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SV2C synaptic vesicle glycoprotein 2C [ Homo sapiens (human) ]

Gene ID: 22987, updated on 7-Apr-2024

Summary

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Official Symbol
SV2Cprovided by HGNC
Official Full Name
synaptic vesicle glycoprotein 2Cprovided by HGNC
Primary source
HGNC:HGNC:30670
See related
Ensembl:ENSG00000122012 MIM:610291; AllianceGenome:HGNC:30670
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLC22B3
Summary
Predicted to enable transmembrane transporter activity. Predicted to be involved in chemical synaptic transmission; neurotransmitter transport; and transmembrane transport. Predicted to be located in plasma membrane and synaptic vesicle. Predicted to be active in neuron projection and synaptic vesicle membrane. Predicted to be integral component of synaptic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 1.2), adrenal (RPKM 0.7) and 8 other tissues See more
Orthologs
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Genomic context

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Location:
5q13.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (75847464..76353939)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (76328570..76835704)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (75379208..75649764)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 5 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22687 Neighboring gene karyopherin subunit alpha 7 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr5:75212667-75212925 Neighboring gene aconitate hydratase, mitochondrial-like Neighboring gene bridging integrator 2 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75332902-75333626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75333627-75334351 Neighboring gene spermine synthase pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75378019-75378572 Neighboring gene MPRA-validated peak5296 silencer Neighboring gene RNA, 5S ribosomal pseudogene 186 Neighboring gene SV2C antisense RNA 1 Neighboring gene SAP18 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22688 Neighboring gene RAP1B like (pseudogene) Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:75566225-75566726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:75566727-75567226 Neighboring gene uncharacterized LOC105379042 Neighboring gene NANOG hESC enhancer GRCh37_chr5:75592019-75592901 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:75590840-75592039 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 4 Neighboring gene GATA motif-containing MPRA enhancer 83 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75621257-75621756 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:75631008-75631638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75632271-75632901 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:75633873-75634098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:75635379-75636148 Neighboring gene programmed cell death 5 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22689 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:75652737-75653716 Neighboring gene Sharpr-MPRA regulatory region 10118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75690574-75691074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:75691075-75691575 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:75699075-75699575 Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:75767824-75769023 Neighboring gene IQ motif containing GTPase activating protein 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75794074-75794996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:75794997-75795918 Neighboring gene sulfiredoxin 1 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A. Yao G, et al. Nat Struct Mol Biol, 2016 Jul. PMID 27294781, Free PMC Article
  2. Botulinum neurotoxins: new questions arising from structural biology. Kammerer RA, et al. Trends Biochem Sci, 2014 Nov. PMID 25282537
  3. Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A. Benoit RM, et al. Nature, 2014 Jan 2. PMID 24240280
  4. Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE study. Ramsey TL, et al. Schizophr Res, 2013 Sep. PMID 23886675, Free PMC Article
  5. Identification of Risk Loci for Parkinson Disease in Asians and Comparison of Risk Between Asians and Europeans: A Genome-Wide Association Study. Foo JN, et al. JAMA Neurol, 2020 Jun 1. PMID 32310270, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Correlation of SV2C rs1423099 single nucleotide polymorphism with sporadic Parkinson's disease in Han population in Southern China.
    Title: Correlation of SV2C rs1423099 single nucleotide polymorphism with sporadic Parkinson's disease in Han population in Southern China.
  2. Differentiation of two human neuroblastoma cell lines alters SV2 expression patterns.
    Title: Differentiation of two human neuroblastoma cell lines alters SV2 expression patterns.
  3. Identification of Risk Loci for Parkinson Disease in Asians and Comparison of Risk Between Asians and Europeans: A Genome-Wide Association Study.
    Title: Identification of Risk Loci for Parkinson Disease in Asians and Comparison of Risk Between Asians and Europeans: A Genome-Wide Association Study.
  4. These data establish SV2C as a mediator of dopamine neuron function and suggest that SV2C disruption is a unique feature of PD that likely contributes to dopaminergic dysfunction.
    Title: Synaptic vesicle glycoprotein 2C (SV2C) modulates dopamine release and is disrupted in Parkinson disease.
  5. N-linked glycosylation of SV2C is required for binding and uptake of botulinum neurotoxin A.
    Title: N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A.
  6. Studies indicate that botulinum neurotoxins (BoNTs) in complex with its protein receptor, synaptic vesicle glycoprotein 2 (SV2) family member C represented a major advance for the detailed molecular understanding of BoNT-host cell receptor interactions.
    Title: Botulinum neurotoxins: new questions arising from structural biology.
  7. A genetic variant in SV2C predicted clinically relevant bevacizumab-induced hypertension in two independent, randomised phase III trials.
    Title: Genetic variant predicts bevacizumab-induced hypertension in ECOG-5103 and ECOG-2100.
  8. In classical mesial temporal sclerosis 1A, the expression of SV2 isoforms is altered with a selective increase of SV2C in sprouting mossy fibres.
    Title: Expression pattern of synaptic vesicle protein 2 (SV2) isoforms in patients with temporal lobe epilepsy and hippocampal sclerosis.
  9. The fact that multiple SNPs in SV2C may impact response to atypical antipsychotics suggests that further evaluation of SNPs in this gene
    Title: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE study.
  10. high-resolution crystal structure of the BoNT/A receptor-binding domain in complex with the SV2C luminal domain
    Title: Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
EBI GWAS Catalog
Genetic variant predicts bevacizumab-induced hypertension in ECOG-5103 and ECOG-2100.
EBI GWAS Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC118874, MGC118875, MGC118876, MGC118877

