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    SH3BP2 SH3 domain binding protein 2 [ Homo sapiens (human) ]

    Gene ID: 6452, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SH3BP2provided by HGNC
    Official Full Name
    SH3 domain binding protein 2provided by HGNC
    Primary source
    HGNC:HGNC:10825
    See related
    Ensembl:ENSG00000087266 MIM:602104; AllianceGenome:HGNC:10825
    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
    3BP2; CRBM; CRPM; 3BP-2; RES4-23
    Summary
    The protein encoded by this gene has an N-terminal pleckstrin homology (PH) domain, an SH3-binding proline-rich region, and a C-terminal SH2 domain. The protein binds to the SH3 domains of several proteins including the ABL1 and SYK protein tyrosine kinases , and functions as a cytoplasmic adaptor protein to positively regulate transcriptional activity in T, natural killer (NK), and basophilic cells. Mutations in this gene result in cherubism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
    Expression
    Ubiquitous expression in spleen (RPKM 16.5), skin (RPKM 14.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SH3BP2 in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2793085..2841096)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2791852..2839552)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2794812..2842823)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2746569-2747069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15180 Neighboring gene TNFAIP3 interacting protein 2 Neighboring gene uncharacterized LOC102723763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2763311-2764135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2764939-2765507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2788339-2788973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2789609-2790243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21189 Neighboring gene nonconserved acetylation island sequence 125 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2821815-2822316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2827676-2828562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2828563-2829448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2838931-2839928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21194 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:2844343-2844854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21197 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2863877-2864589 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:2864590-2865301 Neighboring gene adducin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2876343-2876870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2876871-2877396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21198 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2923771-2924668 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2924669-2925564 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2925565-2926460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2927877-2928392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2935265-2936132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15193 Neighboring gene major facilitator superfamily domain containing 10

    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
    • 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. [Cherubism in three siblings]. Jákob N, et al. Orv Hetil, 2022 Mar 13. PMID 35279646
    2. A missense mutation in the SH3BP2 gene on chromosome 4p16.3 found in a case of nonfamilial cherubism. Imai Y, et al. Cleft Palate Craniofac J, 2003 Nov. PMID 14577811
    3. Novel mutation in the gene encoding c-Abl-binding protein SH3BP2 causes cherubism. Lo B, et al. Am J Med Genet A, 2003 Aug 15. PMID 12900899
    4. DNA analysis of the SH3BP2 gene in patients with aggressive central giant cell granuloma. de Lange J, et al. Br J Oral Maxillofac Surg, 2007 Sep. PMID 16713042
    5. The adapter 3BP2: how it plugs into leukocyte signaling. Deckert M, et al. Adv Exp Med Biol, 2006. PMID 16802602

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Scaffold protein SH3BP2 signalosome is pivotal for immune activation in nephrotic syndrome.
      Title: Scaffold protein SH3BP2 signalosome is pivotal for immune activation in nephrotic syndrome.
    2. Cherubism in three siblings.", trans "A cherubismus elofordulasa harom testverben.
      Title: [Cherubism in three siblings].
    3. SH3BP2-related fibro-osseous disorders of the maxilla and mandible: A systematic review.
      Title: SH3BP2-related fibro-osseous disorders of the maxilla and mandible: A systematic review.
    4. The current study shows that SH3BP2 is expressed in primary tumors and cell lines from Gastrointestinal stromal tumors (GISTs) patients and that SH3BP2 silencing leads to a downregulation of oncogenic KIT and PDGFRA expression and an increase in apoptosis in imatinib-sensitive and imatinib-resistant GIST cells.
      Title: Silencing of adaptor protein SH3BP2 reduces KIT/PDGFRA receptors expression and impairs gastrointestinal stromal tumors growth.
    5. All members featured a heterozygous missense c.1244G>C; p.Arg415Pro SH3BP2 mutation
      Title: Clinicopathologic and Molecular Characteristics of Familial Cherubism with Associated Odontogenic Tumorous Proliferations.
    6. The adaptor 3BP2 is required for KIT receptor expression and human mast cell survival.
      Title: The adaptor 3BP2 is required for KIT receptor expression and human mast cell survival.
    7. A c.1244G>A (p.Arg415Gln) mutation in SH3BP2 gene causes cherubism in a Turkish family
      Title: A c.1244G>A (p.Arg415Gln) mutation in SH3BP2 gene causes cherubism in a Turkish family: report of a family with review of the literature.
    8. Authors conclude that a novel p.Asp419Tyr alteration in SH3BP2 to be a cherubism-causing mutation in a Turkish family.
      Title: A novel c.1255G>T (p.D419Y) mutation in SH3BP2 gene causes cherubism in a Turkish family.
    9. In the first family, a missense mutation Arg415Gln was found in exon 9 of SH3BP2 in all affected individuals. The unaffected individuals did not have the mutation. In the second family, a missense mutation Pro418Thr was identified in exon 9 of the SH3BP2
      Title: Mutations of the SH3BP2 gene in 2 families of cherubism.
    10. These results demonstrate that PARP1 regulates expression of SH3BP2.
      Title: Cloning and characterization of the human SH3BP2 promoter.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    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

