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    SYT2 synaptotagmin 2 [ Homo sapiens (human) ]

    Gene ID: 127833, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYT2provided by HGNC
    Official Full Name
    synaptotagmin 2provided by HGNC
    Primary source
    HGNC:HGNC:11510
    See related
    Ensembl:ENSG00000143858 MIM:600104; AllianceGenome:HGNC:11510
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CMS7; CMS7A; CMS7B; MYSPC; SytII
    Summary
    This gene encodes a synaptic vesicle membrane protein. The encoded protein is thought to function as a calcium sensor in vesicular trafficking and exocytosis. Mutations in this gene are associated with myasthenic syndrome, presynaptic, congenital, with or without motor neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
    Expression
    Broad expression in brain (RPKM 1.4), adrenal (RPKM 1.3) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYT2 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202590596..202710454, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201852402..201972645, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202559724..202679582, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene ribosomal protein S27 pseudogene 8 Neighboring gene Sharpr-MPRA regulatory region 4568 Neighboring gene Sharpr-MPRA regulatory region 13016 Neighboring gene small nucleolar RNA SNORA70 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202536800-202537472 Neighboring gene Sharpr-MPRA regulatory region 13308 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:202557917-202559116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202560242-202561068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202591842-202592466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202606743-202607308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202611908-202612840 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202626482-202626641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202627175-202627676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202640443-202640943 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202645972-202646140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202671295-202671794 Neighboring gene lysine demethylase 5B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202764986-202765486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202765487-202765987 Neighboring gene COX7C pseudogene 2 Neighboring gene solute carrier family 25 member 39 pseudogene 1

    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 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. Identification of a Novel de Novo Variant in the SYT2 Gene Causing a Rare Type of Distal Hereditary Motor Neuropathy. Mironovich O, et al. Genes (Basel), 2020 Oct 22. PMID 33105646, Free PMC Article
    2. Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome. Donkervoort S, et al. Am J Med Genet A, 2020 Oct. PMID 32776697, Free PMC Article
    3. Synaptotagmin II negatively regulates Ca2+-triggered exocytosis of lysosomes in mast cells. Baram D, et al. J Exp Med, 1999 May 17. PMID 10330444, Free PMC Article
    4. Recessive congenital myasthenic syndrome caused by a homozygous mutation in SYT2 altering a highly conserved C-terminal amino acid sequence. Maselli RA, et al. Am J Med Genet A, 2020 Jul. PMID 32250532
    5. Membrane topogenesis of a type I signal-anchor protein, mouse synaptotagmin II, on the endoplasmic reticulum. Kida Y, et al. J Cell Biol, 2000 Aug 21. PMID 10952998, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a Novel de Novo Variant in the SYT2 Gene Causing a Rare Type of Distal Hereditary Motor Neuropathy.
      Title: Identification of a Novel de Novo Variant in the SYT2 Gene Causing a Rare Type of Distal Hereditary Motor Neuropathy.
    2. Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome.
      Title: Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome.
    3. Recessive congenital myasthenic syndrome caused by a homozygous mutation in SYT2 altering a highly conserved C-terminal amino acid sequence.
      Title: Recessive congenital myasthenic syndrome caused by a homozygous mutation in SYT2 altering a highly conserved C-terminal amino acid sequence.
    4. the extended synaptotagmins (E-Syts), endoplasmic reticulum (ER) proteins that function as PtdIns(4,5)P2- and Ca(2+)-regulated tethers to the Pplasma membrane.
      Title: Control of plasma membrane lipid homeostasis by the extended synaptotagmins.
    5. SYT2 mutations cause a novel complex presynaptic congenital myasthenic syndrome characterized by motor neuropathy causing lower limb wasting and foot deformities, reflex potentiation following exercise and a prolonged period of posttetanic potentiation
      Title: Electrophysiologic features of SYT2 mutations causing a treatable neuromuscular syndrome.
    6. Synaptotagmin 2 mutations cause an autosomal-dominant form of lambert-eaton myasthenic syndrome and nonprogressive motor neuropathy.
      Title: Synaptotagmin 2 mutations cause an autosomal-dominant form of lambert-eaton myasthenic syndrome and nonprogressive motor neuropathy.
    7. Human SytII is not an effective receptor for Botulinum neurotoxin D-C.
      Title: Botulinum neurotoxin D-C uses synaptotagmin I and II as receptors, and human synaptotagmin II is not an effective receptor for type B, D-C and G toxins.
    8. synaptotagmin-II is not a high affinity receptor for BoNT/B and G due to a phenylalanine to leucine mutation in its luminal domain present only in humans and chimpanzees
      Title: Human synaptotagmin-II is not a high affinity receptor for botulinum neurotoxin B and G: increased therapeutic dosage and immunogenicity.
    9. Mutation of overexpressed Syt2 transgene leaves intrinsic calcium sensitivity of vesicles intact while it destabilizes the readily releasable pool of vesicles and loosens the tight coupling between calcium influx and release.
      Title: Synaptotagmin has an essential function in synaptic vesicle positioning for synchronous release in addition to its role as a calcium sensor.
    10. A recombinant fragment from the luminal domain of the human receptor protein syt II can bind specifically to botulinum neurotoxin B and its Hc domain.
      Title: Dominant antigenic peptides located at the heavy chain terminal of botulinum neurotoxin B contain receptor-binding sites for synaptotagmin II.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42519

