SYT1 synaptotagmin 1 [Homo sapiens (human)] - Gene

Summary

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

Location:: 12q21.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (78863982..79452008)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (78842458..79430647)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (79257762..79845788)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Modulation of GPR133 (ADGRD1) signaling by its intracellular interaction partner extended synaptotagmin 1.
Title: Modulation of GPR133 (ADGRD1) signaling by its intracellular interaction partner extended synaptotagmin 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.
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.
Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder.
Title: Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder.
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.
The role of synaptic biomarkers in the spectrum of neurodegenerative diseases.
Title: The role of synaptic biomarkers in the spectrum of neurodegenerative diseases.
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.
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.
Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
Title: Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.
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.

Submit: New GeneRIF Correction See all GeneRIFs (57)

Phenotypes

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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	not available

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-31415 (e-PCR)
- UniSTS:33281

WI-22639 (e-PCR)
- UniSTS:76810

SYT1_862 (e-PCR)
- UniSTS:277780

SHGC-31058 (e-PCR)
- UniSTS:64539

G09678 (e-PCR)
- UniSTS:21026

D12S1421 (e-PCR)
- UniSTS:80438

SHGC-155197 (e-PCR)
- UniSTS:182607

SHGC-84895 (e-PCR)
- UniSTS:104788

D12F314S2 (e-PCR)
- UniSTS:70493

SHGC-30056 (e-PCR)
- UniSTS:2399

RH78549 (e-PCR)
- UniSTS:63327

G31550 (e-PCR)
- UniSTS:78177

WI-17968 (e-PCR)
- UniSTS:82536

RH17699 (e-PCR)
- UniSTS:72557

A002S37 (e-PCR)
- UniSTS:55926

D12S64 (e-PCR)
- UniSTS:147835

SHGC-84114 (e-PCR)
- UniSTS:104571

SHGC-110880 (e-PCR)
- UniSTS:168066

SHGC-59569 (e-PCR)
- UniSTS:3474

D37792 (e-PCR)
- UniSTS:124827

SHGC-85231 (e-PCR)
- UniSTS:104367

GDB:384848 (e-PCR)
- UniSTS:157107

SHGC-111536 (e-PCR)
- UniSTS:168385

SHGC-111560 (e-PCR)
- UniSTS:168398

D12S2204 (e-PCR)
- UniSTS:50135

STS-AA040166 (e-PCR)
- UniSTS:30439

G65584 (e-PCR)
- UniSTS:225518

RH44236 (e-PCR)
- UniSTS:34546

D12S1846 (e-PCR)
- UniSTS:9204

RH47944 (e-PCR)
- UniSTS:74237

RH47304 (e-PCR)
- UniSTS:27901

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	IEA Inferred from Electronic Annotation 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 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	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables lipid binding	EXP Inferred from Experiment more info	PubMed
enables lipid binding	IDA Inferred from Direct Assay more info	PubMed
enables low-density lipoprotein particle receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables molecular condensate scaffold activity	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-4,5-bisphosphate binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylserine binding	IEA Inferred from Electronic Annotation 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-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 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 membraneless organelle assembly	IEA Inferred from Electronic Annotation 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 calcium ion-dependent exocytosis	IBA Inferred from Biological aspect of Ancestor 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 regulation of synaptic vesicle exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in spontaneous neurotransmitter secretion	IEA Inferred from Electronic Annotation 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
involved_in vesicle fusion	IEA Inferred from Electronic Annotation more info
involved_in vesicle organization	IDA Inferred from Direct Assay more info	PubMed
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor 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 postsynaptic cytosol	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic active zone	IEA Inferred from Electronic Annotation more info
located_in presynaptic cytosol	IEA Inferred from Electronic Annotation 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)

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

Status: REVIEWED

Source sequence(s)

AC027288, AC073572, AC073606, AC078917

UniProtKB/Swiss-Prot

P21579, Q6AI31
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
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
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
NM_001415942.1 → NP_001402871.1 synaptotagmin-1 isoform 2

Status: REVIEWED

Source sequence(s)

AC027288, AC073572, AC073616, AC078917

UniProtKB/TrEMBL

J3KQA0
NM_001415943.1 → NP_001402872.1 synaptotagmin-1 isoform 2

Status: REVIEWED

Source sequence(s)

AC027288, AC073572, AC073606, AC073616, AC078917, AC090709

UniProtKB/TrEMBL

J3KQA0
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

78863982..79452008

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_047429484.1 → XP_047285440.1 synaptotagmin-1 isoform X2

UniProtKB/TrEMBL

J3KQA0
XM_047429480.1 → XP_047285436.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_047429482.1 → XP_047285438.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_047429483.1 → XP_047285439.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_047429481.1 → XP_047285437.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

78842458..79430647

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_054373098.1 → XP_054229073.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31
XM_054373101.1 → XP_054229076.1 synaptotagmin-1 isoform X2

UniProtKB/TrEMBL

J3KQA0
XM_054373099.1 → XP_054229074.1 synaptotagmin-1 isoform X1

UniProtKB/Swiss-Prot

P21579, Q6AI31