STX1A

gene
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Also known as HPC-1p35-1

Summary

STX1A (syntaxin 1A, HGNC:11433) is a protein-coding gene on chromosome 7q11.23, encoding Syntaxin-1A (Q16623). Plays an essential role in hormone and neurotransmitter calcium-dependent exocytosis and endocytosis.

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.

Source: NCBI Gene 6804 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC) — +2 more curated relationships
  • GWAS associations: 5
  • Clinical variants (ClinVar): 53 total — 2 pathogenic, 5 likely-pathogenic
  • Phenotypes (HPO): 212
  • MANE Select transcript: NM_004603

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11433
Approved symbolSTX1A
Namesyntaxin 1A
Location7q11.23
Locus typegene with protein product
StatusApproved
AliasesHPC-1, p35-1
Ensembl geneENSG00000106089
Ensembl biotypeprotein_coding
OMIM186590
Entrez6804

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 7 protein_coding, 5 retained_intron, 5 protein_coding_CDS_not_defined

ENST00000222812, ENST00000395154, ENST00000395155, ENST00000395156, ENST00000461441, ENST00000462135, ENST00000470878, ENST00000480126, ENST00000484736, ENST00000491427, ENST00000491645, ENST00000494245, ENST00000496216, ENST00000497980, ENST00000910650, ENST00000929307, ENST00000971340

RefSeq mRNA: 2 — MANE Select: NM_004603 NM_001165903, NM_004603

CCDS: CCDS34655, CCDS55120

Canonical transcript exons

ENST00000222812 — 10 exons

ExonStartEnd
ENSE000010174037371960273719669
ENSE000016662297370073073700840
ENSE000034868677370375573703828
ENSE000034888587370414873704256
ENSE000035195987370904573709122
ENSE000035773147370515073705224
ENSE000035965857369921073700484
ENSE000035976857370435073704423
ENSE000036572207370858973708688
ENSE000036763997370284573702982

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 98.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.2435 / max 391.9425, expressed in 1608 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
8432110.90911606
843220.278694
843200.055810

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right frontal lobeUBERON:000281098.24gold quality
right hemisphere of cerebellumUBERON:001489098.02gold quality
prefrontal cortexUBERON:000045197.73gold quality
cerebellar hemisphereUBERON:000224597.70gold quality
cerebellar cortexUBERON:000212997.59gold quality
Brodmann (1909) area 10UBERON:001354197.38gold quality
frontal poleUBERON:000279597.09gold quality
dorsolateral prefrontal cortexUBERON:000983497.00gold quality
anterior cingulate cortexUBERON:000983596.97gold quality
cingulate cortexUBERON:000302796.95gold quality
frontal cortexUBERON:000187096.40gold quality
frontal lobeUBERON:001652596.40gold quality
Brodmann (1909) area 9UBERON:001354096.28gold quality
cerebellumUBERON:000203796.02gold quality
neocortexUBERON:000195095.94gold quality
pituitary glandUBERON:000000795.64gold quality
islet of LangerhansUBERON:000000695.47gold quality
adenohypophysisUBERON:000219695.29gold quality
cortical plateUBERON:000534394.93gold quality
cerebral cortexUBERON:000095694.32gold quality
amygdalaUBERON:000187694.08gold quality
Brodmann (1909) area 46UBERON:000648392.74gold quality
temporal lobeUBERON:000187191.61gold quality
orbitofrontal cortexUBERON:000416791.44gold quality
superior frontal gyrusUBERON:000266191.26gold quality
gall bladderUBERON:000211090.50gold quality
telencephalonUBERON:000189390.20gold quality
forebrainUBERON:000189089.78gold quality
primary visual cortexUBERON:000243689.76gold quality
Ammon’s hornUBERON:000195489.62gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-81547yes516.86
E-HCAD-25yes75.09
E-MTAB-5061yes14.79
E-MTAB-7303no580.31
E-ANND-3no2.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting STX1A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-605-3P99.8869.221833
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-149-3P99.7268.223963
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-548AU-3P99.7068.221373
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-217-5P99.4969.931419
HSA-MIR-806499.4566.92875

Literature-anchored findings (GeneRIF, showing 40)

