1 results in enhanced SYNGR3 expression. This regulatory mechanism suggests that SYNGR3 expression is directly linked to neuronal differentiation programs and may be modulated in disease states."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nMoreover, altered SYNGR3 expression has been associated with Parkinson’s disease (PD). Studies report that reduced SYNGR3 levels, as observed in PD brains, may contribute to impaired synaptic function, consistent with its role in facilitating dopamine uptake through DAT. This finding aligns with the notion that proper presynaptic vesicular dynamics are essential for maintaining dopaminergic signaling, and perturbations in SYNGR3 expression may exacerbate PD pathogenesis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its neuronal functions, SYNGR3 has emerged as a promising biomarker in the context of human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma. In these tumors, robust SYNGR3 expression is observed in both T cells and B cells. When combined with p16 localization, SYNGR3 not only provides enhanced sensitivity and specificity for HPV detection but also correlates with improved patient survival outcomes, underscoring a novel diagnostic and potentially prognostic role for SYNGR3 in oncology."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Loreto A Egaña, Rolando A Cuevas, Tracy B Baust, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Physical and functional interaction between the dopamine transporter and the synaptic vesicle protein synaptogyrin-3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurosci (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1523/JNEUROSCI.4559-08.2009"}], "href": "https://doi.org/10.1523/JNEUROSCI.4559-08.2009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19357284"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19357284"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Roger Belizaire, Cheryl Komanduri, Kerry Wooten, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of synaptogyrin 3 as a new synaptic vesicle protein."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Comp Neurol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/cne.20008"}], "href": "https://doi.org/10.1002/cne.20008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14755516"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14755516"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Lingfei Li, Philip Wing-Lok Ho, Huifang Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional Regulation of the Synaptic Vesicle Protein Synaptogyrin-3 ("}, {"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "SYNGR3"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": ") Gene: The Effects of NURR1 on Its Expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Mol Sci (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3390/ijms23073646"}], "href": "https://doi.org/10.3390/ijms23073646"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35409005"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35409005"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Philip Wing-Lok Ho, Lingfei Li, Hui-Fang Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "In vivo overexpression of synaptogyrin-3 promotes striatal synaptic dopamine uptake in LRRK2"}, {"type": "a", "children": [{"type": "t", "text": "sup"}], "href": "sup"}, {"type": "t", "text": "R1441G"}, {"type": "a", "children": [{"type": "t", "text": "/sup"}], "href": "/sup"}, {"type": "t", "text": " mutant mouse model of Parkinson's disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain Behav (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/brb3.2886"}], "href": "https://doi.org/10.1002/brb3.2886"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36624932"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36624932"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Ryan M Murphy, Jason Tasoulas, Alessandro Porrello, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Tumor Cell Extrinsic Synaptogyrin 3 Expression as a Diagnostic and Prognostic Biomarker in Head and Neck Cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Res Commun (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1158/2767-9764.crc-21-0135"}], "href": "https://doi.org/10.1158/2767-9764.crc-21-0135"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36148399"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36148399"}]}]}]}
Proteins	SNG3_HUMAN
NCBI Gene ID	9143
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SYNGR3 has 6,388 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 103 datasets.

Click the + buttons to view associations for SYNGR3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SYNGR3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SYNGR3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SYNGR3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SYNGR3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SYNGR3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SYNGR3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SYNGR3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SYNGR3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SYNGR3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SYNGR3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of SYNGR3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SYNGR3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SYNGR3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SYNGR3 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SYNGR3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SYNGR3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SYNGR3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of SYNGR3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SYNGR3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SYNGR3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing SYNGR3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SYNGR3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SYNGR3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of SYNGR3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SYNGR3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with SYNGR3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with SYNGR3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by SYNGR3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with SYNGR3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SYNGR3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SYNGR3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SYNGR3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at SYNGR3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SYNGR3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of SYNGR3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing SYNGR3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of SYNGR3 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with SYNGR3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing SYNGR3 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of SYNGR3 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.
	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	gene perturbations changing expression of SYNGR3 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.