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SYT1 synaptotagmin 1 [ Homo sapiens (human) ]

Gene ID: 6857, updated on 11-Apr-2024

Summary

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Official Symbol
SYT1provided by HGNC
Official Full Name
synaptotagmin 1provided by HGNC
Primary source
HGNC:HGNC:11509
See related
Ensembl:ENSG00000067715 MIM:185605; AllianceGenome:HGNC:11509
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
P65; SYT; BAGOS; SVP65
Summary
This gene encodes a member of the synaptotagmin protein family. The synaptotagmins are integral membrane proteins of synaptic vesicles that serve as calcium sensors in the process of vesicular trafficking and exocytosis. The encoded protein participates in triggering neurotransmitter release at the synapse in response to calcium binding. Mutations in this gene are associated with Baker-Gordon syndrome. [provided by RefSeq, Jan 2023]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression
Biased expression in brain (RPKM 173.4) and adrenal (RPKM 11.7) See more
Orthologs
mouse all
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Genomic context

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Location:
12q21.2
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (78863982..79452008)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (78842458..79430647)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (79257762..79845788)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L11 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:79045498-79046127 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:79152976-79154175 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:79187167-79188366 Neighboring gene MPRA-validated peak1851 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr12:79229192-79229693 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79233792-79234605 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79234606-79235418 Neighboring gene RAS like proto-oncogene A pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4680 Neighboring gene uncharacterized LOC105369863 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:79438588-79439174 Neighboring gene uncharacterized LOC124902973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6685 Neighboring gene Sharpr-MPRA regulatory region 15006 Neighboring gene RE1 silencing transcription factor pseudogene Neighboring gene MPRA-validated peak1855 silencer Neighboring gene MPRA-validated peak1856 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:79774873-79775471 Neighboring gene microRNA 1252 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906476-79906976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906977-79907477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:79926619-79927119 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933315-79933826 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933827-79934340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79936391-79936902 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79938953-79939466 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79941058-79941786 Neighboring gene NOP56 ribonucleoprotein pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:80048601-80049285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4681 Neighboring gene PPP1R12A antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4682 Neighboring gene pro-apoptotic WT1 regulator

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. Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder. Melland H, et al. Genet Med, 2022 Apr. PMID 35101335, Free PMC Article
  2. The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore. Caparotta M, et al. J Chem Theory Comput, 2020 Dec 8. PMID 33166466
  3. Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder. Bradberry MM, et al. Neuron, 2020 Jul 8. PMID 32362337, Free PMC Article
  4. Association between cognitive performance and SYT1-rs2251214 among women with cocaine use disorder. Viola TW, et al. J Neural Transm (Vienna), 2019 Dec. PMID 31562556, Free PMC Article
  5. The association between SYT1-rs2251214 and cocaine use disorder further supports its role in psychiatry. da Silva BS, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2019 Aug 30. PMID 31059723

See all (123) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. miRNA-363-3p Hinders Proliferation, Migration, Invasion and Autophagy of Thyroid Cancer Cells by Controlling SYT1 Transcription to affect NF-kappaB.
    Title: miRNA-363-3p Hinders Proliferation, Migration, Invasion and Autophagy of Thyroid Cancer Cells by Controlling SYT1 Transcription to affect NF-κB.
  2. Extended-synaptotagmin 1 engages in unconventional protein secretion mediated via SEC22B(+) vesicle pathway in liver cancer.
    Title: Extended-synaptotagmin 1 engages in unconventional protein secretion mediated via SEC22B(+) vesicle pathway in liver cancer.
  3. Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder.
    Title: Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder.
  4. The neuronal calcium sensor Synaptotagmin-1 and SNARE proteins cooperate to dilate fusion pores.
    Title: The neuronal calcium sensor Synaptotagmin-1 and SNARE proteins cooperate to dilate fusion pores.
  5. The role of synaptic biomarkers in the spectrum of neurodegenerative diseases.
    Title: The role of synaptic biomarkers in the spectrum of neurodegenerative diseases.
  6. The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore.
    Title: The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore.
  7. 12q21 deletion syndrome: Narrowing the critical region down to 1.6 Mb including SYT1 and PPP1R12A.
    Title: 12q21 deletion syndrome: Narrowing the critical region down to 1.6 Mb including SYT1 and PPP1R12A.
  8. Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
    Title: Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
  9. Association between cognitive performance and SYT1-rs2251214 among women with cocaine use disorder.
    Title: Association between cognitive performance and SYT1-rs2251214 among women with cocaine use disorder.
  10. SGIP1alpha is an endocytic adaptor dedicated to the retrieval of surface-stranded Syt1.
    Title: SGIP1α functions as a selective endocytic adaptor for the internalization of synaptotagmin 1 at synapses.
Submit: New GeneRIF Correction See all GeneRIFs (56)

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

Associated conditions

Description Tests
Infantile hypotonia-oculomotor anomalies-hyperkinetic movements-developmental delay syndrome
MedGen: C4748715 OMIM: 618218 GeneReviews: Not available
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EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