  • SNAP-25 traffics to the plasma membrane by a syntaxin-independent mechanism. (PMID:12114505)
  • Munc18b binds to syntaxins 1A, 2, and 3 and regulates vesicle transport to the apical plasma membrane (PMID:12198139)
  • CFTR channels are coordinately regulated by two cognate t-SNAREs, SNAP-23 (synaptosome-associated protein of 23 kDa) and syntaxin 1A. (PMID:12209004)
  • interacts with CFTR protein differently from interactions with SNARE. (PMID:12446681)
  • Syntaxin/Munc18 interactions in the late events during vesicle fusion and release in exocytosis (PMID:15175344)
  • interacts with dopamine transporter (PMID:15202772)
  • A significant genetic association was found between schizophrenia and an intron 7 single nucleotide polymorphism (SNP) tested. Haplotype analysis supported the association with several significant values that appear to be driven by the intron 7 SNP. (PMID:15219469)
  • cleavage of APP but not syntaxin 1 is independent of cell surface regulation by extracellular ligands (PMID:15316009)
  • Syn-1A binds both NBFs of SUR1 and SUR2A but appears to exhibit distinct interactions with NBF2 of these SUR proteins in modulating the KATP channels in islet beta cells and cardiac myocytes (PMID:15339904)
  • Syntaxin-1A actions on sulfonylurea receptor 2A blocks acidic pH-induced cardiac K(ATP) channel activation (PMID:16672225)
  • Norepinephrine transpossrter/syntaxin 1A complex rapidly redistributes, upon amphetamine treatment, when mechanisms supported by the transporter’s NH2 terminus are eliminated. (PMID:17032905)
  • analysis of the spatially distinct modes of munc18-syntaxin 1 interaction (PMID:17264080)
  • the mechanisms involved in Syn1A-K(v) interactions vary significantly between K(v) channels, thus providing a wide scope for Syn1A modulation of exocytosis and membrane excitability (PMID:17506992)
  • the H(abc) domain has a role in membrane trafficking and targeting of syntaxin 1A (PMID:17543282)
  • A lower frequency of the PRM -352T allele of the STX1A gene in overweight/obese subjects impaires glucose regulation, particularly among individuals with combined glucose intolerance and overt diabetes. (PMID:17912268)
  • We have identified a new three-gene classifier that is independent of and improves on stage to stratify early-stage NSCLC patients with significantly different prognoses. (PMID:18065728)
  • The expression of the SNARE protein SNAP-25 and its cellular homologue SNAP-23, as well as syntaxin1 and VAMP (vesicle-associated membrane protein) in samples of normal parathyroid tissue, chief cell adenoma, and parathyroid carcinoma, was examined. (PMID:18457912)
  • SNARE complex-related genes STX1A, VAMP2 and SNAP25 do not play a major role in susceptibility to schizophrenia in the Japanese population (PMID:18512733)
  • STX1A might influence the serotonergic system during neurodevelopment (PMID:18593506)
  • Direct interaction of otoferlin with syntaxin 1A, SNAP-25, and the L-type voltage-gated calcium channel Cav1.3. (PMID:19004828)
  • Homology with vesicle fusion mediator syntaxin-1a predicts determinants of epimorphin/syntaxin-2 function in mammary epithelial morphogenesis.( (PMID:19129200)
  • This analysis revealed significant differences in both allele frequencies and genotype distributions of the STX1A gene in migraine. (PMID:19368856)
  • We confirmed the involvement of syntaxin 1A in migraine susceptibility regarding rs941298. In addition, we found rs6951030 to also be associated in Portuguese migraine patients. (PMID:20385907)
  • syntaxin 1A, a neuronal regulator of presynaptic vesicle release, may play a role in WS and be a component of the cellular pathway determining human intelligence. (PMID:20422020)
  • This protein has been found differentially expressed in thalami from patients with schizophrenia. (PMID:20471030)
  • Results suggest that variants in RNASEL contribute to susceptibility to early onset and familial forms of prostate cancer. (PMID:20564318)
  • association of STX1A with autism in a trio association study; in the anterior cingulate gyrus region, STX1A expression in the autism group was found to be significantly lower than controls; suggests a possible role of STX1A in pathogenesis of autism (PMID:21118708)
  • ATP regulates pancreatic beta-cell K(ATP) channel activity, not only by its direct actions on Kir6.2 pore subunit, but also via ATP modulation of Syn-1A binding to SUR1. (PMID:21173146)
  • Exocytotic dysfunctions in schizophrenia are probably related to an imbalance of the interaction between munc18-1a and SNARE (mainly syntaxin-1A) complex. (PMID:21669024)
  • Recombinant alpha-SNAP-M105I has greater affinity for the cytosolic portion of immunoprecipitated syntaxin than the wild type protein. (PMID:21789195)
  • Forming an acceptor SNARE complex between syntaxin-1A and SNAP-25 weakens but does not abrogate cholesterol-controlled cluster formation and indicates that the reconstitution process results in equal incorporation of protein at either lipid composition. (PMID:21916482)
  • Syntaxin 1A effects may be additive but can be blocked at different concentration ranges of calmodulin, suggesting selective presynaptic targeting to directly regulate exocytosis. (PMID:21976501)
  • A Ca(v)3.2/syntaxin-1A signaling complex controls T-type channel activity and low-threshold exocytosis. (PMID:22130660)
  • Our results provide support for the hypothesis that STX1A represents a susceptibility gene for migraine (PMID:22250207)
  • DrrA activation of the Rab1 GTPase on plasma membrane-derived organelles stimulated the tethering of endoplasmic reticulum-derived vesicles, resulting in vesicle fusion through the pairing of Sec22b with the plasma membrane syntaxin proteins. (PMID:22264512)
  • A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)
  • Nesca directly binds KIF5B, kinesin light-chain and syntaxin-1 (PMID:22404429)
  • Direct interaction between syntaxin 1A and the Kv2.1 C-terminus is required for efficient insulin exocytosis and glucose-stimulated insulin secretion. (PMID:22411134)
  • The histone modification marks were significantly increased in bipolar disorder and major depression and this effect was correlated with significant increases in Syn1a gene expression. (PMID:22571925)
  • Platelets deficient in Munc18b from a Familial Hemophagocytic Lymphohistiocytosis type 5 had secretion defect. (PMID:22791290)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriostx1aENSDARG00000058994
mus_musculusStx1aENSMUSG00000007207
rattus_norvegicusStx1aENSRNOG00000029165
drosophila_melanogasterSyx1AFBGN0013343
caenorhabditis_elegansWBGENE00006798

