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    STXBP5 syntaxin binding protein 5 [ Homo sapiens (human) ]

    Gene ID: 134957, updated on 3-Nov-2024

    Summary

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    Official Symbol
    STXBP5provided by HGNC
    Official Full Name
    syntaxin binding protein 5provided by HGNC
    Primary source
    HGNC:HGNC:19665
    See related
    Ensembl:ENSG00000164506 MIM:604586; AllianceGenome:HGNC:19665
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LGL3; LLGL3; Nbla04300
    Summary
    Syntaxin 1 is a component of the 7S and 20S SNARE complexes which are involved in docking and fusion of synaptic vesicles with the presynaptic plasma membrane. This gene encodes a syntaxin 1 binding protein. In rat, a similar protein dissociates syntaxin 1 from the Munc18/n-Sec1/rbSec1 complex to form a 10S complex, an intermediate which can be converted to the 7S SNARE complex. Thus this protein is thought to be involved in neurotransmitter release by stimulating SNARE complex formation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 8.9), testis (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STXBP5 in Genome Data Viewer
    Location:
    6q24.3
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (147204417..147390473)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (148397706..148583768)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (147525553..147711609)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene STXBP5 antisense RNA 1 Neighboring gene uncharacterized LOC124901422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17649 Neighboring gene lung adenocarcinoma associated transcript 1 Neighboring gene MPRA-validated peak6197 silencer Neighboring gene MPRA-validated peak6199 silencer Neighboring gene MPRA-validated peak6200 silencer Neighboring gene uncharacterized LOC124901421 Neighboring gene uncharacterized LOC105378043 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:147759841-147760442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:147760443-147761044 Neighboring gene YAP1 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. Genetic Variation in the Syntaxin-Binding Protein STXBP5 in Type 1 von Willebrand Disease Patients. Lind-Halldén C, et al. Thromb Haemost, 2018 Aug. PMID 29972863
    2. Tomosyn functions as a PKCδ-regulated fusion clamp in mast cell degranulation. Madera-Salcedo IK, et al. Sci Signal, 2018 Jul 3. PMID 29970602
    3. Genetic evidence for an inhibitory role of tomosyn in insulin-stimulated GLUT4 exocytosis. Wang S, et al. Traffic, 2020 Oct. PMID 32851733, Free PMC Article
    4. Platelet secretion and hemostasis require syntaxin-binding protein STXBP5. Ye S, et al. J Clin Invest, 2014 Oct. PMID 25244094, Free PMC Article
    5. Genetic variation associated with plasma von Willebrand factor levels and the risk of incident venous thrombosis. Smith NL, et al. Blood, 2011 Jun 2. PMID 21163921, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Aberrant hypermethylation induced downregulation of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 correlate with tumorigenesis of glioma.
      Title: Aberrant hypermethylation induced downregulation of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 correlate with tumorigenesis of glioma.
    2. Genetic evidence for an inhibitory role of tomosyn in insulin-stimulated GLUT4 exocytosis.
      Title: Genetic evidence for an inhibitory role of tomosyn in insulin-stimulated GLUT4 exocytosis.
    3. Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells.
      Title: Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells.
    4. STXBP5-AS1 might function as a ceRNA to drive CC cells proliferation and invasion via regulating miR-96-5p/PTEN axis.
      Title: LncRNA STXBP5-AS1 suppressed cervical cancer progression via targeting miR-96-5p/PTEN axis.
    5. Findings identified tomosyn-1 as an inhibitor of mast cell degranulation that required PKCdelta to switch its interaction with STX partners during fusion.
      Title: Tomosyn functions as a PKCδ-regulated fusion clamp in mast cell degranulation.
    6. A haplotype containing the STXBP5 Asn436Ser (rs1039084) mutation is associated with type 1 von Willebrand disease in a Swedish population.
      Title: Genetic Variation in the Syntaxin-Binding Protein STXBP5 in Type 1 von Willebrand Disease Patients.
    7. Assisted by NSF/alpha-SNAP, syntaxin-1 escapes tomosyn arrest and assembles into the Munc18-1/syntaxin-1 complex. Munc13-1 then catalyzes the transit of syntaxin-1 from the Munc18-1/syntaxin-1 complex to the SNARE complex
      Title: Tomosyn guides SNARE complex formation in coordination with Munc18 and Munc13.
    8. Glucose-dependent de-SUMOylation of tomosyn1 at K298 releases syntaxin1A and controls the amplification of exocytosis in concert with a recently-identified tomosyn1-interacting partner; the Ca(2+)-binding protein secretagogin, which dissociates from tomosyn1 in response to Ca(2+)-raising stimuli and is required for insulin granule trafficking and exocytosis downstream of Ca(2+) influx.
      Title: SUMOylation and calcium control syntaxin-1A and secretagogin sequestration by tomosyn to regulate insulin exocytosis in human ß cells.
    9. Using CRISPR/Cas9 genome editing, identified a human nonsynonymous SNP rs1039084 in the STXBP5 locus as a causal variant for a decreased thrombotic phenotype.
      Title: Novel Thrombotic Function of a Human SNP in STXBP5 Revealed by CRISPR/Cas9 Gene Editing in Mice.
    10. Genetic variations in STXBP5 and CLEC4M are associated with VWF level variation in type 1, but not in type 2 von Willebrand disease.
      Title: CLEC4M and STXBP5 gene variations contribute to von Willebrand factor level variation in von Willebrand disease.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
    EBI GWAS Catalog
    Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.
    EBI GWAS Catalog
    Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2.
    EBI GWAS Catalog
    Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30922, MGC141942, MGC141968

