SYT2 synaptotagmin 2 [Homo sapiens (human)] - Gene

Summary

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

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_000001.11 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
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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
Congenital myasthenic syndrome 7 MedGen: C4015038 OMIM: 616040 GeneReviews: Congenital Myasthenic Syndromes Overview	Compare labs
Myasthenic syndrome, congenital, 7B, presynaptic, autosomal recessive MedGen: C5561947 OMIM: 619461 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

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

D1S1724 (e-PCR), detects polymorphism
- UniSTS:14342

D1S1804E (e-PCR)
- UniSTS:29732

D1S2654 (e-PCR)
- UniSTS:81195

NoName (e-PCR)
- UniSTS:482608

NIB1035 (e-PCR)
- UniSTS:64834

D1S2655 (e-PCR), detects polymorphism
- UniSTS:15434

A008L47 (e-PCR)
- UniSTS:34152

A002T08 (e-PCR)
- UniSTS:12394

D1S3420 (e-PCR)
- UniSTS:65707

AL009837 (e-PCR)
- UniSTS:65982

SYT2__5372 (e-PCR)
- UniSTS:464585

D1S2686 (e-PCR), detects polymorphism
- UniSTS:53757

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 metal ion binding	IEA Inferred from Electronic Annotation 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

NG_041776.1 RefSeqGene

Range

4970..124828

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

202590596..202710454 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
XM_017000310.3 → XP_016855799.1 synaptotagmin-2 isoform X2
XM_017000309.3 → XP_016855798.1 synaptotagmin-2 isoform X1