Aliases for SV2C Gene

Aliases for SV2C Gene

  • Synaptic Vesicle Glycoprotein 2C 2 3 4 5
  • Synaptic Vesicle Protein 2C 3
  • KIAA1054 4
  • SV2C 5

External Ids for SV2C Gene

Previous GeneCards Identifiers for SV2C Gene

  • GC05P075417
  • GC05P075463
  • GC05P075414
  • GC05P075379
  • GC05P070632
  • GC05P076083

Summaries for SV2C Gene

GeneCards Summary for SV2C Gene

SV2C (Synaptic Vesicle Glycoprotein 2C) is a Protein Coding gene. Diseases associated with SV2C include Foodborne Botulism and Alcohol-Related Birth Defect. 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 transporter activity and transmembrane transporter activity. An important paralog of this gene is SV2A.

UniProtKB/Swiss-Prot Summary for SV2C 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.
  • (Microbial infection) Receptor for C.botulinum neurotoxin type A (BoNT/A, botA); the toxin probably binds via extracellular loop 4 (PubMed:27313224). Recognition by BoNT/A relies on both protein-protein and protein-N-glycosylation; glycosylation of Asn-559 increases its affinity for BoNT/A (PubMed:27313224). Also serves as a receptor for the closely related C.botulinum neurotoxin type A2; glycosylation is not essential but enhances the interaction (PubMed:29649119).
  • (Microbial infection) Possible receptor for C.botulinum neurotoxin type D (BoNT/D, botD); note that type D does not usually infect humans.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SV2C Gene

Genomics for SV2C Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SV2C 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
GH05J076082 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 600.1 +236.6 236638 2.2 ZNF692 PRDM1 ZIC2 POLR2A PATZ1 EZH2 ZNF341 ZNF561 ZBTB20 SP2 ENSG00000248127 LOC105379041 SV2C IQGAP2
GH05J075845 Enhancer 0.8 Ensembl 600.7 +0.2 238 2.6 SP1 BACH1 STAT3 JUND RELA TCF12 IKZF2 RCOR1 TRIM22 EED SV2C piR-61532-244 IQGAP2
GH05J076425 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.4 +577.5 577538 8 REST IKZF1 KDM1A ZSCAN4 SP1 ZNF140 NFE2 ZNF316 OSR2 ATF3 IQGAP2 ENSG00000272040 POC5 ENSG00000251342 SAP18P1 ENSG00000248127 SV2C piR-57133-481 F2RL2
GH05J076256 Enhancer 0.9 Ensembl ENCODE 11.3 +409.0 409012 1.1 CTCF PRDM10 JUND STAT3 ZNF143 PRDM1 REST RAD21 TRIM22 EED ENSG00000251342 ENSG00000248127 SAP18P1 SV2C RF00951-124 HMGN2P4 IQGAP2
GH05J076176 Enhancer 0.9 ENCODE 10.8 +328.6 328634 1.3 LEF1 IKZF1 JUND STAT3 ZNF143 PHF21A PKNOX1 MTA1 IKZF2 CTCF ENSG00000254893 RAP1BL lnc-F2RL2-6 piR-51037-002 ENSG00000248127 ENSG00000251342 SAP18P1 SV2C HSALNG0042770 IQGAP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SV2C on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SV2C

Top Transcription factor binding sites by QIAGEN in the SV2C gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • FosB
  • Fra-1
  • HOXA5
  • JunB
  • JunD
  • Lmo2
  • Sox5

Genomic Locations for SV2C Gene

Genomic Locations for SV2C Gene
chr5:75,847,463-76,353,939
(GRCh38/hg38)
Size:
506,477 bases
Orientation:
Plus strand
chr5:75,378,997-75,649,764
(GRCh37/hg19)
Size:
270,768 bases
Orientation:
Plus strand

Genomic View for SV2C Gene

Genes around SV2C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SV2C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SV2C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SV2C Gene

Proteins for SV2C Gene

  • Protein details for SV2C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q496J9-SV2C_HUMAN
    Recommended name:
    Synaptic vesicle glycoprotein 2C
    Protein Accession:
    Q496J9
    Secondary Accessions:
    • Q496K1
    • Q9UPU8

    Protein attributes for SV2C Gene

    Size:
    727 amino acids
    Molecular mass:
    82342 Da
    Quaternary structure:
    • Interacts with SYT1 in a calcium-dependent manner.
    • (Microbial infection) Interacts with C.botulinum neurotoxin type A1 and type A2 (BoNT/A, botA) (PubMed:29649119). Interaction is improved by glycosylation of SV2 (PubMed:29649119).