    Associated conditions

    Description Tests
    Fibrous dysplasia of jaw
    MedGen: C0008029 OMIM: 118400 GeneReviews: Cherubism
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • FLJ42079, FLJ54978

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH3 domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphotyrosine residue binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    SH3 domain-binding protein 2
    Names
    Abl-SH3 binding protein 2
    TNFAIP3 interacting protein 2
    epididymis secretory sperm binding 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_011609.1 RefSeqGene

      Range
      5063..53074
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1334

    mRNA and Protein(s)

    1. NM_001122681.2 → NP_001116153.1  SH3 domain-binding protein 2 isoform a

      See identical proteins and their annotated locations for NP_001116153.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of an alternative promoter and 5' UTR and uses a downstream translation start site, compared to variant 3. The resulting isoform (a) has a shorter N-terminus, compared to isoform b. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK225497, AK312286, AL121750
      Consensus CDS
      CCDS33944.1
      UniProtKB/Swiss-Prot
      A6NNC2, B2R5R6, B4DT04, D3DVR0, D6R919, O00500, O15373, P78314, P78315
      UniProtKB/TrEMBL
      A0A384N6E5
      Related
      ENSP00000422168.3, ENST00000503393.8
      Conserved Domains (3) summary
      cd10359
      Location:456 → 556
      SH2_SH3BP2; Src homology 2 domain found in c-Abl SH3 domain-binding protein-2 (SH3BP2)
      cd13308
      Location:19 → 133
      PH_3BP2; SH3 domain-binding protein 2 Pleckstrin homology (PH) domain
      cl25751
      Location:254 → 482
      DUF4045; Domain of unknown function (DUF4045)

    2. NM_001145855.2 → NP_001139327.1  SH3 domain-binding protein 2 isoform c

      See identical proteins and their annotated locations for NP_001139327.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents use of an alternative promoter and 5' UTR and uses an alternate translation start site, compared to variant 3. The resulting isoform (c) has a shorter and distinct N-terminus, compared to isoform b.
      Source sequence(s)
      AK299996, AK312286, AL121750, DC391267
      Consensus CDS
      CCDS54715.1
      UniProtKB/Swiss-Prot
      P78314
      Related
      ENSP00000403231.3, ENST00000435136.8
      Conserved Domains (3) summary
      cd10359
      Location:484 → 584
      SH2_SH3BP2; Src homology 2 domain found in c-Abl SH3 domain-binding protein-2 (SH3BP2)
      cd13308
      Location:47 → 161
      PH_3BP2; SH3 domain-binding protein 2 Pleckstrin homology (PH) domain
      pfam00169
      Location:55 → 157
      PH; PH domain

    3. NM_001145856.2 → NP_001139328.1  SH3 domain-binding protein 2 isoform b

      See identical proteins and their annotated locations for NP_001139328.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (b).
      Source sequence(s)
      AK225497, AL121750, U56386
      Consensus CDS
      CCDS54716.1
      UniProtKB/Swiss-Prot
      P78314
      Related
      ENSP00000424846.2, ENST00000511747.6
      Conserved Domains (3) summary
      PTZ00449
      Location:311 → 539
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd10359
      Location:513 → 613
      SH2_SH3BP2; Src homology 2 domain found in c-Abl SH3 domain-binding protein-2 (SH3BP2)
      cd13308
      Location:76 → 190
      PH_3BP2; SH3 domain-binding protein 2 Pleckstrin homology (PH) domain

    4. NM_003023.4 → NP_003014.3  SH3 domain-binding protein 2 isoform a

      See identical proteins and their annotated locations for NP_003014.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents use of an alternative promoter and 5' UTR and uses a downstream translation start site, compared to variant 3. The resulting isoform (a) has a shorter N-terminus, compared to isoform b. Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AB000462, AK312286, AL121750
      Consensus CDS
      CCDS33944.1
      UniProtKB/Swiss-Prot
      A6NNC2, B2R5R6, B4DT04, D3DVR0, D6R919, O00500, O15373, P78314, P78315
      UniProtKB/TrEMBL
      A0A384N6E5
      Related
      ENST00000356331.10
      Conserved Domains (3) summary
      cd10359
      Location:456 → 556
      SH2_SH3BP2; Src homology 2 domain found in c-Abl SH3 domain-binding protein-2 (SH3BP2)
      cd13308
      Location:19 → 133
      PH_3BP2; SH3 domain-binding protein 2 Pleckstrin homology (PH) domain
      cl25751
      Location:254 → 482
      DUF4045; Domain of unknown function (DUF4045)

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      2793085..2841096
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      2791852..2839552
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78314.2 GenPept UniProtKB/Swiss-Prot:P78314

    Gene LinkOut

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

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