Paralogs (12): STX7 (ENSG00000079950), STX1B (ENSG00000099365), STX4 (ENSG00000103496), STX2 (ENSG00000111450), STX12 (ENSG00000117758), STX16 (ENSG00000124222), STX11 (ENSG00000135604), STX17 (ENSG00000136874), STX5 (ENSG00000162236), STX3 (ENSG00000166900), TSNARE1 (ENSG00000171045), STX19 (ENSG00000178750)

Protein

Protein identifiers

Syntaxin-1AQ16623 (reviewed: Q16623)

Alternative names: Neuron-specific antigen HPC-1

All UniProt accessions (4): Q16623, A0A0C4DFZ1, A8MZ54, Q75ME0

UniProt curated annotations — full annotation on UniProt →

Function. Plays an essential role in hormone and neurotransmitter calcium-dependent exocytosis and endocytosis. Part of the SNARE (Soluble NSF Attachment Receptor) complex composed of SNAP25, STX1A and VAMP2 which mediates the fusion of synaptic vesicles with the presynaptic plasma membrane. STX1A and SNAP25 are localized on the plasma membrane while VAMP2 resides in synaptic vesicles. The pairing of the three SNAREs from the N-terminal SNARE motifs to the C-terminal anchors leads to the formation of the SNARE complex, which brings membranes into close proximity and results in final fusion. Participates in the calcium-dependent regulation of acrosomal exocytosis in sperm. Also plays an important role in the exocytosis of hormones such as insulin or glucagon-like peptide 1 (GLP-1).

Subunit / interactions. Part of the SNARE core complex containing SNAP25, VAMP2 and STX1A; this complex constitutes the basic catalytic machinery of the complex neurotransmitter release apparatus. The SNARE complex interacts with CPLX1. Interacts with STXBP1. The interaction with STXBP1 promotes assembly of the SNARE complex. 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. Interacts with SYTL4. Interacts with STXBP6. Interacts with PLCL1 (via C2 domain). Interacts with OTOF. Interacts with LGI3. Interacts (via the H3 domain) with SLC6A4 (via the N-terminus); this interaction regulates SLC4A6 channel conductance in thalamocortical neurons. Interacts with SYT6 and SYT8; the interaction is Ca(2+)-dependent. Interacts with VAMP8. Interacts with SNAP23. Interacts with VAPA and SYBU. Interacts with PRRT2. Interacts with SEPT8. Interacts with STXBP5L. Interacts with synaptotagmin-1/SYT1. Interacts with SEPTIN5; in the cerebellar cortex. Interacts with SEPTIN4; in the striatum.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane. Synapse. Synaptosome. Cell membrane Secreted.

Tissue specificity. Highly expressed in embryonic spinal cord and ganglia and in adult cerebellum and cerebral cortex. Expressed in heart, liver, fat, skeletal muscle, kidney and brain.

Post-translational modifications. Phosphorylated by CK2. Phosphorylation at Ser-188 by DAPK1 significantly decreases its interaction with STXBP1. Sumoylated, sumoylation is required for regulation of synaptic vesicle endocytosis.

Disease relevance. 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.

Miscellaneous. Expression is up-regulated by phorbol 12-myristate 13-acetate (PMA), but not by forskolin.

Similarity. Belongs to the syntaxin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q16623-11yes
Q16623-22, 1C
Q16623-33

RefSeq proteins (2): NP_001159375, NP_004594* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000727T_SNARE_domDomain
IPR006011Syntaxin_NDomain
IPR006012Syntaxin/epimorphin_CSConserved_site
IPR010989SNAREHomologous_superfamily
IPR045242SyntaxinFamily

Pfam: PF00804, PF05739

UniProt features (20 total): modified residue 4, cross-link 3, mutagenesis site 3, topological domain 2, splice variant 2, sequence conflict 2, chain 1, transmembrane region 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16623-F184.940.49

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (7): 252, 253, 256, 14, 64, 95, 188

Mutagenesis-validated functional residues (3):

PositionPhenotype
252complete loss of sumoylation; when associated with r-253 and r-256.
253complete loss of sumoylation; when associated with r-252 and r-256.
256complete loss of sumoylation; when associated with r-252 and r-253.