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion sensor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium-dependent phospholipid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium-dependent phospholipid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables inositol 1,3,4,5 tetrakisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium-dependent activation of synaptic vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of dendrite extension IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of calcium ion-dependent exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of synaptic vesicle exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromaffin granule membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in dense core granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in exocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    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
    synaptotagmin-2
    Names
    synaptotagmin II

    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.

    Genomic

    1. NG_041776.1 RefSeqGene

      Range
      4970..124828
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136504.1 → NP_001129976.1  synaptotagmin-2

      See identical proteins and their annotated locations for NP_001129976.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC118556, AK094430, BC100815
      Consensus CDS
      CCDS1427.1
      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Related
      ENSP00000356236.1, ENST00000367267.5
      Conserved Domains (2) summary
      cd08385
      Location:139 → 261
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:271 → 406
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

    2. NM_177402.5 → NP_796376.2  synaptotagmin-2

      See identical proteins and their annotated locations for NP_796376.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the more prevalent variant. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC104463, AC118556, BC100815, DA098279
      Consensus CDS
      CCDS1427.1
      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Related
      ENSP00000356237.4, ENST00000367268.5
      Conserved Domains (2) summary
      cd08385
      Location:139 → 261
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:271 → 406
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      202590596..202710454 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509192.3 → XP_011507494.1  synaptotagmin-2 isoform X3

      See identical proteins and their annotated locations for XP_011507494.1

      Conserved Domains (3) summary
      cd08385
      Location:142 → 264
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:274 → 409
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
      cd21964
      Location:4 → 113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins

    2. XM_017000312.2 → XP_016855801.1  synaptotagmin-2 isoform X3

      Conserved Domains (3) summary
      cd08385
      Location:142 → 264
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:274 → 409
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
      cd21964
      Location:4 → 113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins

    3. XM_017000313.2 → XP_016855802.1  synaptotagmin-2 isoform X4

      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Conserved Domains (2) summary
      cd08385
      Location:139 → 261
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:271 → 406
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

    4. XM_017000311.3 → XP_016855800.1  synaptotagmin-2 isoform X3

      Conserved Domains (3) summary
      cd08385
      Location:142 → 264
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:274 → 409
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
      cd21964
      Location:4 → 113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins

    5. XM_017000310.3 → XP_016855799.1  synaptotagmin-2 isoform X2

    6. XM_017000309.3 → XP_016855798.1  synaptotagmin-2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      201852402..201972645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334403.1 → XP_054190378.1  synaptotagmin-2 isoform X3

    2. XM_054334402.1 → XP_054190377.1  synaptotagmin-2 isoform X3

    3. XM_054334404.1 → XP_054190379.1  synaptotagmin-2 isoform X4

      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5

    4. XM_054334401.1 → XP_054190376.1  synaptotagmin-2 isoform X3

    5. XM_054334400.1 → XP_054190375.1  synaptotagmin-2 isoform X2

    6. XM_054334399.1 → XP_054190374.1  synaptotagmin-2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N9I0.2 GenPept UniProtKB/Swiss-Prot:Q8N9I0

    Gene LinkOut

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

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