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STXBP4 syntaxin binding protein 4 [ Homo sapiens (human) ]

Gene ID: 252983, updated on 2-Nov-2024

Summary

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Official Symbol
STXBP4provided by HGNC
Official Full Name
syntaxin binding protein 4provided by HGNC
Primary source
HGNC:HGNC:19694
See related
Ensembl:ENSG00000166263 MIM:610415; AllianceGenome:HGNC:19694
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
Synip
Summary
Enables syntaxin binding activity. Involved in several processes, including positive regulation of cell cycle G1/S phase transition; positive regulation of keratinocyte proliferation; and protein stabilization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in kidney (RPKM 1.4), thyroid (RPKM 1.4) and 25 other tissues See more
Orthologs
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Genomic context

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See STXBP4 in Genome Data Viewer
Location:
17q22
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (54968765..55213273)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (55843691..56088281)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (53046126..53250993)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12406 Neighboring gene uncharacterized LOC124904032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12407 Neighboring gene target of myb1 like 1 membrane trafficking protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:53045085-53046034 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:53046035-53046983 Neighboring gene cytochrome c oxidase copper chaperone COX11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12412 Neighboring gene MPRA-validated peak2901 silencer Neighboring gene uncharacterized LOC107985002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8731 Neighboring gene VISTA enhancer hs2291 Neighboring gene Sharpr-MPRA regulatory regions 2486 and 1497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:53398039-53398539 Neighboring gene Sharpr-MPRA regulatory region 10605 Neighboring gene HLF transcription factor, PAR bZIP family member Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8733 Neighboring gene monocyte to macrophage differentiation associated

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. Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs). Darabi H, et al. Sci Rep, 2016 Sep 7. PMID 27600471, Free PMC Article
  2. Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 17,960 cases and 22,713 controls. Tang L, et al. Arch Med Res, 2012 Jul. PMID 22863968
  3. Germline allelic expression of genes at 17q22 locus associates with risk of breast cancer. Esteves F, et al. Eur J Cancer, 2022 Sep. PMID 35772352
  4. Akt2 phosphorylates Synip to regulate docking and fusion of GLUT4-containing vesicles. Yamada E, et al. J Cell Biol, 2005 Mar 14. PMID 15753124, Free PMC Article
  5. Computational Analysis of Breast Cancer GWAS Loci Identifies the Putative Deleterious Effect of STXBP4 and ZNF404 Gene Variants. Masoodi TA, et al. J Cell Biochem, 2017 Dec. PMID 28422318

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Germline allelic expression of genes at 17q22 locus associates with risk of breast cancer.
    Title: Germline allelic expression of genes at 17q22 locus associates with risk of breast cancer.
  2. Distinctive roles of syntaxin binding protein 4 and its action target, TP63, in lung squamous cell carcinoma: a theranostic study for the precision medicine.
    Title: Distinctive roles of syntaxin binding protein 4 and its action target, TP63, in lung squamous cell carcinoma: a theranostic study for the precision medicine.
  3. Long noncoding RNA LINC00511 involves in breast cancer recurrence and radioresistance by regulating STXBP4 expression via miR-185.
    Title: Long noncoding RNA LINC00511 involves in breast cancer recurrence and radioresistance by regulating STXBP4 expression via miR-185.
  4. Low STXBP4 expression is associated with kidney cancer.
    Title: Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor.
  5. High STXBP4 expression is associated with squamous cell carcinogenesis.
    Title: STXBP4 regulates APC/C-mediated p63 turnover and drives squamous cell carcinogenesis.
  6. The deleterious SNPs localized in STXBP4 and ZNF404 genes were identified which might play a role in breast cancer development by dysregulating its gene expression.
    Title: Computational Analysis of Breast Cancer GWAS Loci Identifies the Putative Deleterious Effect of STXBP4 and ZNF404 Gene Variants.
  7. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus.
    Title: Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs).
  8. Whole transcriptome sequencing followed by pathway analysis indicated that STXBP4 is involved in functional gene networks that regulate cell growth, proliferation, cell death, and survival in cancer. Platelet-derived growth factor receptor alpha (PDGFRalpha) was a key downstream mediator of STXBP4 function. In line with this, shRNA mediated STXBP4 and PDGFRA knockdown suppressed tumor growth in soft-agar and xenograft ...
    Title: STXBP4 Drives Tumor Growth and Is Associated with Poor Prognosis through PDGF Receptor Signaling in Lung Squamous Cell Carcinoma.
  9. meta-analysis suggested that polymorphism STXBP4/COX11 rs6504950 variant was significantly associated with breast cancer risk; the A allele of rs6504950 decreased the risk of breast cancer
    Title: Association of STXBP4/COX11 rs6504950 (G>A) polymorphism with breast cancer risk: evidence from 17,960 cases and 22,713 controls.
  10. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies STXBP4, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ16496, MGC50337, MGC149829