    Three dimensional structures from OCA and Proteopedia for SV2C Gene

neXtProt entry for SV2C Gene

Post-translational modifications for SV2C Gene

  • N-glycosylated. Upon expression in a kidney cell line the most abundant glycan on Asn-534 is GlcNAc(3)Hex(5), while on Asn-559 and Asn-565 the most abundant glycan is GlcNAc2Fuc1Man3GlcNAc3Gal3. Both Asn-559 and Asn-565 have a high degree of glycan heterogeneity (PubMed:27313224).
  • Glycosylation at Asn480, Asn484, Asn534, Asn559, and Asn565
  • Modification sites at PhosphoSitePlus

Other Protein References for SV2C Gene

No data available for DME Specific Peptides for SV2C Gene

Domains & Families for SV2C Gene

Gene Families for SV2C Gene

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

Suggested Antigen Peptide Sequences for SV2C Gene

GenScript: Design optimal peptide antigens:
  • Synaptic vesicle glycoprotein 2C (SV2C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q496J9

UniProtKB/Swiss-Prot:

SV2C_HUMAN :
  • Belongs to the major facilitator superfamily.
Family:
  • Belongs to the major facilitator superfamily.
genes like me logo Genes that share domains with SV2C: view

Function for SV2C Gene

Molecular function for SV2C 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.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Receptor for C.botulinum neurotoxin type A (BoNT/A, botA); the toxin probably binds via extracellular loop 4 (PubMed:27313224). Recognition by BoNT/A relies on both protein-protein and protein-N-glycosylation; glycosylation of Asn-559 increases its affinity for BoNT/A (PubMed:27313224). Also serves as a receptor for the closely related C.botulinum neurotoxin type A2; glycosylation is not essential but enhances the interaction (PubMed:29649119).
UniProtKB/Swiss-Prot Function:
(Microbial infection) Possible receptor for C.botulinum neurotoxin type D (BoNT/D, botD); note that type D does not usually infect humans.

Phenotypes From GWAS Catalog for SV2C Gene

Gene Ontology (GO) - Molecular Function for SV2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24240280
GO:0022857 transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SV2C: view
genes like me logo Genes that share phenotypes with SV2C: view

Animal Models for SV2C Gene

MGI Knock Outs for SV2C:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SV2C

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SV2C Gene

Localization for SV2C Gene

Subcellular locations from UniProtKB/Swiss-Prot for SV2C Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane. Multi-pass membrane protein. Note=Enriched in small synaptic vesicles and adrenal microsomes, not present in chromaffin granules. Associated with both insulin granules and synaptic-like microvesicles in insulin-secreting cells of the pancreas. {ECO:0000250 UniProtKB:Q9Z2I6}.

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 SV2C gene
Compartment Confidence
plasma membrane 5
nucleus 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SV2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0008021 synaptic vesicle IEA,TAS 15217342
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,IBA 21873635
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with SV2C: view

Pathways & Interactions for SV2C Gene

genes like me logo Genes that share pathways with SV2C: view

Gene Ontology (GO) - Biological Process for SV2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006836 neurotransmitter transport IEA --
GO:0007268 chemical synaptic transmission IEA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SV2C: view

No data available for SIGNOR curated interactions for SV2C Gene

Drugs & Compounds for SV2C Gene

(2) Drugs for SV2C Gene - From: PharmGKB and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Olanzapine Approved, Investigational Pharma Antagonist, Agonist, Full agonist, Inverse agonist 442
Calcium Nutra 6556
genes like me logo Genes that share compounds with SV2C: view

Transcripts for SV2C Gene

mRNA/cDNA for SV2C Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 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 SV2C

Alternative Splicing Database (ASD) splice patterns (SP) for SV2C Gene

No ASD Table

Relevant External Links for SV2C Gene

GeneLoc Exon Structure for
SV2C

Expression for SV2C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SV2C Gene

mRNA differential expression in normal tissues according to GTEx for SV2C Gene

This gene is overexpressed in Brain - Hypothalamus (x13.1), Brain - Nucleus accumbens (basal ganglia) (x12.6), Brain - Caudate (basal ganglia) (x6.5), Brain - Putamen (basal ganglia) (x5.3), and Brain - Substantia nigra (x4.1).

Protein differential expression in normal tissues from HIPED for SV2C Gene

This gene is overexpressed in Ovary (33.8) and Urinary Bladder (28.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SV2C Gene



Protein tissue co-expression partners for SV2C Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SV2C

SOURCE GeneReport for Unigene cluster for SV2C Gene:

Hs.663229

Evidence on tissue expression from TISSUES for SV2C Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with SV2C: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SV2C Gene

Orthologs for SV2C Gene

This gene was present in the common ancestor of animals.

