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SH3BP4 SH3 domain binding protein 4 [ Homo sapiens (human) ]

Gene ID: 23677, updated on 3-Nov-2024

Summary

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Official Symbol
SH3BP4provided by HGNC
Official Full Name
SH3 domain binding protein 4provided by HGNC
Primary source
HGNC:HGNC:10826
See related
Ensembl:ENSG00000130147 MIM:605611; AllianceGenome:HGNC:10826
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TTP; BOG25
Summary
This gene encodes a protein with 3 Asn-Pro-Phe (NPF) motifs, an SH3 domain, a PXXP motif, a bipartite nuclear targeting signal, and a tyrosine phosphorylation site. This protein is involved in cargo-specific control of clathrin-mediated endocytosis, specifically controlling the internalization of a specific protein receptor. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in salivary gland (RPKM 12.0), gall bladder (RPKM 8.4) and 24 other tissues See more
Orthologs
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Genomic context

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See SH3BP4 in Genome Data Viewer
Location:
2q37.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (234952017..235055714)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (235441072..235544683)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (235860661..235964358)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373937 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235810653-235811216 Neighboring gene uncharacterized LOC105373938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235840873-235841418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235843604-235844104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:235861114-235861763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235873459-235874021 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235882781-235883348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235883349-235883916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235883917-235884484 Neighboring gene uncharacterized LOC105373939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235885570-235886122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235888982-235889719 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:235892104-235892818 and GRCh37_chr2:235892819-235893532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235899889-235900660 Neighboring gene Sharpr-MPRA regulatory region 6611 Neighboring gene Sharpr-MPRA regulatory region 6657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235907423-235908052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235908168-235908844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235911298-235912136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235913425-235914014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235914015-235914602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235914603-235915192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235916550-235917186 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235920146-235920722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235920723-235921298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235921299-235921875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235939804-235940432 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:235952107-235952608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235960919-235961880 Neighboring gene Sharpr-MPRA regulatory region 15714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235970623-235971123 Neighboring gene Sharpr-MPRA regulatory region 6954 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:235991995-235993194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235996100-235996600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236022675-236023222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236035311-236035906 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:236045748-236045962 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236066308-236066890 Neighboring gene CEP19 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:236080141-236080327 Neighboring gene uncharacterized LOC124907998

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. Cloning, chromosomal localization, and characterization of cDNA from a novel gene, SH3BP4, expressed by human corneal fibroblasts. Dunlevy JR, et al. Genomics, 1999 Dec 15. PMID 10644451
  2. Nuclear and plasma membrane localization of SH3BP4 in retinal pigment epithelial cells. Khanobdee K, et al. Mol Vis, 2004 Dec 13. PMID 15616480
  3. MC159 of Molluscum Contagiosum Virus Suppresses Autophagy by Recruiting Cellular SH3BP4 via an SH3 Domain-Mediated Interaction. Schmotz C, et al. J Virol, 2019 May 15. PMID 30842330, Free PMC Article
  4. SH3BP4, a novel pigmentation gene, is inversely regulated by miR-125b and MITF. Kim KH, et al. Exp Mol Med, 2017 Aug 18. PMID 28819321, Free PMC Article
  5. MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma. Wilkins OM, et al. Cancer Epidemiol Biomarkers Prev, 2019 Jan. PMID 29880533, Free PMC Article

