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Aliases for SH3BP4 Gene

Aliases for SH3BP4 Gene

  • SH3 Domain Binding Protein 4 2 3 5
  • Transferrin Receptor-Trafficking Protein 3 4
  • EH-Binding Protein 10 3 4
  • BOG25 3 4
  • TTP 3 4
  • SH3 Domain-Binding Protein 4 3
  • EHB10 4

External Ids for SH3BP4 Gene

Previous GeneCards Identifiers for SH3BP4 Gene

  • GC02P233898
  • GC02P234542
  • GC02P235876
  • GC02P236147
  • GC02P235642
  • GC02P235525
  • GC02P227701

Summaries for SH3BP4 Gene

Entrez Gene Summary for SH3BP4 Gene

  • 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]

GeneCards Summary for SH3BP4 Gene

SH3BP4 (SH3 Domain Binding Protein 4) is a Protein Coding gene. Diseases associated with SH3BP4 include Cataract 8, Multiple Types. Among its related pathways are PI3K / Akt Signaling. Gene Ontology (GO) annotations related to this gene include identical protein binding and GDP-dissociation inhibitor activity. An important paralog of this gene is MACC1.

UniProtKB/Swiss-Prot for SH3BP4 Gene

  • May function in transferrin receptor internalization at the plasma membrane through a cargo-specific control of clathrin-mediated endocytosis. Alternatively, may act as a negative regulator of the amino acid-induced TOR signaling by inhibiting the formation of active Rag GTPase complexes. Preferentially binds inactive Rag GTPase complexes and prevents their interaction with the mTORC1 complex inhibiting its relocalization to lysosomes and its activation. Thereby, may indirectly regulate cell growth, proliferation and autophagy.

Gene Wiki entry for SH3BP4 Gene

Additional gene information for SH3BP4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SH3BP4 Gene

Genomics for SH3BP4 Gene

GeneHancer (GH) Regulatory Elements for SH3BP4 Gene

Promoters and enhancers for SH3BP4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I234948 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 554.2 +1.8 1833 10.2 FOXA2 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF48 ZNF335 GLIS2 FOS SH3BP4 GC02M234968 LOC105373938
GH02I234288 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 5.4 -659.4 -659414 7.9 FOXA2 MLX SIN3A FEZF1 ZNF2 IRF4 YY1 ZNF143 ATF7 FOS ARL4C SH3BP4 LOC105373933 ENSG00000261298
GH02I234994 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 4 +44.1 44071 3.9 ELF3 FOXA2 ARID4B RAD21 THRB ZNF48 ZSCAN9 RARA HSF1 ZNF143 GC02P234996 SH3BP4 GC02M234987
GH02I234630 Enhancer 1.1 FANTOM5 Ensembl ENCODE 4.4 -319.3 -319291 4.3 NCOA3 PKNOX1 CLOCK FOXA2 NEUROD1 BACH1 CTBP1 ARID3A GATA3 FOS LOC105373936 SH3BP4 ARL4C
GH02I234968 Enhancer 1.4 Ensembl ENCODE dbSUPER 0.4 +18.2 18185 3.3 HDGF PKNOX1 YBX1 FEZF1 GLI4 ZNF2 ATF7 FOS TSHZ1 ZNF488 GC02M234968 LOC105373939 SH3BP4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SH3BP4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SH3BP4 gene promoter:

Genomic Locations for SH3BP4 Gene

Genomic Locations for SH3BP4 Gene
chr2:234,951,973-235,055,714
(GRCh38/hg38)
Size:
103,742 bases
Orientation:
Plus strand
chr2:235,860,617-235,964,358
(GRCh37/hg19)

Genomic View for SH3BP4 Gene

Genes around SH3BP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SH3BP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SH3BP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SH3BP4 Gene

Proteins for SH3BP4 Gene

  • Protein details for SH3BP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P0V3-SH3B4_HUMAN
    Recommended name:
    SH3 domain-binding protein 4
    Protein Accession:
    Q9P0V3
    Secondary Accessions:
    • O95082
    • Q309A3
    • Q53QD0
    • Q53TD1

    Protein attributes for SH3BP4 Gene

    Size:
    963 amino acids
    Molecular mass:
    107496 Da
    Quaternary structure:
    • Homodimer or homooligomer. Interacts with DNM2, EPS15, clathrin, the adapter protein complex 2/AP-2 and TFRC. Interacts with the Rag GTPases RRAGA, RRAGB, RRAGC and RRAGD; the interaction is most probably direct, preferentially occurs with their inactive GDP-bound form and is negatively regulated by amino acids.
    Miscellaneous:
    • Overexpression or depletion of SH3BP4 result in a specific decrease of the transferrin receptor endocytosis that can be rescued by DNM2 overexpression.