Orthologs for SV2C Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SV2C 30 31
  • 99.31 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SV2C 31
  • 93 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SV2C 31
  • 93 (a)
OneToOne
LOC488943 30
  • 90.1 (n)
Cow
(Bos Taurus)
Mammalia SV2C 30 31
  • 89.9 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sv2c 30
  • 89.23 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SV2C 31
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Sv2c 30 17 31
  • 88.86 (n)
OneToOne
Chicken
(Gallus gallus)
Aves SV2C 30 31
  • 80.79 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SV2C 31
  • 83 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sv2c 30
  • 75.26 (n)
Zebrafish
(Danio rerio)
Actinopterygii sv2c 30 31
  • 70.11 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG3168 31
  • 28 (a)
ManyToMany
CG31106 31
  • 25 (a)
ManyToMany
CG31272 31
  • 23 (a)
ManyToMany
CG15221 31
  • 22 (a)
ManyToMany
CG14691 31
  • 21 (a)
ManyToMany
CG31103 31
  • 21 (a)
ManyToMany
CG3690 31
  • 20 (a)
ManyToMany
CG12783 31
  • 20 (a)
ManyToMany
CG33234 31
  • 19 (a)
ManyToMany
CG33233 31
  • 18 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
OneToMany
Species where no ortholog for SV2C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 SV2C Gene

ENSEMBL:
Gene Tree for SV2C (if available)
TreeFam:
Gene Tree for SV2C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SV2C: view image

Paralogs for SV2C Gene

Paralogs for SV2C Gene

(3) SIMAP similar genes for SV2C Gene using alignment to 2 proteins:

  • SV2C_HUMAN
  • B3KT41_HUMAN
genes like me logo Genes that share paralogs with SV2C: view

Variants for SV2C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SV2C Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
714993 Benign: not provided 76,132,339(+) G/A INTRON_VARIANT
740483 Likely Benign: not provided 76,301,471(+) G/T SYNONYMOUS_VARIANT
777396 Benign: not provided 76,132,245(+) C/T SYNONYMOUS_VARIANT
786058 Benign: not provided 76,300,793(+) G/A SYNONYMOUS_VARIANT
rs2270927 - p.Thr482Ser

Additional dbSNP identifiers (rs#s) for SV2C Gene

Structural Variations from Database of Genomic Variants (DGV) for SV2C Gene

Variant ID Type Subtype PubMed ID
dgv1107e214 CNV gain 21293372
dgv360e215 CNV deletion 23714750
dgv5700n100 CNV gain 25217958
dgv5701n100 CNV gain 25217958
esv1004475 CNV insertion 20482838
esv1726251 CNV insertion 17803354
esv2487643 CNV deletion 19546169
esv2588798 CNV deletion 19546169
esv2730318 CNV deletion 23290073
esv2759351 CNV gain 17122850
esv2759352 CNV gain 17122850
esv2763917 CNV gain 21179565
esv3302975 CNV tandem duplication 20981092
esv3326642 CNV duplication 20981092
esv3353515 CNV duplication 20981092
esv3362900 CNV duplication 20981092
esv3425598 CNV duplication 20981092
esv34707 CNV gain 17911159
esv34958 CNV gain 17911159
esv3566119 CNV deletion 23714750
esv3575857 CNV gain 25503493
esv3605461 CNV loss 21293372
esv989228 CNV deletion 20482838
nsv1015349 CNV gain 25217958
nsv1033350 CNV gain 25217958
nsv1074843 CNV deletion 25765185
nsv1120508 CNV tandem duplication 24896259
nsv1129259 CNV insertion 24896259
nsv1137009 CNV deletion 24896259
nsv1145064 CNV deletion 24896259
nsv327180 CNV deletion 16902084
nsv329230 CNV insertion 16902084
nsv509074 CNV insertion 20534489
nsv513243 CNV loss 21212237
nsv516875 CNV gain 19592680
nsv518475 CNV gain 19592680
nsv526084 CNV gain 19592680
nsv598676 CNV gain 21841781
nsv598677 CNV gain 21841781
nsv598678 CNV loss 21841781
nsv818353 CNV gain 17921354
nsv955875 CNV deletion 24416366
nsv964896 CNV duplication 23825009
nsv968951 CNV duplication 23825009

Variation tolerance for SV2C Gene

Residual Variation Intolerance Score: 47.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.84; 86.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SV2C Gene

Human Gene Mutation Database (HGMD)
SV2C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SV2C

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SV2C Gene

Disorders for SV2C Gene

MalaCards: The human disease database

(5) MalaCards diseases for SV2C Gene - From: DISEASES

Disorder Aliases PubMed IDs
foodborne botulism
  • wound botulism
alcohol-related birth defect
  • fetal alcohol syndrome
intestinal botulism
  • intestinal colonization botulism
infant botulism
  • infant intestinal botulism
alternating hemiplegia of childhood
  • ahc
- elite association - COSMIC cancer census association via MalaCards
Search SV2C in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SV2C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SV2C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SV2C Gene

Publications for SV2C Gene

  1. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A. (PMID: 27294781) Yao G … Jin R (Nature structural & molecular biology 2016) 3 4
  3. Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A. (PMID: 24240280) Benoit RM … Kammerer RA (Nature 2014) 3 4
  4. 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 41
  5. No major role of common SV2A variation for predisposition or levetiracetam response in epilepsy. (PMID: 18977120) Lynch JM … Sisodiya SM (Epilepsy research 2009) 3 41

Products for SV2C Gene

Sources for SV2C Gene