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SV2A Gene(Protein Coding)

Synaptic Vesicle Glycoprotein 2A

GCID:
GC01M149903
GIFtS:
53
Genes Participants
UDN Logo

Aliases for SV2A Gene

Aliases for SV2A Gene

  • Synaptic Vesicle Glycoprotein 2A 2 3 5
  • KIAA0736 4
  • SV2 3

External Ids for SV2A Gene

Previous GeneCards Identifiers for SV2A Gene

  • GC01M145617
  • GC01M146649
  • GC01M147091
  • GC01M146688
  • GC01M148141
  • GC01M149874
  • GC01M121255

Summaries for SV2A Gene

Entrez Gene Summary for SV2A Gene

  • The protein encoded by this gene is one of three related synaptic vesicle proteins. The encoded protein may interact with synaptotagmin to enhance low frequency neurotransmission in quiescent neurons. [provided by RefSeq, Jun 2016]

GeneCards Summary for SV2A Gene

SV2A (Synaptic Vesicle Glycoprotein 2A) is a Protein Coding gene. Diseases associated with SV2A include Alcohol-Related Birth Defect and Photosensitive Epilepsy. Among its related pathways are Toxicity of botulinum toxin type F (BoNT/F) and Uptake and actions of bacterial toxins. Gene Ontology (GO) annotations related to this gene include protein kinase binding and transporter activity. An important paralog of this gene is SV2C.

UniProtKB/Swiss-Prot for SV2A Gene

  • Plays a role in the control of regulated secretion in neural and endocrine cells, enhancing selectively low-frequency neurotransmission. Positively regulates vesicle fusion by maintaining the readily releasable pool of secretory vesicles (By similarity).

Tocris Summary for SV2A Gene

  • Once proteins are translated, they must be directed to the appropriate localization within, or outside of the cell. Protein translocation occurs either during translation or after translation and depends on the N'-terminal signal-recognition particle (SRP) interacting with its receptor.

Gene Wiki entry for SV2A Gene

Additional gene information for SV2A Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SV2A Gene

Genomics for SV2A Gene

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  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SV2A Gene

Promoters and enhancers for SV2A 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
GH01I149916 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 571.8 +0.2 227 1.6 TFAP4 MXI1 SAP130 KLF17 MZF1 SIN3A FEZF1 ZNF2 HIC1 ZNF335 SV2A ENSG00000261716 PIR37951
GH01I149915 Enhancer 0.7 ENCODE 550.8 +1.7 1700 0.7 HDAC1 TEAD4 TAL1 ZSCAN4 TCF12 CTBP1 POLR2A NCOR1 CBFA2T2 CREM SV2A PIR37951
GH01I149883 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 29 +31.2 31179 5.9 CLOCK MLX ZFP64 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 HIST2H2AB BOLA1 GC01M149896 HIST2H2AC HIST2H2BE PRPF3 SF3B4 UBE2D3P3 ARNT GOLPH3L
GH01I149926 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 21.7 -10.9 -10923 4.1 PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 POLR2B SF3B4 GC01M149927 PIR45673 SETDB1 SV2A PRPF3 GOLPH3L UBE2D3P3 RPRD2 APH1A
GH01I149934 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.1 -19.9 -19940 6.3 HDGF PKNOX1 CLOCK FOXA2 ARNT ARID4B NEUROD1 SIN3A FEZF1 YY1 MTMR11 PIR49087 SV2A ARNT PRPF3 SETDB1 SF3B4 GOLPH3L UBE2D3P3 CTSK
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SV2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SV2A gene promoter:

Genomic Locations for SV2A Gene

Genomic Locations for SV2A Gene
chr1:149,903,318-149,917,882
(GRCh38/hg38)
Size:
14,565 bases
Orientation:
Minus strand
chr1:149,874,870-149,889,434
(GRCh37/hg19)

Genomic View for SV2A Gene

Genes around SV2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SV2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SV2A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SV2A Gene

Proteins for SV2A Gene

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  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SV2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7L0J3-SV2A_HUMAN
    Recommended name:
    Synaptic vesicle glycoprotein 2A
    Protein Accession:
    Q7L0J3
    Secondary Accessions:
    • D3DUZ7
    • O94841
    • Q5QNX8
    • Q7Z3L6
    • Q8NBJ6
    • Q9BVZ9

    Protein attributes for SV2A Gene

    Size:
    742 amino acids
    Molecular mass:
    82695 Da
    Quaternary structure:
    • Interacts with SYT1/synaptotagmin-1 in a calcium-dependent manner. Binds the adapter protein complex AP-2 (By similarity).
    Miscellaneous:
    • Identified as the brain binding-site for the antiepileptic drug levetiracetam/lev.
    SequenceCaution:
    • Sequence=BAA34456.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI12573.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SV2A Gene

    Alternative splice isoforms for SV2A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SV2A Gene

Protein Expression for SV2A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SV2A Gene