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin II binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin-1 binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of exocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of synaptic vesicle exocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synaptic vesicle priming IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of acetylcholine-gated channel complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extrinsic component of neuronal dense core vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    syntaxin-binding protein 5
    Names
    lethal(2) giant larvae protein homolog 3
    putative protein product of Nbla04300
    tomosyn
    tomosyn-1

    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.

    mRNA and Protein(s)

    1. NM_001127715.4 → NP_001121187.1  syntaxin-binding protein 5 isoform b

      See identical proteins and their annotated locations for NP_001121187.1

      Status: VALIDATED

      Source sequence(s)
      AL355365, AL356415, AL590709
      Consensus CDS
      CCDS47499.1
      UniProtKB/Swiss-Prot
      Q14DF3, Q5T5C0, Q5T5C1, Q5T5C2, Q8NBG8, Q96NG9
      UniProtKB/TrEMBL
      Q14DD4
      Related
      ENSP00000321826.6, ENST00000321680.11
      Conserved Domains (5) summary
      COG2319
      Location:236 → 538
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1084 → 1144
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:61 → 94
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:276 → 383
      LLGL; LLGL2
      cl25539
      Location:61 → 279
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. NM_001394409.1 → NP_001381338.1  syntaxin-binding protein 5 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL355365, AL356415, AL590709
      UniProtKB/TrEMBL
      H0Y332, Q14DD4
      Related
      ENSP00000356445.3, ENST00000367475.7
      Conserved Domains (5) summary
      COG2319
      Location:236 → 538
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1068 → 1128
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:61 → 94
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:275 → 383
      LLGL; LLGL2
      cl29593
      Location:61 → 279
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. NM_139244.6 → NP_640337.3  syntaxin-binding protein 5 isoform a

      See identical proteins and their annotated locations for NP_640337.3

      Status: VALIDATED

      Source sequence(s)
      AL355365, AL356415, AL590709
      Consensus CDS
      CCDS5211.1
      UniProtKB/TrEMBL
      Q14DD4
      Related
      ENSP00000356451.3, ENST00000367481.7
      Conserved Domains (5) summary
      COG2319
      Location:236 → 538
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1048 → 1108
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:61 → 94
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:276 → 383
      LLGL; LLGL2
      cl25539
      Location:61 → 279
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      147204417..147390473
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418197.1 → XP_047274153.1  syntaxin-binding protein 5 isoform X1

    2. XM_047418198.1 → XP_047274154.1  syntaxin-binding protein 5 isoform X2

    3. XM_047418199.1 → XP_047274155.1  syntaxin-binding protein 5 isoform X3

    4. XM_047418202.1 → XP_047274158.1  syntaxin-binding protein 5 isoform X6

    5. XM_047418204.1 → XP_047274160.1  syntaxin-binding protein 5 isoform X8

    6. XM_047418203.1 → XP_047274159.1  syntaxin-binding protein 5 isoform X7

      UniProtKB/TrEMBL
      A0A9L9PXY2
      Related
      ENSP00000516592.1, ENST00000706851.1

    7. XM_047418205.1 → XP_047274161.1  syntaxin-binding protein 5 isoform X10

    8. XM_017010268.3 → XP_016865757.1  syntaxin-binding protein 5 isoform X9

    9. XM_047418200.1 → XP_047274156.1  syntaxin-binding protein 5 isoform X4

    10. XM_047418201.1 → XP_047274157.1  syntaxin-binding protein 5 isoform X5

    RNA

    1. XR_007059202.1 RNA Sequence

    2. XR_007059201.1 RNA Sequence

    3. XR_007059203.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      148397706..148583768
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354260.1 → XP_054210235.1  syntaxin-binding protein 5 isoform X1

    2. XM_054354261.1 → XP_054210236.1  syntaxin-binding protein 5 isoform X2

    3. XM_054354262.1 → XP_054210237.1  syntaxin-binding protein 5 isoform X3

    4. XM_054354265.1 → XP_054210240.1  syntaxin-binding protein 5 isoform X6

    5. XM_054354267.1 → XP_054210242.1  syntaxin-binding protein 5 isoform X8

    6. XM_054354266.1 → XP_054210241.1  syntaxin-binding protein 5 isoform X7

      UniProtKB/TrEMBL
      A0A9L9PXY2

    7. XM_054354269.1 → XP_054210244.1  syntaxin-binding protein 5 isoform X10

    8. XM_054354268.1 → XP_054210243.1  syntaxin-binding protein 5 isoform X9

    9. XM_054354263.1 → XP_054210238.1  syntaxin-binding protein 5 isoform X4

    10. XM_054354264.1 → XP_054210239.1  syntaxin-binding protein 5 isoform X5

    RNA

    1. XR_008487255.1 RNA Sequence

    2. XR_008487254.1 RNA Sequence

    3. XR_008487256.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T5C0.1 GenPept UniProtKB/Swiss-Prot:Q5T5C0

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