Function

Pathways and Gene Ontology

Reactome pathways

34 pathways

IDPathway
R-HSA-181429Serotonin Neurotransmitter Release Cycle
R-HSA-181430Norepinephrine Neurotransmitter Release Cycle
R-HSA-210500Glutamate Neurotransmitter Release Cycle
R-HSA-212676Dopamine Neurotransmitter Release Cycle
R-HSA-264642Acetylcholine Neurotransmitter Release Cycle
R-HSA-264876Insulin processing
R-HSA-422356Regulation of insulin secretion
R-HSA-449836Other interleukin signaling
R-HSA-5250971Toxicity of botulinum toxin type C (botC)
R-HSA-5682910LGI-ADAM interactions
R-HSA-6794361Neurexins and neuroligins
R-HSA-888590GABA synthesis, release, reuptake and degradation
R-HSA-9609523Insertion of tail-anchored proteins into the endoplasmic reticulum membrane
R-HSA-9662360Sensory processing of sound by inner hair cells of the cochlea
R-HSA-112310Neurotransmitter release cycle
R-HSA-112315Transmission across Chemical Synapses
R-HSA-112316Neuronal System
R-HSA-1266738Developmental Biology
R-HSA-1280215Cytokine Signaling in Immune system
R-HSA-1430728Metabolism
R-HSA-163685Integration of energy metabolism
R-HSA-1643685Disease
R-HSA-168256Immune System
R-HSA-168799Neurotoxicity of clostridium toxins
R-HSA-2980736Peptide hormone metabolism
R-HSA-392499Metabolism of proteins
R-HSA-449147Signaling by Interleukins
R-HSA-5339562Uptake and actions of bacterial toxins
R-HSA-5663205Infectious disease
R-HSA-6794362Protein-protein interactions at synapses

MSigDB gene sets: 860 (showing top): GGGACCA_MIR133A_MIR133B, TGGTGCT_MIR29A_MIR29B_MIR29C, MODULE_92, BENPORATH_ES_WITH_H3K27ME3, GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_DEPENDENT_EXOCYTOSIS, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_INSULIN_SECRETION, MODULE_563, GOBP_MEMBRANE_FUSION, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_REGULATION_OF_HORMONE_LEVELS

GO Biological Process (28): positive regulation of neurotransmitter secretion (GO:0001956), intracellular protein transport (GO:0006886), exocytosis (GO:0006887), vesicle fusion (GO:0006906), response to gravity (GO:0009629), positive regulation of norepinephrine secretion (GO:0010701), regulation of synaptic vesicle priming (GO:0010807), synaptic vesicle exocytosis (GO:0016079), obsolete synaptic vesicle docking (GO:0016081), protein sumoylation (GO:0016925), calcium-ion regulated exocytosis (GO:0017156), insulin secretion (GO:0030073), secretion by cell (GO:0032940), positive regulation of catecholamine secretion (GO:0033605), SNARE complex assembly (GO:0035493), positive regulation of calcium ion-dependent exocytosis (GO:0045956), obsolete vesicle docking (GO:0048278), synaptic vesicle endocytosis (GO:0048488), regulation of insulin secretion (GO:0050796), protein localization to membrane (GO:0072657), positive regulation of excitatory postsynaptic potential (GO:2000463), neurotransmitter transport (GO:0006836), vesicle-mediated transport (GO:0016192), regulation of exocytosis (GO:0017157), regulated exocytosis (GO:0045055), positive regulation of exocytosis (GO:0045921), hormone secretion (GO:0046879), modulation of excitatory postsynaptic potential (GO:0098815)

GO Molecular Function (14): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), calcium channel inhibitor activity (GO:0019855), chloride channel inhibitor activity (GO:0019869), kinase binding (GO:0019900), myosin head/neck binding (GO:0032028), identical protein binding (GO:0042802), ATP-dependent protein binding (GO:0043008), transmembrane transporter binding (GO:0044325), protein-containing complex binding (GO:0044877), calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515), myosin binding (GO:0017022), protein-macromolecule adaptor activity (GO:0030674)

GO Cellular Component (25): extracellular region (GO:0005576), cytosol (GO:0005829), plasma membrane (GO:0005886), voltage-gated potassium channel complex (GO:0008076), endomembrane system (GO:0012505), secretory granule (GO:0030141), axon (GO:0030424), synaptic vesicle membrane (GO:0030672), SNARE complex (GO:0031201), nuclear membrane (GO:0031965), actomyosin (GO:0042641), neuron projection (GO:0043005), presynaptic active zone membrane (GO:0048787), synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032), synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033), synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044), Schaffer collateral - CA1 synapse (GO:0098685), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), synaptic vesicle (GO:0008021), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), protein-containing complex (GO:0032991), presynaptic membrane (GO:0042734), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-12 pathways:

CategoryPathways
Neurotransmitter release cycle6
Peptide hormone metabolism1
Integration of energy metabolism1
Signaling by Interleukins1
Neurotoxicity of clostridium toxins1
Developmental Biology1
Protein-protein interactions at synapses1
Protein localization1
Sensory processing of sound1
Transmission across Chemical Synapses1
Neuronal System1
Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding6
cellular anatomical structure4
SNARE complex3
neurotransmitter secretion2
positive regulation of secretion by cell2
intracellular protein localization2
vesicle-mediated transport2
regulated exocytosis2
presynapse2
ion channel inhibitor activity2
binding2
cytoplasm2
synapse2
regulation of neurotransmitter secretion1
positive regulation of synaptic transmission1
positive regulation of neurotransmitter transport1
protein transport1
intracellular transport1
secretion by cell1
vesicle fusion to plasma membrane1
vesicle organization1
organelle membrane fusion1
response to abiotic stimulus1
regulation of norepinephrine secretion1
positive regulation of catecholamine secretion1
norepinephrine secretion1
synaptic vesicle priming1
regulation of protein-containing complex assembly1
establishment of localization in cell1
vesicle-mediated transport in synapse1
synaptic vesicle cycle1
signal release from synapse1
peptidyl-lysine modification1
protein modification by small protein conjugation1
protein secretion1
peptide hormone secretion1
secretion1
export from cell1
catecholamine secretion1
regulation of catecholamine secretion1

Protein interactions and networks

STRING

2265 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STX1ASNAP25P13795999
STX1AVAMP2P19065999
STX1ASTXBP1P61764998
STX1ASYT1P21579986
STX1ASNAP23O00161971
STX1AKCNB1Q14721962
STX1AST8SIA2Q92186940
STX1ASTXBP5Q5T5C0938
STX1AVAMP1P23763935
STX1ACPLX1O14810934
STX1AKCNA1Q09470904
STX1ACACNA1BQ00975898
STX1ASLC6A2P23975888
STX1ANAPAP54920888
STX1AVAMP3Q15836871

IntAct

386 interactions, top by confidence:

ABTypeScore
SNAP25VAMP2psi-mi:“MI:0914”(association)0.760
VAMP2SNAP25psi-mi:“MI:0914”(association)0.760
SNAP25VAMP2psi-mi:“MI:0915”(physical association)0.760
STX1ANAPBpsi-mi:“MI:0915”(physical association)0.670
STX1ASTX1Apsi-mi:“MI:0915”(physical association)0.670
STX1ATXLNApsi-mi:“MI:0915”(physical association)0.670
VAMP2SNCApsi-mi:“MI:0914”(association)0.630
SNAP23STX1Apsi-mi:“MI:0915”(physical association)0.550
SNAP29STX1Apsi-mi:“MI:0915”(physical association)0.550
STX1ASNAP23psi-mi:“MI:0915”(physical association)0.550
STX1ASNAP29psi-mi:“MI:0915”(physical association)0.550
SNAP25SNCApsi-mi:“MI:0914”(association)0.500
SNCASNAP25psi-mi:“MI:0914”(association)0.500
SNAP25SNCApsi-mi:“MI:0915”(physical association)0.500
SNAP25STX1Apsi-mi:“MI:0915”(physical association)0.500
SNCASTX1Apsi-mi:“MI:0915”(physical association)0.500
DPP8STX1Apsi-mi:“MI:0915”(physical association)0.400
STX1APSMA3psi-mi:“MI:0915”(physical association)0.370
STX1ASUMO1P1psi-mi:“MI:0915”(physical association)0.370
STX1ATXLNBpsi-mi:“MI:0915”(physical association)0.370
STX1AStxbp1psi-mi:“MI:2364”(proximity)0.270
DISC1STX1Apsi-mi:“MI:0915”(physical association)0.000
STXBP1STX1Apsi-mi:“MI:0915”(physical association)0.000
MALSTX1Apsi-mi:“MI:0915”(physical association)0.000
TSNARE1STX1Apsi-mi:“MI:0915”(physical association)0.000
SMIM1STX1Apsi-mi:“MI:0915”(physical association)0.000
UPK1BSTX1Apsi-mi:“MI:0915”(physical association)0.000
STX1Apsi-mi:“MI:0915”(physical association)0.000
TMEM128STX1Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (272): STXBP1 (Reconstituted Complex), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Two-hybrid), STX1A (Two-hybrid), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS), STX1A (Affinity Capture-MS)

ESM2 similar proteins: A8WVD0, O15400, O16000, O35526, O70257, O70439, P32850, P32851, P32856, P32867, P39926, P50279, P61264, P61265, P61266, P61267, P61268, P70452, Q00262, Q08849, Q08850, Q0VCI2, Q12846, Q13277, Q16623, Q16932, Q20024, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q59YF0, Q5R4L2, Q5R602, Q5TX47, Q64704, Q7XIE2, Q8N4C7, Q8R1Q0, Q8VZU2

Diamond homologs: A8WVD0, O16000, O35526, O75558, P32850, P32851, P32854, P32856, P50279, P61264, P61265, P61266, P61267, P61268, P70452, P91409, Q00262, Q08849, Q08850, Q12846, Q13277, Q16623, Q16932, Q20797, Q24547, Q3SWZ3, Q5R4L2, Q5TX47, Q64704, Q6F3B4, Q8R1Q0, Q9D3G5, G3V7P1, O14662, O15400, O64791, O65359, O70257, O70439, O94651

SIGNOR signaling

8 interactions.