  • N-glycosylated.
  • Phosphorylation by CK1 of the N-terminal cytoplasmic domain regulates interaction with SYT1.
  • Ubiquitination at isoforms=2366, posLast=375375, and isoforms=2515
  • Glycosylation at posLast=498498, posLast=548548, and isoforms=2573
  • Modification sites at PhosphoSitePlus

Other Protein References for SV2A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SV2A Gene

Domains & Families for SV2A Gene

Gene Families for SV2A Gene

Human Protein Atlas (HPA):
  • FDA approved drug targets
  • Predicted membrane proteins

Protein Domains for SV2A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SV2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7L0J3

UniProtKB/Swiss-Prot:

SV2A_HUMAN :
  • Belongs to the major facilitator superfamily.
Family:
  • Belongs to the major facilitator superfamily.
genes like me logo Genes that share domains with SV2A: view

Function for SV2A Gene

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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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  6. Cell Line

Molecular function for SV2A Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the control of regulated secretion in neural and endocrine cells, enhancing selectively low-frequency neurotransmission. Positively regulates vesicle fusion by maintaining the readily releasable pool of secretory vesicles (By similarity).

Phenotypes From GWAS Catalog for SV2A Gene

Gene Ontology (GO) - Molecular Function for SV2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IEA --
GO:0005215 transporter activity IEA --
GO:0019901 protein kinase binding ISS --
GO:0022857 transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SV2A: view
genes like me logo Genes that share phenotypes with SV2A: view

Animal Models for SV2A Gene

MGI Knock Outs for SV2A:

Animal Model Products

miRNA for SV2A Gene

miRTarBase miRNAs that target SV2A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SV2A Gene

Localization for SV2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SV2A Gene

Cell junction, synapse. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein. Note=Enriched in chromaffin granules, not present in adrenal microsomes. Associated with both insulin granules and synaptic-like microvesicles in insulin-secreting cells of the pancreas (By similarity). Colocalizes with ATP2B1 at photoreceptor synaptic terminals. {ECO:0000250 UniProtKB:Q02563, ECO:0000250 UniProtKB:Q9JIS5}.

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 SV2A gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 4
peroxisome 2
cytosol 2
extracellular 1
cytoskeleton 1
endosome 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SV2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA --
GO:0005886 plasma membrane TAS --
GO:0005911 cell-cell junction IEA --
GO:0008021 synaptic vesicle TAS 15217342
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SV2A: view

Pathways & Interactions for SV2A Gene

genes like me logo Genes that share pathways with SV2A: view

Pathways by source for SV2A Gene

1 KEGG pathway for SV2A Gene
1 Cell Signaling Technology pathway for SV2A Gene

Gene Ontology (GO) - Biological Process for SV2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006836 neurotransmitter transport IEA --
GO:0006874 cellular calcium ion homeostasis IEA --
GO:0007268 chemical synaptic transmission IEA --
GO:0014052 regulation of gamma-aminobutyric acid secretion IEA --
genes like me logo Genes that share ontologies with SV2A: view

No data available for SIGNOR curated interactions for SV2A Gene

Drugs & Compounds for SV2A Gene

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  1. Drug

(14) Drugs for SV2A Gene - From: DrugBank, ClinicalTrials, ApexBio, DGIdb, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Levetiracetam Approved, Investigational Pharma Target, agonist, blocker 0
Brivaracetam Approved, Investigational Pharma Target, unknown, inhibitor ligand for SV2A, selective and high-affinity 0
calcium Approved Nutra 0
Piracetam Approved, Investigational Pharma Positive, Allosteric regulator 176
Seletracetam Investigational Pharma Target, modulator, binder 0

(6) Additional Compounds for SV2A Gene - From: Novoseek and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Exo1
461681-88-9
leptomycin b
87081-35-4

(4) Tocris Compounds for SV2A Gene

Compound Action Cas Number
Brefeldin A Disrupts protein translocation to Golgi 20350-15-6
DBeQ Selective and reversible p97 ATPase inhibitor 177355-84-9
Exo1 Inhibits Golgi-ER traffic; blocks exocytosis 461681-88-9
Leptomycin B Inhibits nuclear export of proteins; antitumor 87081-35-4

(1) ApexBio Compounds for SV2A Gene

Compound Action Cas Number
Brivaracetam ligand for SV2A, selective and high-affinity 357336-20-0
genes like me logo Genes that share compounds with SV2A: view

Drug Products

Transcripts for SV2A Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SV2A Gene

(5) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(205) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SV2A Gene

Synaptic vesicle glycoprotein 2A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SV2A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15
SP1: -
SP2:
SP3:
SP4: -
SP5: - -

Relevant External Links for SV2A Gene

GeneLoc Exon Structure for
SV2A
ECgene alternative splicing isoforms for
SV2A

Expression for SV2A Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SV2A Gene

mRNA expression in normal human tissues for SV2A Gene
mRNA expression by GTEx for SV2A GenemRNA expression by BioGPS for SV2A Gene

mRNA differential expression in normal tissues according to GTEx for SV2A Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.8), Brain - Anterior cingulate cortex (BA24) (x5.2), Brain - Cortex (x5.0), Brain - Cerebellum (x4.2), and Brain - Cerebellar Hemisphere (x4.1).