    Alternative splice isoforms for SH3BP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SH3BP4 Gene

Post-translational modifications for SH3BP4 Gene

  • Phosphorylated upon EGF stimulation. Phosphorylation prevents interaction with DNM2.
  • Ubiquitination at isoforms=657

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SH3BP4 (SH3BP4)
  • Abcam antibodies for SH3BP4
  • Santa Cruz Biotechnology (SCBT) Antibodies for SH3BP4

No data available for DME Specific Peptides for SH3BP4 Gene

Domains & Families for SH3BP4 Gene

Gene Families for SH3BP4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SH3BP4 Gene

Graphical View of Domain Structure for InterPro Entry

Q9P0V3

UniProtKB/Swiss-Prot:

SH3B4_HUMAN :
  • The SH3 domain mediates localization to the clathrin-coated pits and vesicles. The SH3 domain mediates interaction with DNM2 and the cytoplasmic part of TFRC with a lower affinity. The SH3 domain also mediates interaction with RRAGB, RRAGC and is required for the negative regulation of mTORC1.
Domain:
  • The SH3 domain mediates localization to the clathrin-coated pits and vesicles. The SH3 domain mediates interaction with DNM2 and the cytoplasmic part of TFRC with a lower affinity. The SH3 domain also mediates interaction with RRAGB, RRAGC and is required for the negative regulation of mTORC1.
genes like me logo Genes that share domains with SH3BP4: view

Function for SH3BP4 Gene

Molecular function for SH3BP4 Gene

GENATLAS Biochemistry:
SMC homology domain 3 (SH3) binding protein 4,expressed by corneal fibroblast and other tissues with higher levels in pancreas,placenta,heart,kidney,localized in the nucleus,may be involved in a newly cascade of proteins involved in endocytosis,intracellular sorting and the cell cycle
UniProtKB/Swiss-Prot Function:
May function in transferrin receptor internalization at the plasma membrane through a cargo-specific control of clathrin-mediated endocytosis. Alternatively, may act as a negative regulator of the amino acid-induced TOR signaling by inhibiting the formation of active Rag GTPase complexes. Preferentially binds inactive Rag GTPase complexes and prevents their interaction with the mTORC1 complex inhibiting its relocalization to lysosomes and its activation. Thereby, may indirectly regulate cell growth, proliferation and autophagy.

Phenotypes From GWAS Catalog for SH3BP4 Gene

Gene Ontology (GO) - Molecular Function for SH3BP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005092 GDP-dissociation inhibitor activity IMP 22575674
GO:0005515 protein binding IPI 16325581
GO:0017016 Ras GTPase binding IEA,IPI 22575674
GO:0042802 identical protein binding IPI 16325581
genes like me logo Genes that share ontologies with SH3BP4: view
genes like me logo Genes that share phenotypes with SH3BP4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SH3BP4 Gene

Localization for SH3BP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SH3BP4 Gene

Membrane, clathrin-coated pit. Cytoplasmic vesicle, clathrin-coated vesicle. Nucleus. Note=Specifically associated with transferrin receptor-containing clathrin-coated pits and clathrin-coated vesicles. May also localize to the nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SH3BP4 gene
Compartment Confidence
extracellular 5
nucleus 4
cytosol 3

Gene Ontology (GO) - Cellular Components for SH3BP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IDA 22575674
GO:0005905 clathrin-coated pit IEA --
GO:0016020 membrane IEA --
GO:0030136 clathrin-coated vesicle IEA --
genes like me logo Genes that share ontologies with SH3BP4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SH3BP4 Gene

Pathways & Interactions for SH3BP4 Gene

SuperPathways for SH3BP4 Gene

SuperPathway Contained pathways
1 PI3K / Akt Signaling
genes like me logo Genes that share pathways with SH3BP4: view

Pathways by source for SH3BP4 Gene

1 Cell Signaling Technology pathway for SH3BP4 Gene

SIGNOR curated interactions for SH3BP4 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for SH3BP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0008285 negative regulation of cell proliferation IMP 22575674
GO:0010508 positive regulation of autophagy IMP 22575674
GO:0030308 negative regulation of cell growth IMP 22575674
GO:0032007 negative regulation of TOR signaling IMP,IEA 22575674
genes like me logo Genes that share ontologies with SH3BP4: view

Drugs & Compounds for SH3BP4 Gene

No Compound Related Data Available

Transcripts for SH3BP4 Gene

Unigene Clusters for SH3BP4 Gene

SH3-domain binding protein 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SH3BP4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c · 9d ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c
SP1: - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: - - - -
SP5: -
SP6:
SP7: - - - - - - - -
SP8:
SP9: -
SP10:

Relevant External Links for SH3BP4 Gene

GeneLoc Exon Structure for
SH3BP4
ECgene alternative splicing isoforms for
SH3BP4

Expression for SH3BP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SH3BP4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SH3BP4 Gene

This gene is overexpressed in Minor Salivary Gland (x4.3).