AEffectBMechanism
CSNK2A1up-regulatesSTX1Aphosphorylation
DAPK1“down-regulates activity”STX1Aphosphorylation
STX1A“form complex”SNARE_complexbinding
CADPS“up-regulates activity”STX1Abinding
CADPS2“up-regulates activity”STX1Abinding
SYBU“up-regulates activity”STX1Arelocalization
CSNK2A2unknownSTX1Aphosphorylation
STXBP1“up-regulates activity”STX1Abinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 122 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Other interleukin signaling536.0×1e-05
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane536.0×1e-05
Intra-Golgi traffic623.6×1e-05
Retrograde transport at the Trans-Golgi-Network620.0×2e-05
COPII-mediated vesicle transport614.8×1e-04
Intra-Golgi and retrograde Golgi-to-ER traffic812.7×1e-05
ER-Phagosome pathway611.8×4e-04
ER to Golgi Anterograde Transport510.1×3e-03

GO biological processes:

GO termPartnersFoldFDR
obsolete vesicle docking1286.7×5e-19
vesicle fusion1479.5×2e-21
synaptic vesicle priming645.4×3e-07
membrane fusion741.2×3e-08
exocytosis1115.8×1e-08
long-term synaptic potentiation513.2×3e-03
cellular response to type II interferon611.8×1e-03
retrograde transport, endosome to Golgi611.6×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

53 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic5
Uncertain significance22
Likely benign15
Benign1

Top pathogenic / likely-pathogenic (7)

Variant IDHGVSClassification
1679128NM_004603.4(STX1A):c.284-1G>APathogenic
814991GRCh37/hg19 7q11.23(chr7:72996564-73597315)x1Pathogenic
1679129NM_004603.4(STX1A):c.554C>G (p.Ser185Cys)Likely pathogenic
1679130NM_004603.4(STX1A):c.668_670del (p.Val223del)Likely pathogenic
1679131NM_004603.4(STX1A):c.677A>G (p.Gln226Arg)Likely pathogenic
1679132NM_004603.4(STX1A):c.722_724del (p.Val241del)Likely pathogenic
984555NM_004603.4(STX1A):c.435C>G (p.Cys145Trp)Likely pathogenic

SpliceAI

2099 predictions. Top by Δscore:

VariantEffectΔscore
7:73700927:TGAGG:Tacceptor_gain1.0000
7:73700928:GAGG:Gacceptor_gain1.0000
7:73700930:GG:Gacceptor_gain1.0000
7:73700932:C:CCacceptor_gain1.0000
7:73702840:CTCA:Cdonor_loss1.0000
7:73702841:TCA:Tdonor_loss1.0000
7:73702842:CA:Cdonor_loss1.0000
7:73702843:A:ACdonor_gain1.0000
7:73702844:C:CCdonor_gain1.0000
7:73702844:C:CGdonor_loss1.0000
7:73702844:CCTGG:Cdonor_gain1.0000
7:73702982:TCT:Tacceptor_loss1.0000
7:73702983:C:CCacceptor_gain1.0000
7:73702983:CTGG:Cacceptor_loss1.0000
7:73702984:T:Gacceptor_loss1.0000
7:73703750:CTCA:Cdonor_loss1.0000
7:73703751:TCA:Tdonor_loss1.0000
7:73703752:CA:Cdonor_loss1.0000
7:73703753:A:ACdonor_gain1.0000
7:73703753:A:AGdonor_loss1.0000
7:73703753:AC:Adonor_gain1.0000
7:73703753:ACC:Adonor_gain1.0000
7:73703754:C:CAdonor_loss1.0000
7:73703754:C:CCdonor_gain1.0000
7:73703754:CC:Cdonor_gain1.0000
7:73703754:CCC:Cdonor_gain1.0000
7:73703825:CCGG:Cacceptor_gain1.0000
7:73703826:CGG:Cacceptor_gain1.0000
7:73703826:CGGC:Cacceptor_gain1.0000
7:73703829:C:CCacceptor_gain1.0000

