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

Summary

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

Location:: 6q24.3

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (147204417..147390473)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (148397706..148583768)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (147525553..147711609)

Chromosome 6 - NC_000006.12 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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed

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

RH66550 (e-PCR)
- UniSTS:34306

STXBP5_1310 (e-PCR)
- UniSTS:277778

SGC32886 (e-PCR)
- UniSTS:17941

RH98677 (e-PCR)
- UniSTS:86571

STS-H95256 (e-PCR)
- UniSTS:51558

D6S1205E (e-PCR)
- UniSTS:23162

RH119481 (e-PCR)
- UniSTS:133521

SHGC-57989 (e-PCR)
- UniSTS:27287

RH118645 (e-PCR)
- UniSTS:138137

G35014 (e-PCR)
- UniSTS:80537

RH98706 (e-PCR)
- UniSTS:93084

SHGC-36574 (e-PCR)
- UniSTS:61108

RH119689 (e-PCR)
- UniSTS:133058

Homology

Homologs of the STXBP5 gene: The STXBP5 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, and frog.
Orthologs from Annotation Pipeline: 342 organisms have orthologs with human gene STXBP5
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables myosin II binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables syntaxin-1 binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in exocytosis	IEA Inferred from Electronic Annotation 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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in regulation of exocytosis	TAS Traceable Author Statement more info	PubMed
involved_in regulation of protein secretion	IBA Inferred from Biological aspect of Ancestor 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	PubMed
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	PubMed
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	PubMed
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)

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

Q5T5C0, Q96NG9

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

Status: VALIDATED

Source sequence(s)

AL355365, AL356415, AL590709

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 ...
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/Swiss-Prot

Q5T5C0

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 ...