Protein differential expression in normal tissues from HIPED for SV2A Gene

This gene is overexpressed in Frontal cortex (31.1) and Brain (27.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SV2A Gene



Protein tissue co-expression partners for SV2A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SV2A Gene:

SV2A

SOURCE GeneReport for Unigene cluster for SV2A Gene:

Hs.516153

Evidence on tissue expression from TISSUES for SV2A Gene

  • Nervous system(5)
  • Eye(4.5)
  • Pancreas(2.7)
  • Muscle(2.3)
  • Heart(2.2)
  • Kidney(2)
  • Liver(2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with SV2A: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SV2A Gene

Orthologs for SV2A Gene

This gene was present in the common ancestor of animals.

Orthologs for SV2A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SV2A 33 34
  • 99.78 (n)
oppossum
(Monodelphis domestica)
 Mammalia SV2A 34
  • 96 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia SV2A 33 34
  • 92.63 (n)
dog
(Canis familiaris)
 Mammalia SV2A 33 34
  • 91.87 (n)
rat
(Rattus norvegicus)
 Mammalia Sv2a 33
  • 90.97 (n)
mouse
(Mus musculus)
 Mammalia Sv2a 33 16 34
  • 90.48 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SV2A 34
  • 52 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SV2A 34
  • 71 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia sv2a 33
  • 74.76 (n)
zebrafish
(Danio rerio)
 Actinopterygii SV2A 34
  • 80 (a)
 OneToOne
LOC568033 33
  • 72.5 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG3168 34
  • 27 (a)
 ManyToMany
CG31106 34
  • 22 (a)
 ManyToMany
CG15221 34
  • 21 (a)
 ManyToMany
CG31103 34
  • 21 (a)
 ManyToMany
CG31272 34
  • 21 (a)
 ManyToMany
CG3690 34
  • 21 (a)
 ManyToMany
CG14691 34
  • 20 (a)
 ManyToMany
CG33234 34
  • 19 (a)
 ManyToMany
CG12783 34
  • 18 (a)
 ManyToMany
CG33233 34
  • 18 (a)
 ManyToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 28 (a)
 OneToMany
Species where no ortholog for SV2A 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)
  • lizard (Anolis carolinensis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SV2A Gene

ENSEMBL:
Gene Tree for SV2A (if available)
TreeFam:
Gene Tree for SV2A (if available)

Paralogs for SV2A Gene

Paralogs for SV2A Gene

(2) SIMAP similar genes for SV2A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SV2A: view

Variants for SV2A Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SV2A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs782514088 uncertain-significance, Inborn genetic diseases 149,909,832(-) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000695415 -- 149,916,428(-) G/C genic_upstream_transcript_variant, intron_variant
rs1001150107 -- 149,916,160(-) C/T genic_upstream_transcript_variant, intron_variant
rs1001254212 -- 149,917,171(-) C/T genic_upstream_transcript_variant, intron_variant
rs1001346872 -- 149,904,067(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for SV2A Gene

Variant ID Type Subtype PubMed ID
nsv508037 OTHER sequence alteration 20534489
nsv831525 CNV gain 17160897
nsv831537 CNV loss 17160897

Variation tolerance for SV2A Gene

Residual Variation Intolerance Score: 4.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.85; 34.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SV2A Gene

Human Gene Mutation Database (HGMD)
SV2A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SV2A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SV2A Gene

Disorders for SV2A Gene

MalaCards: The human disease database

(2) MalaCards diseases for SV2A Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
alcohol-related birth defect
  • arbd
photosensitive epilepsy
  • photogenic epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search SV2A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SV2A

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 SV2A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SV2A Gene

Publications for SV2A Gene

  1. No major role of common SV2A variation for predisposition or levetiracetam response in epilepsy. (PMID: 18977120) Lynch JM … Sisodiya SM (Epilepsy research 2009) 3 22 44 58
  2. The synaptic vesicle protein SV2A is the binding site for the antiepileptic drug levetiracetam. (PMID: 15210974) Lynch BA … Fuks B (Proceedings of the National Academy of Sciences of the United States of America 2004) 3 4 25 58
  3. Expression of synaptic vesicle protein 2A in epilepsy-associated brain tumors and in the peritumoral cortex. (PMID: 20167814) de Groot M … Reijneveld JC (Neuro-oncology 2010) 3 22 58
  4. Expression patterns of synaptic vesicle protein 2A in focal cortical dysplasia and TSC-cortical tubers. (PMID: 19220410) Toering ST … Aronica E (Epilepsia 2009) 3 22 58
  5. Botulinum toxin type A inhibits the growth of LNCaP human prostate cancer cells in vitro and in vivo. (PMID: 19399787) Karsenty G … Corcos J (The Prostate 2009) 3 22 58

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