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

    Gene ID: 23677, updated on 10-Dec-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
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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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    NEW Try the new Transcript table

    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
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594
      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
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594

    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
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594

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

      UniProtKB/Swiss-Prot
      O95082, Q309A3, Q53QD0, Q53TD1, Q9P0V3
      UniProtKB/TrEMBL
      A8K594
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P0V3.1 GenPept UniProtKB/Swiss-Prot:Q9P0V3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools