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Aliases for STX1A Gene

Aliases for STX1A Gene

  • Syntaxin 1A 2 3 5
  • Neuron-Specific Antigen HPC-1 3 4
  • Syntaxin 1A (Brain) 2 3
  • STX1 3 4
  • Syntaxin-1A 3
  • HPC-1 3
  • P35-1 3
  • SYN1A 3

External Ids for STX1A Gene

Previous HGNC Symbols for STX1A Gene

  • STX1

Previous GeneCards Identifiers for STX1A Gene

  • GC07M071753
  • GC07M072511
  • GC07M072525
  • GC07M072500
  • GC07M072558
  • GC07M072751
  • GC07M073113
  • GC07M068995

Summaries for STX1A Gene

Entrez Gene Summary for STX1A Gene

  • 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]

GeneCards Summary for STX1A Gene

STX1A (Syntaxin 1A) is a Protein Coding gene. Diseases associated with STX1A include Cystic Fibrosis and Osteogenesis Imperfecta, Type Xv. Among its related pathways are Peptide hormone metabolism and Cytokine Signaling in Immune system. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and protein N-terminus binding. An important paralog of this gene is STX1B.

UniProtKB/Swiss-Prot for STX1A Gene

  • Plays a role in hormone and neurotransmitter exocytosis (By similarity). Potentially involved in docking of synaptic vesicles at presynaptic active zones. May mediate Ca(2+)-regulation of exocytosis acrosomal reaction in sperm.

Gene Wiki entry for STX1A Gene

Additional gene information for STX1A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for STX1A Gene

Genomics for STX1A Gene

GeneHancer (GH) Regulatory Elements for STX1A Gene

Promoters and enhancers for STX1A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I073715 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.8 +2.1 2148 4.9 CLOCK SMAD1 FOXA2 ARNT ZFP64 ARID4B NEUROD1 SIN3A FEZF1 ZNF766 STX1A POM121B POM121 TBL2 STAG3L3 NSUN5P2 MIR590 NSUN5 PMS2P7 RFC2
GH07I073721 Enhancer 0.8 ENCODE dbSUPER 556.3 -1.9 -1887 1.1 CTCF RXRA RAD21 YY1 ZNF121 ZFHX2 ZNF341 HNF4A EGR2 STX1A GC07M073734
GH07I073612 Enhancer 1.1 ENCODE 13.1 +106.2 106220 2.6 PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 ENSG00000274080 BCL7B STX1A VPS37D BUD23 DNAJC30 TBL2 RNU6-1198P METTL27 PMS2P7
GH07I073606 Enhancer 0.9 Ensembl ENCODE 13.1 +112.4 112449 1.1 CTCF RB1 ZMYM3 RAD21 CC2D1A MTA3 ZBTB48 ARID2 PATZ1 SMC3 STX1A VPS37D BUD23 DNAJC30 TBL2 RNU6-1198P GTF2IP4 ENSG00000274080 GC07P073590 MLXIPL
GH07I073602 Enhancer 0.6 Ensembl 13 +116.5 116489 1.2 PAF1 PKNOX1 NFYC ZNF48 SP1 SSRP1 POLR2A PBX2 GLIS1 MYNN MLXIPL BCL7B STX1A BUD23 DNAJC30 VPS37D ENSG00000274080 GC07P073590
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around STX1A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the STX1A gene promoter:

Genomic Locations for STX1A Gene

Genomic Locations for STX1A Gene
20,498 bases
Minus strand

Genomic View for STX1A Gene

Genes around STX1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
STX1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for STX1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for STX1A Gene

Proteins for STX1A Gene

  • Protein details for STX1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • O15447
    • O15448
    • Q12936
    • Q75MD9
    • Q7Z5K3
    • Q9BPZ6

    Protein attributes for STX1A Gene

    288 amino acids
    Molecular mass:
    33023 Da
    Quaternary structure:
    • Interacts (via C-terminus) with KCNB1 (via C-terminus); the interaction increases in a calcium-dependent manner and induces a pore-independent enhancement of exocytosis in neuroendocrine cells, chromaffin cells, pancreatic beta cells and from the soma of dorsal root ganglia (DRG) neurons (By similarity). Part of the SNARE core complex containing SNAP25, VAMP2 and STX1A (By similarity). This complex binds to CPLX1 (By similarity). Binds SYTL4 and STXBP6 (By similarity). Found in a ternary complex with STX1A and SNAP25 (By similarity). Interacts with PLCL1 (via C2 domain) (By similarity). Interacts with OTOF and LGI3 (By similarity). Interacts with SLC6A4 (By similarity). Interacts with SYT6 and SYT8; the interaction is Ca(2+)-dependent (By similarity). Found in a complex with VAMP8 and SNAP23 (PubMed:12130530). Interacts with VAPA and SYBU (PubMed:15459722). Interacts with STXBP1 and DAPK1 (PubMed:12730201).
    • Sequence=AAA20940.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for STX1A Gene


neXtProt entry for STX1A Gene

Post-translational modifications for STX1A Gene

  • Phosphorylated by CK2 (By similarity). Phosphorylation at Ser-188 by DAPK1 significantly decreases its interaction with STXBP1.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for STX1A Gene

