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

Summary

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, Apr 2022]
Expression: Ubiquitous expression in kidney (RPKM 1.4), thyroid (RPKM 1.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q22

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (54968765..55213273)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (55843691..56088281)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (53046126..53250993)

Chromosome 17 - NC_000017.11 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?

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.
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.
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.
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.
High STXBP4 expression is associated with squamous cell carcinogenesis.
Title: STXBP4 regulates APC/C-mediated p63 turnover and drives squamous cell carcinogenesis.
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.
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).
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.
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.
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 EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. 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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 glucose transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasmic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	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)

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
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) ...
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) ...
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

54968765..55213273

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047435714.1 → XP_047291670.1 syntaxin-binding protein 4 isoform X4
XM_017024410.2 → XP_016879899.1 syntaxin-binding protein 4 isoform X1

UniProtKB/TrEMBL

E7EPP7
XM_017024411.3 → XP_016879900.1 syntaxin-binding protein 4 isoform X2

UniProtKB/TrEMBL

E7EPP7
XM_047435716.1 → XP_047291672.1 syntaxin-binding protein 4 isoform X6
XM_047435715.1 → XP_047291671.1 syntaxin-binding protein 4 isoform X5
XM_047435717.1 → XP_047291673.1 syntaxin-binding protein 4 isoform X7
XM_047435713.1 → XP_047291669.1 syntaxin-binding protein 4 isoform X3
XM_017024414.3 → XP_016879903.1 syntaxin-binding protein 4 isoform X9
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) ...
XM_017024413.2 → XP_016879902.1 syntaxin-binding protein 4 isoform X8

UniProtKB/TrEMBL

E7EPP7