STX1A syntaxin 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: STX1Aprovided by HGNC
Official Full Name: syntaxin 1Aprovided by HGNC
Primary source: HGNC:HGNC:11433
See related: Ensembl:ENSG00000106089 MIM:186590
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: STX1; HPC-1; P35-1; SYN1A
Summary: This gene encodes a member of the syntaxin superfamily. Syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins possess a single C-terminal transmembrane domain, a SNARE [Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein REceptor] domain (known as H3), and an N-terminal regulatory domain (Habc). Syntaxins bind synaptotagmin in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels via the C-terminal H3 domain. This gene product is a key molecule in ion channel regulation and synaptic exocytosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
Expression: Biased expression in brain (RPKM 28.2), bone marrow (RPKM 2.7) and 3 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 7q11.23

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
109.20191205	current	GRCh38.p13 (GCF_000001405.39)	7	NC_000007.14 (73699210..73719673, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (73113535..73134032, complement)

Chromosome 7 - NC_000007.14 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?

Results suggest a role of Stx-1A rs4717806 SNP in ischemic heart disease, possibly due to its influence in Stx-1A expression and, at cascade, to insulin secretion and to glucose dependent metabolism.
Title: The Syntaxin-1A gene single nucleotide polymorphism rs4717806 associates with the risk of ischemic heart disease.
Some Autism spectrum disorder patients had haploidy of STX1A gene and lower STX1A gene expression.
Title: A part of patients with autism spectrum disorder has haploidy of HPC-1/syntaxin1A gene that possibly causes behavioral disturbance as in experimentally gene ablated mice.
Analysing protein mobility, cluster size and accessibility to myc-epitopes the authors show that forces acting on the transmembrane segment produce loose clusters, while cytoplasmic protein interactions mediate a tightly packed state.
Title: The packing density of a supramolecular membrane protein cluster is controlled by cytoplasmic interactions.
Our results suggest that, as in the CNS, CADM1 interactions drive exocytic site assembly and promote actin network formation. These results support the broader hypothesis that the effects of cell-cell contact on beta-cell maturation and function are mediated by the same extracellular protein interactions that drive the formation of the presynaptic exocytic machinery. These interactions may be therapeutic targets for re...
Title: Extracellular CADM1 interactions influence insulin secretion by rat and human islet β-cells and promote clustering of syntaxin-1.
A significant interactive two-locus model of STX1A_rs4363087|VAMP2_rs2278637 (presynaptic genes) was observed among SVC variants in all epilepsy cases.
Title: Synergistic association of STX1A and VAMP2 with cryptogenic epilepsy in North Indian population.
Mislocalization of syntaxin-1 was found in pluripotent stem cells from epileptic encephalopathy patient.
Title: Mislocalization of syntaxin-1 and impaired neurite growth observed in a human iPSC model for STXBP1-related epileptic encephalopathy.
Blockade of the SNARE protein syntaxin 1 inhibits glioblastoma tumor growth.
Title: Blockade of the SNARE protein syntaxin 1 inhibits glioblastoma tumor growth.
SNARE complex genes and their interactions may play a significant role in susceptibility and working memory of ADHD.
Title: Synaptosome-related (SNARE) genes and their interactions contribute to the susceptibility and working memory of attention-deficit/hyperactivity disorder in males.
We described clinical, genetic, and functional data from 17 families with a diagnosis of benign familial neonatal epilepsy caused by KCNQ2 or KCNQ3 mutations and we showed that some mutations lead to a reduction of Q2 channel regulation by syntaxin-1A.
Title: Novel KCNQ2 and KCNQ3 mutations in a large cohort of families with benign neonatal epilepsy: first evidence for an altered channel regulation by syntaxin-1A.
no associaton with idiopathic generalized epilepsy was found regarding Intron 7 rs1569061 of Syntaxin 1A gene, MnlI rs3746544 and DdeI rs1051312 polymorphisms of SNAP-25 gene compared with healthy subjects
Title: Genetic variants of synaptic vesicle and presynaptic plasma membrane proteins in idiopathic generalized epilepsy.

Submit: New GeneRIF Correction See all GeneRIFs (59)

