This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced varia... See more...

Aliases for SYNGR1 Gene

Aliases for SYNGR1 Gene

  • Synaptogyrin 1 2 3 5
  • Synaptogyrin-1 3 4

External Ids for SYNGR1 Gene

Previous GeneCards Identifiers for SYNGR1 Gene

  • GC22P036360
  • GC22P037989
  • GC22P037988
  • GC22P038070
  • GC22P039745
  • GC22P022711

Summaries for SYNGR1 Gene

Entrez Gene Summary for SYNGR1 Gene

  • This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for SYNGR1 Gene

SYNGR1 (Synaptogyrin 1) is a Protein Coding gene. Diseases associated with SYNGR1 include Megalencephalic Leukoencephalopathy With Subcortical Cysts 1 and Berylliosis. Among its related pathways are Innate Immune System. An important paralog of this gene is SYNGR3.

UniProtKB/Swiss-Prot Summary for SYNGR1 Gene

  • May play a role in regulated exocytosis. Modulates the localization of synaptophysin/SYP into synaptic-like microvesicles and may therefore play a role in synaptic-like microvesicle formation and/or maturation (By similarity). Involved in the regulation of short-term and long-term synaptic plasticity (By similarity).

Gene Wiki entry for SYNGR1 Gene

Additional gene information for SYNGR1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYNGR1 Gene

Genomics for SYNGR1 Gene

GeneHancer (GH) Regulatory Elements for SYNGR1 Gene

Promoters and enhancers for SYNGR1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J039348 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 523.5 +0.8 842 3.9 ZBTB40 JUND CTCF ZNF639 ZIC2 ZBTB11 ZNF423 ZBTB26 TRIM28 EZH2 SYNGR1 RPL3 DDX17 SNORD83B PRDX3P1 JOSD1 TNRC6B ENSG00000280216
GH22J039362 Promoter/Enhancer 1.3 EPDnew ENCODE CraniofacialAtlas dbSUPER 510.3 +13.5 13521 2.7 NRF1 ZIC2 GABPA HDAC2 TCF12 NFE2 TAL1 POLR2A MAFG GATA2 SYNGR1 RPL3 TAB1 FUNDC2P4 CBX7 MGAT3 ENSG00000280216
GH22J039452 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 23.3 +104.2 104222 3.3 ZBTB40 PHB2 ZBTB11 MYC CTBP1 ZNF341 RBM25 HDAC3 NCOR1 KDM1A MGAT3 SYNGR1 MGAT3-AS1 MIEF1 lnc-RPS19BP1-4
GH22J039399 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 19.7 +50.0 49976 2.2 FOXK2 EP300 CTCF SIN3A NRF1 MYC POLR2G PHF8 ZFX ZNF639 TAB1 piR-32214-449 SYNGR1 lnc-MGAT3-4
GH22J039388 Promoter/Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas 27.8 +38.9 38937 1.7 NRF1 USF1 ZBTB26 SAP30 KLF7 CTBP1 MYC HDAC2 KMT2B KLF9 SYNGR1 MGAT3 RPL3 MIEF1 CACNA1I CBX7 APOBEC3G APOBEC3D RF00017-3844 piR-55667
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYNGR1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYNGR1

Top Transcription factor binding sites by QIAGEN in the SYNGR1 gene promoter:
  • GATA-1
  • Pax-2
  • Pax-2a
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for SYNGR1 Gene

Genomic Locations for SYNGR1 Gene
chr22:39,349,925-39,385,588
(GRCh38/hg38)
Size:
35,664 bases
Orientation:
Plus strand
chr22:39,745,930-39,781,593
(GRCh37/hg19)
Size:
35,664 bases
Orientation:
Plus strand

Genomic View for SYNGR1 Gene

Genes around SYNGR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNGR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNGR1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNGR1 Gene

Proteins for SYNGR1 Gene

  • Protein details for SYNGR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43759-SNG1_HUMAN
    Recommended name:
    Synaptogyrin-1
    Protein Accession:
    O43759
    Secondary Accessions:
    • A6NP69
    • A8K0E2
    • O43757
    • O43758
    • Q53Y02
    • Q96J56
    • Q9UGZ4

