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

Gene ID: 6452, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2793085..2841096)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2791852..2839552)
105.20220307 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. SH3BP2-related fibro-osseous disorders of the maxilla and mandible: A systematic review. Kueper J, et al. Int J Oral Maxillofac Surg, 2022 Jan. PMID 33941395
  3. Clinicopathologic and Molecular Characteristics of Familial Cherubism with Associated Odontogenic Tumorous Proliferations. Argyris PP, et al. Head Neck Pathol, 2018 Mar. PMID 28721660, Free PMC Article
  4. 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. Sekerci AE, et al. Med Oral Patol Oral Cir Bucal, 2014 Jul 1. PMID 24608212, Free PMC Article
  5. A novel c.1255G>T (p.D419Y) mutation in SH3BP2 gene causes cherubism in a Turkish family. Dinckan N, et al. Oral Surg Oral Med Oral Pathol Oral Radiol, 2012 Nov. PMID 23083484

See all (70) 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)

Genotypes

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 IBA
Inferred from Biological aspect of Ancestor
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
    ENSP00000348685.5, ENST00000356331.9
    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_2023_10

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

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