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

    Gene ID: 22987, updated on 10-Dec-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 several processes, including chemical synaptic transmission; neurotransmitter transport; and regulation of synaptic vesicle exocytosis. Predicted to be located in plasma membrane and synaptic vesicle. Predicted to be active in dopaminergic synapse and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in brain (RPKM 1.2), adrenal (RPKM 0.7) and 8 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SV2C in Genome Data Viewer
    Location:
    5q13.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (75847464..76353939)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (76328570..76835704)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Correlation of SV2C rs1423099 single nucleotide polymorphism with sporadic Parkinson's disease in Han population in Southern China. Tan Z, et al. Neurosci Lett, 2023 Sep 14. PMID 37544580

    See all (28) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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