    Protein attributes for SYNGR1 Gene

    Size:
    233 amino acids
    Molecular mass:
    25456 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SYNGR1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNGR1 Gene

Post-translational modifications for SYNGR1 Gene

  • Ubiquitination at Lys10
  • Modification sites at PhosphoSitePlus

Other Protein References for SYNGR1 Gene

No data available for DME Specific Peptides for SYNGR1 Gene

Domains & Families for SYNGR1 Gene

Gene Families for SYNGR1 Gene

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

Protein Domains for SYNGR1 Gene

Blocks:
  • Marvel
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYNGR1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52856, highly similar to Synaptogyrin-1 (B5MCD7_HUMAN)
  • Synaptogyrin-1 (SNG1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43759

UniProtKB/Swiss-Prot:

SNG1_HUMAN :
  • Belongs to the synaptogyrin family.
Family:
  • Belongs to the synaptogyrin family.
genes like me logo Genes that share domains with SYNGR1: view

Function for SYNGR1 Gene

Molecular function for SYNGR1 Gene

UniProtKB/Swiss-Prot Function:
May play a role in regulated exocytosis. Modulates the localization of synaptophysin/SYP into synaptic-like microvesicles and may therefore play a role in synaptic-like microvesicle formation and/or maturation (By similarity). Involved in the regulation of short-term and long-term synaptic plasticity (By similarity).
GENATLAS Biochemistry:
synaptogyrin,putative vesicle protein,expressed in neurons of the central nervous system,with three alternatively spliced isoforms,SYNGR1a,SYNGR1b,SYNGR1c

Phenotypes From GWAS Catalog for SYNGR1 Gene

Gene Ontology (GO) - Molecular Function for SYNGR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SYNGR1: view
genes like me logo Genes that share phenotypes with SYNGR1: view

Animal Models for SYNGR1 Gene

MGI Knock Outs for SYNGR1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SYNGR1

CRISPR Products

miRNA for SYNGR1 Gene

miRTarBase miRNAs that target SYNGR1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNGR1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYNGR1 Gene

Localization for SYNGR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNGR1 Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. {ECO:0000269 PubMed:17081065}.

Subcellular locations from

COMPARTMENTS
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 SYNGR1 gene
Compartment Confidence
plasma membrane 5
lysosome 4
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SYNGR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0008021 synaptic vesicle IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with SYNGR1: view

Pathways & Interactions for SYNGR1 Gene

PathCards logo

SuperPathways for SYNGR1 Gene

genes like me logo Genes that share pathways with SYNGR1: view

Pathways by source for SYNGR1 Gene

3 Reactome pathways for SYNGR1 Gene

Gene Ontology (GO) - Biological Process for SYNGR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006605 protein targeting IEA --
GO:0043312 neutrophil degranulation TAS --
GO:0045055 regulated exocytosis ISS --
GO:0048169 regulation of long-term neuronal synaptic plasticity ISS --
GO:0048172 regulation of short-term neuronal synaptic plasticity ISS --
genes like me logo Genes that share ontologies with SYNGR1: view

No data available for SIGNOR curated interactions for SYNGR1 Gene

Drugs & Compounds for SYNGR1 Gene

No Compound Related Data Available

Transcripts for SYNGR1 Gene

mRNA/cDNA for SYNGR1 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYNGR1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNGR1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8
SP1: - - -
SP2: - - - -
SP3: - - - - - -
SP4: - -
SP5: - - -
SP6: - - -
SP7: - - -

Relevant External Links for SYNGR1 Gene

GeneLoc Exon Structure for
SYNGR1

Expression for SYNGR1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYNGR1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNGR1 Gene

This gene is overexpressed in Brain - Cerebellum (x6.0), Brain - Cortex (x5.8), Brain - Cerebellar Hemisphere (x5.2), Brain - Frontal Cortex (BA9) (x4.7), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for SYNGR1 Gene

