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; AllianceGenome:HGNC:11433
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
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Genomic context

Location:: 7q11.23

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (73699210..73719669, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (74900126..74920586, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (73113540..73133999, 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?

Heterozygous and homozygous variants in STX1A cause a neurodevelopmental disorder with or without epilepsy.
Title: Heterozygous and homozygous variants in STX1A cause a neurodevelopmental disorder with or without epilepsy.
Syntaxin-1 and Insulinoma-Associated Protein 1 Expression in Breast Neoplasms with Neuroendocrine Features.
Title: Syntaxin-1 and Insulinoma-Associated Protein 1 Expression in Breast Neoplasms with Neuroendocrine Features.
Oligomeric alpha-Syn and SNARE complex proteins in peripheral extracellular vesicles of neural origin are biomarkers for Parkinson's disease.
Title: Oligomeric α-Syn and SNARE complex proteins in peripheral extracellular vesicles of neural origin are biomarkers for Parkinson's disease.
De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A.
Title: De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A.
Syntaxin 1: A Novel Robust Immunophenotypic Marker of Neuroendocrine Tumors.
Title: Syntaxin 1: A Novel Robust Immunophenotypic Marker of Neuroendocrine Tumors.
The N-terminal of the SNAP25 loop region binds with membrane, and this interaction induced a disorder-to-order conformational change of the loop, resulting in enhanced interaction between the C-terminal of the SNAP25 loop and syx-1. SNARE-complex assembly efficiency decreased when the electrostatic interaction between C-terminal of the SNAP25 loop and syx-1 was disrupted.
Title: Membrane-mediated disorder-to-order transition of SNAP25 flexible linker facilitates its interaction with syntaxin-1 and SNARE-complex assembly.
Using a case-control study to explore the association between STX1A gene and children with ADHD in Chinese Han population, our results suggest STX1A genetic variants might contribute to the susceptibility of children ADHD.
Title: STX1A gene variations contribute to the susceptibility of children attention-deficit/hyperactivity disorder: a case-control association study.
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.

Submit: New GeneRIF Correction See all GeneRIFs (66)

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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables calcium channel inhibitor activity	IEA Inferred from Electronic Annotation more info
enables chloride channel inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
part_of SNARE complex	TAS Traceable Author Statement more info	PubMed
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed
is_active_in presynaptic active zone membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
part_of synaptobrevin 2-SNAP-25-syntaxin-1a complex	IEA Inferred from Electronic Annotation 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

O15447, O15448, Q12936, Q16623, Q75MD9, Q7Z5K3, Q9BPZ6

UniProtKB/TrEMBL

Q75ME0, X5D7S1

Related

ENSP00000222812.3, ENST00000222812.8

Conserved Domains (2) summary

pfam00804
Location:30 → 227

Syntaxin

pfam05739
Location:228 → 279

SNARE; SNARE domain