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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
STX1A
syntaxin 1A
Chromosome 7 Β· 7q11.23
NCBI Gene: 6804Ensembl: ENSG00000106089.12HGNC: HGNC:11433UniProt: A0A0C4DFZ1
203PubMed Papers
20Diseases
0Drugs
6Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTransporter
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
synaptic vesicle endocytosischloride channel inhibitor activityplasma membranesynaptic vesicle exocytosisIntellectual disabilityautismNeurodevelopmental disordercystic fibrosis
✦AI Summary

STX1A (syntaxin 1A) is a Qa-SNARE protein that plays essential roles in calcium-dependent exocytosis and membrane fusion processes across multiple cellular contexts. The protein functions as part of the canonical SNARE complex, pairing with SNAP25 and VAMP2 to mediate synaptic vesicle fusion with the presynaptic plasma membrane for neurotransmitter release 1. Beyond synaptic function, STX1A exhibits dual subcellular localization, residing primarily in lysosomes while also localizing to the plasma membrane, where it regulates lysosomal exocytosis through SNARE complex formation with SNAP23/SNAP25 and VAMP2 2. Recent studies have identified a novel mitochondrial localization for STX1A in gastric cancer cells, where it modulates mitochondrial respiration and ferroptosis, contributing to chemoresistance mechanisms 3. Clinically, STX1A variants are associated with neurodevelopmental disorders, as mutations in the synaptic SNARE complex components, including STX1A, can produce phenotypes involving autism, intellectual disability, movement disorders, and epilepsy 1. The gene is also implicated in Williams syndrome, a microdeletion disorder affecting chromosome 7.23 that includes STX1A among the deleted genes, contributing to the syndrome's complex phenotype 4. Additionally, STX1A has been identified as a candidate gene in ADHD pathogenesis and consanguineous families with neurodevelopmental disorders 56.

Sources cited
1
STX1A functions in the canonical synaptic SNARE complex with SNAP25 and VAMP2, and mutations cause autism, intellectual disability, movement disorders, and epilepsy
PMID: 32959907
2
STX1A localizes to lysosomes and plasma membrane, regulating lysosomal exocytosis through SNARE complex formation
PMID: 41123944
3
STX1A localizes to mitochondria in gastric cancer cells and regulates mitochondrial respiration and ferroptosis
PMID: 40056239
4
STX1A is among genes deleted in Williams syndrome on chromosome 7q11.23
PMID: 34140529
5
STX1A is identified as a candidate gene in ADHD pathogenesis
PMID: 36211978
6
STX1A variants identified in consanguineous families with neurodevelopmental disorders
PMID: 28097321
Disease Associationsβ“˜20
Intellectual disabilityOpen Targets
0.57Moderate
autismOpen Targets
0.44Moderate
Neurodevelopmental disorderOpen Targets
0.38Weak
cystic fibrosisOpen Targets
0.37Weak
botulismOpen Targets
0.37Weak
SeizureOpen Targets
0.37Weak
genetic disorderOpen Targets
0.19Weak
complex neurodevelopmental disorderOpen Targets
0.18Weak
Neurodevelopmental abnormalityOpen Targets
0.11Weak
Myocardial IschemiaOpen Targets
0.06Suggestive
Familial exudative vitreoretinopathyOpen Targets
0.05Suggestive
X-linked retinal dysplasiaOpen Targets
0.05Suggestive
neoplasmOpen Targets
0.05Suggestive
childhood disintegrative disorderOpen Targets
0.05Suggestive
severe early-childhood-onset retinal dystrophyOpen Targets
0.05Suggestive
Stargardt diseaseOpen Targets
0.05Suggestive
glioblastoma multiformeOpen Targets
0.04Suggestive
hemolytic-uremic syndromeOpen Targets
0.04Suggestive
Abruptio PlacentaeOpen Targets
0.04Suggestive
X-linked retinoschisisOpen Targets
0.04Suggestive
Pathogenic Variants6
NM_004603.4(STX1A):c.435C>G (p.Cys145Trp)Likely pathogenic
Neurodevelopmental abnormality|Intellectual disability;Seizure
β˜…β˜†β˜†β˜†2022β†’ Residue 145
NM_004603.4(STX1A):c.554C>G (p.Ser185Cys)Likely pathogenic
Intellectual disability;Seizure
β˜…β˜†β˜†β˜†2022β†’ Residue 185
NM_004603.4(STX1A):c.668_670del (p.Val223del)Likely pathogenic
Autism;Intellectual disability
β˜…β˜†β˜†β˜†2022β†’ Residue 223
NM_004603.4(STX1A):c.677A>G (p.Gln226Arg)Likely pathogenic
Intellectual disability;Seizure
β˜…β˜†β˜†β˜†2022β†’ Residue 226
NM_004603.4(STX1A):c.722_724del (p.Val241del)Likely pathogenic
Autism;Intellectual disability
β˜…β˜†β˜†β˜†2022β†’ Residue 241
NM_004603.4(STX1A):c.284-1G>APathogenic
Autism;Intellectual disability
β˜…β˜†β˜†β˜†2022
View on ClinVar β†—
Related Genes
BNIP1Protein interaction100%NSFProtein interaction100%SNAP23Protein interaction100%STX6Protein interaction100%STX7Protein interaction100%STX10Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
71%
Ovary
10%
Lung
8%
Liver
7%
Heart
3%
Gene Interaction Network
Click a node to explore
STX1ABNIP1NSFSNAP23STX6STX7STX10
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q16623
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.26Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.11 [0.05–0.26]
RankingsWhere STX1A stands among ~20K protein-coding genes
  • #2,076of 20,598
    Most Researched203 Β· top quartile
  • #3,307of 5,498
    Most Pathogenic Variants6
  • #812of 17,882
    Most Constrained (LOEUF)0.26 Β· top 5%
Genes detectedSTX1A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
Williams syndrome.
PMID: 34140529
Nat Rev Dis Primers Β· 2021
1.00
2
Shiga Toxin (Stx) Classification, Structure, and Function.
PMID: 25530917
Microbiol Spectr Β· 2014
0.90
3
Attention-deficit/hyperactive disorder updates.
PMID: 36211978
Front Mol Neurosci Β· 2022
0.80
4
Diagnostic Yield and Novel Candidate Genes by Exome Sequencing in 152 Consanguineous Families With Neurodevelopmental Disorders.
PMID: 28097321
JAMA Psychiatry Β· 2017
0.70
5
YKT6 Is Essential for Male Fertility by Promoting Meiosis Progression During Spermatogenesis of Mice.
PMID: 40528727
Cell Prolif Β· 2026
0.60