This gene is overexpressed in Nasal epithelium (20.1), Frontal cortex (19.4), and Retina (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYNGR1 Gene



Protein tissue co-expression partners for SYNGR1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYNGR1

SOURCE GeneReport for Unigene cluster for SYNGR1 Gene:

Hs.216226

Evidence on tissue expression from TISSUES for SYNGR1 Gene

  • Nervous system(4.9)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with SYNGR1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNGR1 Gene

Orthologs for SYNGR1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYNGR1 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Syngr1 17 31 30
  • 90.56 (n)
rat
(Rattus norvegicus)
Mammalia Syngr1 30
  • 89.95 (n)
chimpanzee
(Pan troglodytes)
Mammalia SYNGR1 31
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SYNGR1 31
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SYNGR1 31
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYNGR1 31
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYNGR1 31 30
  • 78.3 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYNGR1 31
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syngr1 30
  • 69.12 (n)
zebrafish
(Danio rerio)
Actinopterygii syngr1a 31 30
  • 66.83 (n)
OneToMany
syngr1b 31
  • 52 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011318 30
  • 59.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta synaptogyrin 31 32 30
  • 57.5 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sng-1 31 30
  • 44.86 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 48 (a)
OneToMany
Species where no ortholog for SYNGR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 SYNGR1 Gene

ENSEMBL:
Gene Tree for SYNGR1 (if available)
TreeFam:
Gene Tree for SYNGR1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYNGR1: view image

Paralogs for SYNGR1 Gene

Paralogs for SYNGR1 Gene

(3) SIMAP similar genes for SYNGR1 Gene using alignment to 5 proteins:

  • SNG1_HUMAN
  • A2A283_HUMAN
  • B5MCD7_HUMAN
  • F8WCE4_HUMAN
  • L0R6Q9_HUMAN
genes like me logo Genes that share paralogs with SYNGR1: view

Variants for SYNGR1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYNGR1 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
rs193920982 Uncertain Significance: Malignant tumor of prostate 39,377,595(+) C/T INTRON_VARIANT
VAR_060490 - p.Asp222Gly

Additional dbSNP identifiers (rs#s) for SYNGR1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYNGR1 Gene

Variant ID Type Subtype PubMed ID
esv3647763 CNV loss 21293372
nsv817996 CNV gain 17921354
nsv834198 CNV loss 17160897
nsv834199 CNV loss 17160897

Variation tolerance for SYNGR1 Gene

Residual Variation Intolerance Score: 28.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.65; 14.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNGR1 Gene

Human Gene Mutation Database (HGMD)
SYNGR1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYNGR1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNGR1 Gene

Disorders for SYNGR1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SYNGR1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
megalencephalic leukoencephalopathy with subcortical cysts 1
  • mlc1
berylliosis
  • beryllium poisoning
schizophrenia
  • sczd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SYNGR1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SYNGR1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYNGR1 Gene

Publications for SYNGR1 Gene

  1. Association study and mutational screening of SYNGR1 as a candidate susceptibility gene for schizophrenia. (PMID: 19641478) Iatropoulos P … Barlati S (Psychiatric genetics 2009) 3 23 41 54
  2. Identification of rare mutations of synaptogyrin 1 gene in patients with schizophrenia. (PMID: 17049558) Cheng MC … Chen CH (Journal of psychiatric research 2007) 3 4 23 54
  3. A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia. (PMID: 14732601) Verma R … Brahmachari SK (Biological psychiatry 2004) 3 23 41 54
  4. Characterization of the human synaptogyrin gene family. (PMID: 9760194) Kedra D … Dumanski JP (Human genetics 1998) 2 3 4 54
  5. No association between bipolar disorder and syngr1 or synapsin II polymorphisms in the Han Chinese population. (PMID: 19665806) Wang Y … Li S (Psychiatry research 2009) 3 41 54

Products for SYNGR1 Gene

Sources for SYNGR1 Gene