  • DKFZp781D2042

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables SNARE binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion sensor activity IEA
Inferred from Electronic Annotation
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 calcium-dependent phospholipid binding TAS
Traceable Author Statement
more info
 PubMed 
enables calcium-dependent protein binding IEA
Inferred from Electronic Annotation
more info
  
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
  
enables clathrin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables low-density lipoprotein particle receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-4,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables syntaxin-1 binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables syntaxin-3 binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in calcium ion-regulated exocytosis of neurotransmitter IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in calcium-dependent activation of synaptic vesicle fusion IEA
Inferred from Electronic Annotation
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chemical synaptic transmission TAS
Traceable Author Statement
more info
 PubMed 
involved_in detection of calcium ion TAS
Traceable Author Statement
more info
 PubMed 
involved_in fast, calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neurotransmitter secretion TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendrite extension IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of dopamine secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein heterooligomerization IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of exocytosis TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of regulated secretory pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spontaneous neurotransmitter secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synchronous neurotransmitter secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle docking IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
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
  
located_in clathrin-sculpted acetylcholine transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in clathrin-sculpted glutamate transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in clathrin-sculpted monoamine transport vesicle membrane TAS
Traceable Author Statement
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in dense core granule IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in excitatory synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in exocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
  
located_in neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in neuron projection terminus IEA
Inferred from Electronic Annotation
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
  
located_in presynaptic membrane IEA
Inferred from Electronic Annotation
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
synaptotagmin-1
Names
synaptotagmin I
sytI

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_001135805.2 → NP_001129277.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_001129277.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC073606, AK094616, AK126908, BC041373, BM668697, DA174824
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579, Q6AI31
    UniProtKB/TrEMBL
    A0A994J5A7
    Related
    ENSP00000376932.3, ENST00000393240.7
    Conserved Domains (3) summary
    cd08385
    Location:143 → 265
    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
    cd21963
    Location:6 → 113
    Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins

  2. NM_001135806.2 → NP_001129278.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_001129278.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    BC041373, BM668697, CR627387, DA174824
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579, Q6AI31
    UniProtKB/TrEMBL
    A0A994J5A7
    Related
    ENSP00000447575.1, ENST00000552744.5
    Conserved Domains (3) summary
    cd08385
    Location:143 → 265
    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
    cd21963
    Location:6 → 113
    Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins

  3. NM_001291901.2 → NP_001278830.1  synaptotagmin-1 isoform 2

    See identical proteins and their annotated locations for NP_001278830.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC027288, AC073572, AC073606, AC078917
    Consensus CDS
    CCDS76582.1
    UniProtKB/TrEMBL
    A0A994J5A7, J3KQA0
    Related
    ENSP00000391056.2, ENST00000457153.6
    Conserved Domains (3) summary
    cd08385
    Location:140 → 262
    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
    cd21963
    Location:6 → 113
    Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins

  4. NM_001415938.1 → NP_001402867.1  synaptotagmin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073606, AC078917
    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  5. NM_001415939.1 → NP_001402868.1  synaptotagmin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917
    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  6. NM_001415940.1 → NP_001402869.1  synaptotagmin-1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917, AC090709
    UniProtKB/Swiss-Prot
    P21579, Q6AI31
    Related
    ENSP00000516009.1, ENST00000704714.1

  7. NM_001415941.1 → NP_001402870.1  synaptotagmin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917
    UniProtKB/TrEMBL
    J3KQA0
    Related
    ENSP00000515996.1, ENST00000704699.1

  8. NM_001415942.1 → NP_001402871.1  synaptotagmin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073616, AC078917
    UniProtKB/TrEMBL
    J3KQA0

  9. NM_001415943.1 → NP_001402872.1  synaptotagmin-1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917, AC090709
    UniProtKB/TrEMBL
    J3KQA0

  10. NM_005639.3 → NP_005630.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_005630.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579, Q6AI31
    UniProtKB/TrEMBL
    A0A994J5A7
    Related
    ENSP00000261205.4, ENST00000261205.9
    Conserved Domains (3) summary
    cd08385
    Location:143 → 265
    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
    cd21963
    Location:6 → 113
    Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    78863982..79452008
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429479.1 → XP_047285435.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  2. XM_047429484.1 → XP_047285440.1  synaptotagmin-1 isoform X2

    UniProtKB/TrEMBL
    J3KQA0

  3. XM_047429480.1 → XP_047285436.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  4. XM_047429482.1 → XP_047285438.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  5. XM_047429483.1 → XP_047285439.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  6. XM_047429481.1 → XP_047285437.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    78842458..79430647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373100.1 → XP_054229075.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  2. XM_054373098.1 → XP_054229073.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31

  3. XM_054373101.1 → XP_054229076.1  synaptotagmin-1 isoform X2

    UniProtKB/TrEMBL
    J3KQA0

  4. XM_054373099.1 → XP_054229074.1  synaptotagmin-1 isoform X1

    UniProtKB/Swiss-Prot
    P21579, Q6AI31
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P21579.1 GenPept UniProtKB/Swiss-Prot:P21579

Gene LinkOut

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