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables syntaxin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to type II interferon IEA
Inferred from Electronic Annotation
more info
  
involved_in insulin receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell cycle G1/S phase transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein targeting IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of D-glucose transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in phagocytic vesicle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
syntaxin-binding protein 4
Names
STX4-interacting protein
syntaxin 4 interacting protein

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_001398481.1 → NP_001385410.1  syntaxin-binding protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC005177, AC007485
    Conserved Domains (3) summary
    COG1196
    Location:298 → 463
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd00992
    Location:22 → 100
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00397
    Location:500 → 529
    WW; WW domain

  2. NM_001398482.1 → NP_001385411.1  syntaxin-binding protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC007485
    Consensus CDS
    CCDS92360.1
    UniProtKB/TrEMBL
    B5MCT9
    Related
    ENSP00000385944.1, ENST00000405898.5
    Conserved Domains (1) summary
    cd00992
    Location:22 → 98
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  3. NM_001398483.1 → NP_001385412.1  syntaxin-binding protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC007485
    Conserved Domains (2) summary
    COG1196
    Location:296 → 461
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd00992
    Location:22 → 98
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  4. NM_178509.6 → NP_848604.3  syntaxin-binding protein 4 isoform 1

    See identical proteins and their annotated locations for NP_848604.3

    Status: VALIDATED

    Source sequence(s)
    AC005177, AK122865, AK123793, BC041485, CA848494
    Consensus CDS
    CCDS11584.2
    UniProtKB/Swiss-Prot
    Q6ZWJ1, Q8IVZ5
    UniProtKB/TrEMBL
    E7EPP7
    Related
    ENSP00000365530.2, ENST00000376352.6
    Conserved Domains (4) summary
    cd00992
    Location:22 → 98
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam00397
    Location:498 → 527
    WW; WW domain
    pfam06050
    Location:304 → 411
    HGD-D; 2-hydroxyglutaryl-CoA dehydratase, D-component
    pfam08467
    Location:189 → 341
    Luteo_P1-P2; Luteovirus RNA polymerase P1-P2/replicase

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    54968765..55213273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435714.1 → XP_047291670.1  syntaxin-binding protein 4 isoform X4

  2. XM_017024410.2 → XP_016879899.1  syntaxin-binding protein 4 isoform X1

    UniProtKB/TrEMBL
    E7EPP7

  3. XM_017024411.3 → XP_016879900.1  syntaxin-binding protein 4 isoform X2

    UniProtKB/TrEMBL
    E7EPP7

  4. XM_047435716.1 → XP_047291672.1  syntaxin-binding protein 4 isoform X6

  5. XM_047435715.1 → XP_047291671.1  syntaxin-binding protein 4 isoform X5

  6. XM_047435717.1 → XP_047291673.1  syntaxin-binding protein 4 isoform X7

  7. XM_047435713.1 → XP_047291669.1  syntaxin-binding protein 4 isoform X3

  8. XM_017024414.3 → XP_016879903.1  syntaxin-binding protein 4 isoform X9

  9. XM_006721797.5 → XP_006721860.1  syntaxin-binding protein 4 isoform X10

    Conserved Domains (1) summary
    cd00992
    Location:22 → 100
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  10. XM_017024413.2 → XP_016879902.1  syntaxin-binding protein 4 isoform X8

    UniProtKB/TrEMBL
    E7EPP7

RNA

  1. XR_007065289.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    55843691..56088281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315640.1 → XP_054171615.1  syntaxin-binding protein 4 isoform X4

  2. XM_054315637.1 → XP_054171612.1  syntaxin-binding protein 4 isoform X1

  3. XM_054315638.1 → XP_054171613.1  syntaxin-binding protein 4 isoform X2

  4. XM_054315641.1 → XP_054171616.1  syntaxin-binding protein 4 isoform X6

  5. XM_054315639.1 → XP_054171614.1  syntaxin-binding protein 4 isoform X3

  6. XM_054315643.1 → XP_054171618.1  syntaxin-binding protein 4 isoform X10

  7. XM_054315642.1 → XP_054171617.1  syntaxin-binding protein 4 isoform X8

RNA

  1. XR_008484801.1 RNA Sequence

  2. XR_008484802.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZWJ1.2 GenPept UniProtKB/Swiss-Prot:Q6ZWJ1

Gene LinkOut

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