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in neurotransmitter transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of synaptic vesicle exocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in dopaminergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in synaptic vesicle TAS
Traceable Author Statement
more info
 PubMed 
is_active_in synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synaptic vesicle membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
synaptic vesicle glycoprotein 2C
Names
solute carrier family 22 member B3
synaptic vesicle protein 2C

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001297716.2 → NP_001284645.1  synaptic vesicle glycoprotein 2C isoform 2

    See identical proteins and their annotated locations for NP_001284645.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 3' terminal exon, compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC026774, AC026783, AC108091, AK094917
    Consensus CDS
    CCDS75261.1
    UniProtKB/TrEMBL
    B3KT41
    Related
    ENSP00000316983.7, ENST00000322285.7
    Conserved Domains (3) summary
    cd06174
    Location:155 → 348
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR01299
    Location:1 → 667
    synapt_SV2; synaptic vesicle protein SV2
    pfam13576
    Location:507 → 561
    Pentapeptide_3; Pentapeptide repeats (9 copies)

  2. NM_014979.4 → NP_055794.3  synaptic vesicle glycoprotein 2C isoform 1

    See identical proteins and their annotated locations for NP_055794.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB028977, AC026774, AC108091, AC113404, AK094917, BC100825, DA725900, R44558
    Consensus CDS
    CCDS43331.1
    UniProtKB/Swiss-Prot
    Q496J9, Q496K1, Q9UPU8
    Related
    ENSP00000423541.2, ENST00000502798.7
    Conserved Domains (3) summary
    cd06174
    Location:155 → 719
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR01299
    Location:1 → 727
    synapt_SV2; synaptic vesicle protein SV2
    pfam13576
    Location:507 → 561
    Pentapeptide_3; Pentapeptide repeats (9 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    75847464..76353939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543282.4 → XP_011541584.2  synaptic vesicle glycoprotein 2C isoform X1

    UniProtKB/Swiss-Prot
    Q496J9, Q496K1, Q9UPU8
    Conserved Domains (3) summary
    cd06174
    Location:155 → 719
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR01299
    Location:1 → 727
    synapt_SV2; synaptic vesicle protein SV2
    pfam13576
    Location:507 → 561
    Pentapeptide_3; Pentapeptide repeats (9 copies)

  2. XM_047416961.1 → XP_047272917.1  synaptic vesicle glycoprotein 2C isoform X2

  3. XM_011543281.4 → XP_011541583.1  synaptic vesicle glycoprotein 2C isoform X1

    See identical proteins and their annotated locations for XP_011541583.1

    UniProtKB/Swiss-Prot
    Q496J9, Q496K1, Q9UPU8
    Conserved Domains (3) summary
    cd06174
    Location:155 → 719
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR01299
    Location:1 → 727
    synapt_SV2; synaptic vesicle protein SV2
    pfam13576
    Location:507 → 561
    Pentapeptide_3; Pentapeptide repeats (9 copies)

  4. XM_017009244.3 → XP_016864733.1  synaptic vesicle glycoprotein 2C isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    76328570..76835704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352101.1 → XP_054208076.1  synaptic vesicle glycoprotein 2C isoform X1

  2. XM_054352104.1 → XP_054208079.1  synaptic vesicle glycoprotein 2C isoform X4

  3. XM_054352103.1 → XP_054208078.1  synaptic vesicle glycoprotein 2C isoform X2

  4. XM_054352102.1 → XP_054208077.1  synaptic vesicle glycoprotein 2C isoform X1

  5. XM_054352105.1 → XP_054208080.1  synaptic vesicle glycoprotein 2C isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q496J9.1 GenPept UniProtKB/Swiss-Prot:Q496J9

Gene LinkOut

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