AlphaMissense

1942 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:73700780:C:GA247P1.000
7:73700801:C:GA240P1.000
7:73702875:G:CF216L1.000
7:73702875:G:TF216L1.000
7:73702877:A:GF216L1.000
7:73702888:A:GL212P1.000
7:73702909:A:GL205P1.000
7:73704156:A:GL153P1.000
7:73704189:C:GR142P1.000
7:73704246:A:GL123P1.000
7:73700758:G:TA254D0.999
7:73700759:C:GA254P0.999
7:73700779:G:TA247D0.999
7:73700821:A:TI233N0.999
7:73700840:C:GG227R0.999
7:73700840:C:TG227R0.999
7:73702858:A:GL222P0.999
7:73702865:C:GA220P0.999
7:73702876:A:CF216C0.999
7:73702876:A:GF216S0.999
7:73702930:C:GR198P0.999
7:73703764:A:CF177L0.999
7:73703764:A:TF177L0.999
7:73703765:A:CF177C0.999
7:73703765:A:GF177S0.999
7:73703766:A:GF177L0.999
7:73703789:A:GL169P0.999
7:73703801:A:GL165P0.999
7:73704161:C:AR151S0.999
7:73704161:C:GR151S0.999

dbSNP variants (sampled 300 via entrez): RS1000259461 (7:73706967 G>C), RS1000307837 (7:73707159 G>A,C), RS1000468722 (7:73701729 C>T), RS1000821349 (7:73701399 G>A), RS1001769417 (7:73714882 C>T), RS1001821782 (7:73715495 C>T), RS1002100064 (7:73716827 G>C,T), RS1002155583 (7:73717099 G>A), RS1002263780 (7:73709752 G>A,C), RS1002378824 (7:73704117 G>A,C,T), RS1002422872 (7:73704480 C>A,T), RS1002706055 (7:73705476 C>T), RS1002741640 (7:73699673 G>A), RS1002758471 (7:73705717 A>C), RS1003836745 (7:73718600 C>A,T)

Disease associations

OMIM: gene MIM:186590 | disease phenotypes: MIM:209850

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorderStrongAutosomal dominant
complex neurodevelopmental disorderModerateAutosomal dominant
cystic fibrosisSupportiveAutosomal recessive

Mondo (5): intellectual disability (MONDO:0001071), autism (MONDO:0005260), cystic fibrosis (MONDO:0009061), neurodevelopmental disorder (MONDO:0700092), complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

212 total (30 of 212 shown, HPO-id order):

HPOTerm
HP:0000010Recurrent urinary tract infections
HP:0000014Abnormality of the bladder
HP:0000015Bladder diverticulum
HP:0000023Inguinal hernia
HP:0000025Functional abnormality of male internal genitalia
HP:0000028Cryptorchidism
HP:0000044Hypogonadotropic hypogonadism
HP:0000075Renal duplication
HP:0000076Vesicoureteral reflux
HP:0000083Renal insufficiency
HP:0000089Renal hypoplasia
HP:0000093Proteinuria
HP:0000121Nephrocalcinosis
HP:0000125Pelvic kidney
HP:0000147Polycystic ovaries
HP:0000154Wide mouth
HP:0000158Macroglossia
HP:0000179Thick lower lip vermilion
HP:0000212Gingival overgrowth
HP:0000232Everted lower lip vermilion
HP:0000246Sinusitis
HP:0000252Microcephaly
HP:0000275Narrow face
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000307Pointed chin
HP:0000337Broad forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead

GWAS associations

5 associations (top):

StudyTraitp-value
GCST010244_44Triglyceride levels8.000000e-45
GCST010725_13Malaria8.000000e-06
GCST010725_74Malaria6.000000e-06
GCST010725_91Malaria7.000000e-06
GCST90020028_167Hip circumference adjusted for BMI2.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (4)

DescriptorNameTree numbers
D001321Autistic DisorderF03.625.164.113.500
D003550Cystic FibrosisC06.689.202; C08.381.187; C16.320.190; C16.614.213
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

53 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, decreases methylation2
sodium arsenitedecreases expression, increases expression2
(+)-JQ1 compoundincreases expression, affects cotreatment, decreases expression2
Arsenicincreases expression, affects methylation, increases abundance2
Estradiolaffects expression, increases expression2
Cyclosporineincreases expression2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Iincreases expression1
alpha-pineneincreases expression, increases abundance, affects cotreatment1
methylselenic acidaffects expression1
sodium arsenateincreases abundance, increases expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
tamibarotenedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
cylindrospermopsinincreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001decreases expression1
abrineincreases expression1
mirdametinibaffects cotreatment, decreases expression1
jinfukangincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Troglitazoneincreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1

Clinical trials (associated diseases)