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SH3BP4 promotes neuropilin-1 and alpha5-integrin endocytosis and is inhibited by Akt.
    Title: SH3BP4 promotes neuropilin-1 and α5-integrin endocytosis and is inhibited by Akt.
  2. The data uncover the tumor-suppressive role of SH3BP4 that functions as a negative feedback regulator of Wnt signaling through modulating beta-catenin's subcellular localization.
    Title: SH3BP4 Regulates Intestinal Stem Cells and Tumorigenesis by Modulating β-Catenin Nuclear Localization.
  3. A SNP in the 3'UTR of SH3BP4 (rs56161233) that overlaps predicted miR-100-binding sites and is predicted to disrupt several miRNA-mRNA interactions was associated with overall survival of laryngeal cancer.
    Title: MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma.
  4. SH3BP4 has been identified as a novel pigmentation gene. The SH3BP4 is a direct target of miR-125b. The SH3BP4 is transcriptionally regulated by MITF as its direct target.
    Title: SH3BP4, a novel pigmentation gene, is inversely regulated by miR-125b and MITF.
  5. SH3BP4 is a negative regulator of the Rag GTPase complex and amino acid-dependent mTORC1 signaling.
    Title: SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. Results show that TTP (SH3BP4), a SH3-containing protein, specifically regulates the internalization of the transferrin receptor (TfR).
    Title: TTP specifically regulates the internalization of the transferrin receptor.
Submit: New GeneRIF Correction

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
Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
EBI GWAS Catalog
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
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 SH3BP4, 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GDP-dissociation inhibitor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
NOT involved_in amino acid import IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to amino acid stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to lysosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of catalytic activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in clathrin-coated pit IEA
Inferred from Electronic Annotation
more info
  
located_in clathrin-coated vesicle IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
SH3 domain-binding protein 4
Names
EH-binding protein 10
transferrin receptor-trafficking 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.

Genomic

  1. NG_033930.1 RefSeqGene

    Range
    5034..108731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001371302.1 → NP_001358231.1  SH3 domain-binding protein 4

    Status: REVIEWED

    Source sequence(s)
    AC010148, AC114814
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

  2. NM_001371303.1 → NP_001358232.1  SH3 domain-binding protein 4

    Status: REVIEWED

    Source sequence(s)
    AC010148, AC114814
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

  3. NM_001371304.1 → NP_001358233.1  SH3 domain-binding protein 4

    Status: REVIEWED

    Source sequence(s)
    AC010148, AC114814
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Related
    ENSP00000340237.4, ENST00000344528.8
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

  4. NM_001371305.1 → NP_001358234.1  SH3 domain-binding protein 4

    Status: REVIEWED

    Source sequence(s)
    AC010148, AC114814
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

  5. NM_001371306.1 → NP_001358235.1  SH3 domain-binding protein 4

    Status: REVIEWED

    Source sequence(s)
    AC010148, AC114814
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

  6. NM_014521.3 → NP_055336.1  SH3 domain-binding protein 4

    See identical proteins and their annotated locations for NP_055336.1

    Status: REVIEWED

    Source sequence(s)
    AF147747, BC057396
    Consensus CDS
    CCDS2513.1
    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Related
    ENSP00000375867.2, ENST00000392011.7
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    234952017..235055714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443849.1 → XP_047299805.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  2. XM_047443850.1 → XP_047299806.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    Related
    ENSP00000386862.1, ENST00000409212.5

  3. XM_047443851.1 → XP_047299807.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  4. XM_047443848.1 → XP_047299804.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  5. XM_011510893.2 → XP_011509195.1  SH3 domain-binding protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011509195.1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
    UniProtKB/TrEMBL
    A8K594
    Conserved Domains (3) summary
    cd11757
    Location:59 → 110
    SH3_SH3BP4; Src Homology 3 domain of SH3 domain-binding protein 4
    pfam07653
    Location:658 → 722
    SH3_2; Variant SH3 domain
    cl02517
    Location:324 → 404
    ZU5; ZU5 domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    235441072..235544683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341233.1 → XP_054197208.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  2. XM_054341234.1 → XP_054197209.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  3. XM_054341236.1 → XP_054197211.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  4. XM_054341232.1 → XP_054197207.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3

  5. XM_054341235.1 → XP_054197210.1  SH3 domain-binding protein 4 isoform X1

    UniProtKB/Swiss-Prot
    O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P0V3.1 GenPept UniProtKB/Swiss-Prot:Q9P0V3

Gene LinkOut

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