Protein differential expression in normal tissues from HIPED for SH3BP4 Gene

This gene is overexpressed in Plasma (23.8), Lung (8.6), Placenta (8.2), and Pancreas (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SH3BP4 Gene



NURSA nuclear receptor signaling pathways regulating expression of SH3BP4 Gene:

SH3BP4

SOURCE GeneReport for Unigene cluster for SH3BP4 Gene:

Hs.516777

mRNA Expression by UniProt/SwissProt for SH3BP4 Gene:

Q9P0V3-SH3B4_HUMAN
Tissue specificity: Expressed in all tissues tested with higher expression in pancreas. Expressed by retinal pigment epithelial cells (at protein level).

Evidence on tissue expression from TISSUES for SH3BP4 Gene

  • Liver(4.3)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with SH3BP4: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SH3BP4 Gene

Orthologs for SH3BP4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SH3BP4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SH3BP4 33 34
  • 99.27 (n)
dog
(Canis familiaris)
Mammalia SH3BP4 33 34
  • 87.84 (n)
cow
(Bos Taurus)
Mammalia SH3BP4 33 34
  • 87.26 (n)
oppossum
(Monodelphis domestica)
Mammalia SH3BP4 34
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SH3BP4 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sh3bp4 33
  • 86.26 (n)
mouse
(Mus musculus)
Mammalia Sh3bp4 33 16 34
  • 85.92 (n)
chicken
(Gallus gallus)
Aves SH3BP4 33 34
  • 77.71 (n)
lizard
(Anolis carolinensis)
Reptilia SH3BP4 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sh3bp4 33
  • 68.86 (n)
Str.458 33
zebrafish
(Danio rerio)
Actinopterygii sh3bp4a 33 34
  • 67.92 (n)
sh3bp4 34
  • 66 (a)
OneToMany
Dr.17077 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7319 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1683 34
  • 26 (a)
OneToMany
Species where no ortholog for SH3BP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SH3BP4 Gene

ENSEMBL:
Gene Tree for SH3BP4 (if available)
TreeFam:
Gene Tree for SH3BP4 (if available)

Paralogs for SH3BP4 Gene

Paralogs for SH3BP4 Gene

(2) SIMAP similar genes for SH3BP4 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for SH3BP4 Gene

genes like me logo Genes that share paralogs with SH3BP4: view

Variants for SH3BP4 Gene

Sequence variations from dbSNP and Humsavar for SH3BP4 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000006154 -- 234,990,634(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000024534 -- 235,038,662(+) A/C intron_variant
rs1000028771 -- 235,002,698(+) C/G intron_variant
rs1000137896 -- 234,987,032(+) AAA/AA genic_upstream_transcript_variant, intron_variant
rs1000140993 -- 235,033,315(+) C/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SH3BP4 Gene

Variant ID Type Subtype PubMed ID
nsv214423 CNV deletion 16902084
nsv3220 CNV insertion 18451855
nsv460140 CNV loss 19166990
nsv476127 CNV novel sequence insertion 20440878
nsv527654 CNV gain 19592680
nsv584719 CNV loss 21841781
nsv999839 CNV gain 25217958
nsv1151814 CNV deletion 26484159
nsv1151042 CNV insertion 26484159
nsv1143969 CNV deletion 24896259
nsv1143072 CNV deletion 24896259
nsv1136317 CNV deletion 24896259
nsv1072501 CNV deletion 25765185
nsv1072500 CNV deletion 25765185
nsv1072081 CNV deletion 25765185
esv993755 CNV deletion 20482838
esv7240 CNV loss 19470904
esv3796 CNV loss 18987735
esv2721684 CNV deletion 23290073
esv2721682 CNV deletion 23290073
esv2721681 CNV deletion 23290073
esv2721680 CNV deletion 23290073
esv2721679 CNV deletion 23290073
esv2721678 CNV deletion 23290073
esv1367526 CNV deletion 17803354

Variation tolerance for SH3BP4 Gene

Residual Variation Intolerance Score: 70% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.60; 56.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SH3BP4 Gene

Human Gene Mutation Database (HGMD)
SH3BP4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SH3BP4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SH3BP4 Gene

Disorders for SH3BP4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SH3BP4 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
cataract 8, multiple types
  • ctrct8
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SH3BP4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SH3BP4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SH3BP4 Gene

Publications for SH3BP4 Gene

  1. Cloning, chromosomal localization, and characterization of cDNA from a novel gene, SH3BP4, expressed by human corneal fibroblasts. (PMID: 10644451) Dunlevy JR … Hassell JR (Genomics 1999) 2 3 4 22 58
  2. SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. (PMID: 22575674) Kim YM … Kim DH (Molecular cell 2012) 3 4 58
  3. Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts. (PMID: 22419666) Shi M … Beaty TH (American journal of medical genetics. Part A 2012) 3 44 58
  4. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. (PMID: 21546767) Murea M … Freedman BI (American journal of nephrology 2011) 3 44 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for SH3BP4 Gene

Sources for SH3BP4 Gene

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