600 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00157690PHASE4COMPLETEDStudy of Alendronate to Prevent and Treat Osteoporosis in Cystic Fibrosis Patients
NCT00208078PHASE4TERMINATEDEffect of Non-Invasive Ventilation in Cystic Fibrosis Patient With Chronic Respiratory Failure.
NCT00244270PHASE4COMPLETEDCystic Fibrosis and Totally Implantable Vascular Access Devices
NCT00333385PHASE4TERMINATEDContinuous Versus Short Infusions of Ceftazidime in Cystic Fibrosis
NCT00411736PHASE4COMPLETEDScandinavian Cystic Fibrosis Azithromycin Study
NCT00418470PHASE4TERMINATEDProlonging the Duration of Peripheral Venous Catheters in Cystic Fibrosis People
NCT00431964PHASE4COMPLETEDEffect of Azithromycin on Lung Function in 6-18 Year-olds With Cystic Fibrosis (CF) Not Infected With P. Aeruginosa
NCT00434278PHASE4TERMINATEDA Trial of Pulmozyme Withdrawal on Exercise Tolerance in Cystic Fibrosis Subjects With Severe Lung Disease (TOPIC)
NCT00483769PHASE4COMPLETEDOne Year Glargine Treatment in CFRD Children and Adolescents
NCT00528190PHASE4COMPLETEDTreatment of Aspergillus Fumigatus (a Fungal Infection) in Patients With Cystic Fibrosis
NCT00557089PHASE4COMPLETEDThe Effect of rhDNase on Ventilation Inhomogeneity in Patients With Cystic Fibrosis
NCT00572975PHASE4COMPLETEDMalabsorption Blood Test:Toward a Novel Approach to Quantify Steatorrhea
NCT00680316PHASE4TERMINATEDA Study of Pulmozyme® (Dornase Alpha) in 3- to 5-Year-Old Patients With Cystic Fibrosis
NCT00685035PHASE4COMPLETEDComparison of Airway Clearance Therapy in Cystic Fibrosis Using the Same VEST Therapy Device But With Different Settings
NCT00744250PHASE4TERMINATEDIntraduodenal Aspiration Study to Assess the Bioavailability of Oral Pancrecarb® Compared to Placebo Control
NCT00787917PHASE4TERMINATEDAn Exploratory Study to Assess Multiple Doses of Omalizumab in Patients With Cystic Fibrosis Complicated by Acute Bronchopulmonary Aspergillosis (ABPA)
NCT00843817PHASE4COMPLETEDRhDNase and Biodistribution of PMN Serine Proteases in Cystic Fibrosis Sputum
NCT00890370PHASE4COMPLETEDShould Any One Airway Clearance Technique be Recommended for People With Cystic Fibrosis?
NCT00996424PHASE4TERMINATEDThe Effect of Inhaled N-Acetylcysteine Compared to Normal Saline on Sputum Rheology and Lung Function
NCT01044719PHASE4UNKNOWNDuration of Antibiotics in Infective Exacerbations of Cystic Fibrosis
NCT01100606PHASE4COMPLETEDA Study to Evaluate the Mode of Administration and Safety of EUR-1008 (APT-1008) in Infants 1 to 12 Months of Age
NCT01131507PHASE4COMPLETEDPR-018: An Open-Label, Safety Extension of Study PR-011
NCT01207245PHASE4COMPLETEDCircadian Rhythm In Tobramycin Elimination In Cystic Fibrosis
NCT01323101PHASE4COMPLETEDDoxycycline Effects on Inflammation in Cystic Fibrosis
NCT01327703PHASE4COMPLETEDControl of Steatorrhea in Participants With Cystic Fibrosis and Exocrine Pancreatic Insufficiency
NCT01377792PHASE4COMPLETEDStudy of Long-term Treatment With Hypertonic Saline in Patients With Cystic Fibrosis
NCT01400750PHASE4COMPLETEDComparison of 2 Treatment Regimens for Eradication of P Aeruginosa Infection in Children With Cystic Fibrosis
NCT01429259PHASE4COMPLETEDPopulation Pharmacokinetics of Prolonged Infusion Meropenem in Cystic Fibrosis (CF) Children
NCT01608555PHASE4COMPLETEDTobramycin 300 mg Once-a-day (o.d.) Aerosol in Adults With Cystic Fibrosis
NCT01667094PHASE4UNKNOWNA Study Comparing Continuous Infusion Antibiotics to Standard Treatment for Lung Infections in Cystic Fibrosis
NCT01694069PHASE4TERMINATEDContinuous Infusion Piperacillin-tazobactam for the Treatment of Cystic Fibrosis
NCT01702415PHASE4WITHDRAWNZoledronic Acid in Cystic Fibrosis
NCT01712334PHASE4COMPLETEDA Study of the Comparable Efficacy and Safety of Pulmozyme (Dornase Alfa) Delivered by the eRapid Nebulizer System in Patients With Cystic Fibrosis
NCT01737983PHASE4COMPLETEDEffect of Lactobacillus Reuteri in Cystic Fibrosis
NCT01844778PHASE4COMPLETEDEase of Use and Microbial Contamination of Tobramycin Inhalation Powder (TIP) Versus Nebulised Tobramycin Inhalation Solution (TIS) and Nebulised Colistimethate (COLI)
NCT01880346PHASE4COMPLETEDComparison of Absorption of Vitamin D in Cystic Fibrosis
NCT01882400PHASE4COMPLETEDAssessment of Response to Treatment of Osteoporosis With Oral Bisphosphonates in Patients With Muscular Dystrophy
NCT01937325PHASE4UNKNOWNCPET in CF Patients With One G551D Mutation Taking VX770
NCT02015663PHASE4TERMINATEDTobramycin Inhalation Powder (TIP) Administered Once Daily Continuously Versus TIP Administered BID in 28 Day on / 28 Day Off Cycles
NCT02048592PHASE4UNKNOWNImpact of Immunonutrition on the Patients With Cystic Fibrosis