No data available for DME Specific Peptides for STX1A Gene

Domains & Families for STX1A Gene

Gene Families for STX1A Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for STX1A Gene

Suggested Antigen Peptide Sequences for STX1A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the syntaxin family.
  • Belongs to the syntaxin family.
genes like me logo Genes that share domains with STX1A: view

Function for STX1A Gene

Molecular function for STX1A Gene

GENATLAS Biochemistry:
syntaxin 1A,expressed in the nervous system at the early stage of embryogenesis,strongly related to the cognitive processes,forming a synaptic core complex with synaptosome associated proteins and synaptobrevin,binding to N-type Ca2+ channels,involved in the intracellular membrane transport and exocytosis process of neurotransmitters,deleted in Williams syndrome,soluble N ethylmaleimide-sensitive factor-attachment protein receptor,SNARE protein
UniProtKB/Swiss-Prot Function:
Plays a role in hormone and neurotransmitter exocytosis (By similarity). Potentially involved in docking of synaptic vesicles at presynaptic active zones. May mediate Ca(2+)-regulation of exocytosis acrosomal reaction in sperm.

Phenotypes From GWAS Catalog for STX1A Gene

Gene Ontology (GO) - Molecular Function for STX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA --
GO:0005484 SNAP receptor activity IBA --
GO:0005515 protein binding IPI 10321247
GO:0017022 myosin binding IBA --
GO:0019855 calcium channel inhibitor activity IEA --
genes like me logo Genes that share ontologies with STX1A: view
genes like me logo Genes that share phenotypes with STX1A: view

Human Phenotype Ontology for STX1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for STX1A Gene

MGI Knock Outs for STX1A:

Animal Model Products

  • Taconic Biosciences Mouse Models for STX1A

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for STX1A Gene

Localization for STX1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for STX1A Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass type IV membrane protein. Cell junction, synapse, synaptosome. Cell membrane. Note=Colocalizes with KCNB1 at the cell membrane. {ECO:0000250 UniProtKB:P32851}.
Isoform 2: Secreted.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for STX1A gene
Compartment Confidence
plasma membrane 5
cytosol 5
extracellular 4
cytoskeleton 3
nucleus 2
golgi apparatus 2
endoplasmic reticulum 1
lysosome 1
endosome 1

Gene Ontology (GO) - Cellular Components for STX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane TAS 10099709
GO:0005887 integral component of plasma membrane IEA --
GO:0008021 synaptic vesicle IBA --
genes like me logo Genes that share ontologies with STX1A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for STX1A Gene

Pathways & Interactions for STX1A Gene

genes like me logo Genes that share pathways with STX1A: view

SIGNOR curated interactions for STX1A Gene

Is activated by:

Gene Ontology (GO) - Biological Process for STX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001956 positive regulation of neurotransmitter secretion IEA --
GO:0006810 transport IEA --
GO:0006836 neurotransmitter transport IEA --
GO:0006886 intracellular protein transport IBA --
GO:0006887 exocytosis IEA --
genes like me logo Genes that share ontologies with STX1A: view

Drugs & Compounds for STX1A Gene

(13) Drugs for STX1A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(9) Additional Compounds for STX1A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with STX1A: view

Transcripts for STX1A Gene

Unigene Clusters for STX1A Gene

Syntaxin 1A (brain):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for STX1A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c · 11d · 11e ^ 12a · 12b · 12c
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - -
SP4: - -
SP5: - - -
SP6: - -
SP7: - -
SP8: - - -

Relevant External Links for STX1A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for STX1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for STX1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for STX1A Gene

This gene is overexpressed in Brain - Cortex (x8.5), Brain - Frontal Cortex (BA9) (x6.8), Brain - Anterior cingulate cortex (BA24) (x6.3), and Pituitary (x4.6).

Protein differential expression in normal tissues from HIPED for STX1A Gene

This gene is overexpressed in Frontal cortex (40.2) and Brain (23.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for STX1A Gene

Protein tissue co-expression partners for STX1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of STX1A Gene:


SOURCE GeneReport for Unigene cluster for STX1A Gene:


mRNA Expression by UniProt/SwissProt for STX1A Gene:

Tissue specificity: Isoform 1 is highly expressed in embryonic spinal chord and ganglia and in adult cerebellum and cerebral cortex. Isoform 2 is expressed in heart, liver, fat, skeletal muscle, kidney and brain.