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

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

STX1A_264 (e-PCR)
- UniSTS:277776

STS-L37792 (e-PCR)
- UniSTS:18981

RH78389 (e-PCR)
- UniSTS:6754

D7S2927 (e-PCR)
- UniSTS:42596

MARC_14487-14488:1010605685:1 (e-PCR)
- UniSTS:267687

RH103672 (e-PCR)
- UniSTS:97997

Homology

Homologs of the STX1A gene: The STX1A gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 232 organisms have orthologs with human gene STX1A
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
ATP-dependent protein binding	IEA Inferred from Electronic Annotation more info
SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
SNARE binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
calcium channel inhibitor activity	IEA Inferred from Electronic Annotation more info
calcium-dependent protein binding	IEA Inferred from Electronic Annotation more info
chloride channel inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
ion channel binding	IEA Inferred from Electronic Annotation more info
kinase binding	IPI Inferred from Physical Interaction more info	PubMed
myosin head/neck binding	IEA Inferred from Electronic Annotation more info
protein N-terminus binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding, bridging	IEA Inferred from Electronic Annotation more info
protein domain specific binding	IEA Inferred from Electronic Annotation more info
protein heterodimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
SNARE complex assembly	IEA Inferred from Electronic Annotation more info
calcium ion regulated exocytosis	IEA Inferred from Electronic Annotation more info
cytokine-mediated signaling pathway	TAS Traceable Author Statement more info
exocytosis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
glutamate secretion	TAS Traceable Author Statement more info
insulin secretion	IEA Inferred from Electronic Annotation more info
intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
neurotransmitter secretion	TAS Traceable Author Statement more info
positive regulation of calcium ion-dependent exocytosis	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of catecholamine secretion	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of excitatory postsynaptic potential	IEA Inferred from Electronic Annotation more info
positive regulation of neurotransmitter secretion	IEA Inferred from Electronic Annotation more info
positive regulation of norepinephrine secretion	ISS Inferred from Sequence or Structural Similarity more info
protein localization to membrane	IEA Inferred from Electronic Annotation more info
protein sumoylation	IDA Inferred from Direct Assay more info	PubMed
regulation of insulin secretion	TAS Traceable Author Statement more info	PubMed
regulation of synaptic vesicle priming	IEA Inferred from Electronic Annotation more info
response to gravity	IEA Inferred from Electronic Annotation more info
secretion by cell	IDA Inferred from Direct Assay more info	PubMed
synaptic vesicle docking	IEA Inferred from Electronic Annotation more info
synaptic vesicle endocytosis	IDA Inferred from Direct Assay more info	PubMed
synaptic vesicle exocytosis	IDA Inferred from Direct Assay more info	PubMed
synaptic vesicle fusion to presynaptic active zone membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
vesicle docking	IBA Inferred from Biological aspect of Ancestor more info	PubMed
vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
SNARE complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
SNARE complex	IDA Inferred from Direct Assay more info	PubMed
SNARE complex	TAS Traceable Author Statement more info	PubMed
actomyosin	IEA Inferred from Electronic Annotation more info
axon	IEA Inferred from Electronic Annotation more info
cell junction	IEA Inferred from Electronic Annotation more info
cytosol	TAS Traceable Author Statement more info
endomembrane system	IBA Inferred from Biological aspect of Ancestor more info	PubMed
extracellular region	IEA Inferred from Electronic Annotation more info
glutamatergic synapse	IEA Inferred from Electronic Annotation more info
integral component of membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
integral component of presynaptic membrane	IEA Inferred from Electronic Annotation more info
integral component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
neuron projection	IDA Inferred from Direct Assay more info	PubMed
nuclear membrane	IEA Inferred from Electronic Annotation more info
plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
plasma membrane	IDA Inferred from Direct Assay more info	PubMed
plasma membrane	TAS Traceable Author Statement more info	PubMed
postsynaptic density	IEA Inferred from Electronic Annotation more info
presynaptic active zone membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
presynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
secretory granule	IEA Inferred from Electronic Annotation more info
synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info	PubMed
synaptobrevin 2-SNAP-25-syntaxin-1a complex	IEA Inferred from Electronic Annotation more info
synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex	IEA Inferred from Electronic Annotation more info
synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex	IEA Inferred from Electronic Annotation more info
colocalizes_with voltage-gated potassium channel complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: syntaxin-1A

Names: neuron-specific antigen HPC-1; syntaxin 1A (brain)

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_013360.1 RefSeqGene

Range

5019..25478

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001165903.2 → NP_001159375.1 syntaxin-1A isoform 2

See identical proteins and their annotated locations for NP_001159375.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal segment in the 3' coding region, as compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus, as compared to isoform 1.

Source sequence(s)

BC000444, BC064644, DA159446

Consensus CDS

CCDS55120.1

UniProtKB/Swiss-Prot

Q16623

Related

ENSP00000378585.3, ENST00000395156.7

Conserved Domains (1) summary

pfam00804
Location:30 → 226

Syntaxin; Syntaxin
NM_004603.4 → NP_004594.1 syntaxin-1A isoform 1

See identical proteins and their annotated locations for NP_004594.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BC003011, BC064644, DA159446

Consensus CDS

CCDS34655.1

UniProtKB/Swiss-Prot

Q16623

UniProtKB/TrEMBL

Q75ME0

Related

ENSP00000222812.3, ENST00000222812.8

Conserved Domains (2) summary

pfam00804
Location:30 → 227

Syntaxin; Syntaxin

pfam05739
Location:228 → 279

SNARE; SNARE domain