Evidence on tissue expression from TISSUES for STX1A Gene

  • Nervous system(5)
  • Lung(4.1)
  • Intestine(2.6)
  • Pancreas(2.5)
  • Adrenal gland(2.3)
  • Kidney(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for STX1A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • urinary
Head and neck:
  • brain
  • ear
  • head
  • bronchus
  • heart
  • lung
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
  • anus
  • rectum
  • testicle
  • blood
  • blood vessel
  • coagulation system
  • skin
  • sweat gland
  • white blood cell
genes like me logo Genes that share expression patterns with STX1A: view

Orthologs for STX1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for STX1A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia STX1A 33 34
  • 99.77 (n)
(Monodelphis domestica)
Mammalia STX1A 34
  • 95 (a)
(Canis familiaris)
Mammalia STX1A 33 34
  • 91.97 (n)
(Rattus norvegicus)
Mammalia Stx1a 33
  • 91.55 (n)
(Mus musculus)
Mammalia Stx1a 33 16 34
  • 91.2 (n)
(Bos Taurus)
Mammalia STX1A 33 34
  • 87.92 (n)
(Gallus gallus)
Aves -- 34
  • 83 (a)
-- 34
  • 79 (a)
(Anolis carolinensis)
Reptilia STX1A 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia stx1a 33
  • 80.9 (n)
(Danio rerio)
Actinopterygii stx1a 34
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta Syx1A 35 33 34
  • 71.17 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007698 33
  • 65.25 (n)
(Caenorhabditis elegans)
Secernentea unc-64 33 34
  • 62.55 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL139W 33
  • 49.51 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SSO2 33 36
  • 47.65 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C15961g 33
  • 45.83 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons SYP132 33
  • 45.16 (n)
(Oryza sativa)
Liliopsida Os06g0168500 33
  • 47.36 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU04244 33
  • 44.17 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes psy1 33
  • 40.94 (n)
Species where no ortholog for STX1A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for STX1A Gene

Gene Tree for STX1A (if available)
Gene Tree for STX1A (if available)

Paralogs for STX1A Gene

Paralogs for STX1A Gene

(10) SIMAP similar genes for STX1A Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with STX1A: view

Variants for STX1A Gene

Sequence variations from dbSNP and Humsavar for STX1A Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000259461 -- 73,706,967(-) G/C intron_variant
rs1000307837 -- 73,707,159(-) G/A intron_variant
rs1000468722 -- 73,701,729(-) C/T downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000821349 -- 73,701,399(-) G/A genic_downstream_transcript_variant, intron_variant
rs1001769417 -- 73,714,882(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for STX1A Gene

Variant ID Type Subtype PubMed ID
nsv469841 CNV loss 16826518
nsv831028 CNV loss 17160897

Variation tolerance for STX1A Gene

Residual Variation Intolerance Score: 32.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.38; 8.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for STX1A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for STX1A Gene

Disorders for STX1A Gene

MalaCards: The human disease database

(7) MalaCards diseases for STX1A Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search STX1A in MalaCards View complete list of genes associated with diseases


  • Note=STX1A is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. {ECO:0000305 PubMed:9311751}.

Additional Disease Information for STX1A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with STX1A: view

No data available for Genatlas for STX1A Gene

Publications for STX1A Gene

  1. Evidence of syntaxin 1A involvement in migraine susceptibility: a Portuguese study. (PMID: 20385907) Lemos C … Sousa A (Archives of neurology 2010) 3 22 44 58
  2. Contribution of syntaxin 1A to the genetic susceptibility to migraine: a case-control association study in the Spanish population. (PMID: 19368856) Corominas R … Cormand B (Neuroscience letters 2009) 3 22 44 58
  3. Search for genetic variants of the SYNTAXIN 1A (STX1A) gene: the -352 A>T variant in the STX1A promoter associates with impaired glucose metabolism in an Italian obese population. (PMID: 17912268) Romeo S … Baroni MG (International journal of obesity (2005) 2008) 3 22 44 58
  4. No association between tagging SNPs of SNARE complex genes (STX1A, VAMP2 and SNAP25) and schizophrenia in a Japanese population. (PMID: 18512733) Kawashima K … Iwata N (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 22 44 58
  5. Genetic and expression analyses reveal elevated expression of syntaxin 1A ( STX1A) in high functioning autism. (PMID: 18593506) Nakamura K … Mori N (The international journal of neuropsychopharmacology 2008) 3 22 44 58

Products for STX1A Gene

Sources for STX1A Gene

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