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TBC1D3 Gene

protein-coding   GIFtS: 35
GCID: GC17M036338

TBC1 Domain Family, Member 3

  See TBC1D3-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
TBC1 Domain Family, Member 31 2     Rab GTPase-Activating Protein PRC172 3
PRC172 3 5     Prostate Cancer Gene 171
TBC1D3A2 3 5     TBC1D3F2
Prostate Cancer Gene 17 Protein2 3     TBC1 Domain Family Member 32
Protein TRE17-Alpha2 3     TBC1 Domain Family, Member 3F2

External Ids:    HGNC: 190311   Entrez Gene: 7298732   Ensembl: ENSG000001976817   OMIM: 6077415   UniProtKB: Q8IZP13   

Export aliases for TBC1D3 gene to outside databases

Previous GC identifers: GC17P036015 GC17M036712 GC17P033358 GC17M033413 GC17M033592 GC17M033594


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TBC1D3 Gene:
TBC1D3 (TBC1 domain family, member 3) is a protein-coding gene. Diseases associated with TBC1D3 include prostate cancer. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D3H.

UniProtKB/Swiss-Prot: TBC3A_HUMAN, Q8IZP1
Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D3 gene promoter:
         STAT1   GATA-3   STAT4   STAT1beta   STAT5A   STAT1alpha   c-Rel   STAT2   STAT3   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D3 promoter sequence
   Search Chromatin IP Primers for TBC1D3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q12   Ensembl cytogenetic band:  17q12   HGNC cytogenetic band: 17q12

TBC1D3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D3 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M036338:  view genomic region     (about GC identifiers)

Start:
36,337,528 bp from pter      End:
36,358,166 bp from pter
Size:
20,639 bases      Orientation:
minus strand

1 alternative location:
Chr17+,NW_003315949 208,603-219,515     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TBC3A_HUMAN, Q8IZP1 (See protein sequence)
Recommended Name: TBC1 domain family member 3  
Size: 549 amino acids; 62168 Da
Miscellaneous: TBC1D3 is encoded by a collection of very similar paralogs with multiple copies of each paralog,
some human genomes encoding well over 50 copies depending on ethnic origin of the donor
Secondary accessions: A6NGX2 A8K007 Q9H0B9 Q9UDD4

Explore the universe of human proteins at neXtProt for TBC1D3: NX_Q8IZP1

Explore proteomics data for TBC1D3 at MOPED

Post-translational modifications: 

  • Ubiquitinated by a CUL7-based E3 ligase, which leads to proteasomal degradation1
  • Palmitoylation is required for membrane localization and protects TBC1D3 from ubiquination1
  • Modification sites at neXtProt

  • See TBC1D3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001116863.3  
    ENSEMBL proteins: 
     ENSP00000428847   ENSP00000427748   ENSP00000429762   ENSP00000346691   ENSP00000429926  
     ENSP00000439621   ENSP00000339993  

    TBC1D3 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry Q8IZP1

    ProtoNet protein and cluster: Q8IZP1

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: TBC3A_HUMAN, Q8IZP1
    Similarity: Contains 1 Rab-GAP TBC domain


    Find genes that share domains with TBC1D3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC3A_HUMAN, Q8IZP1
    Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    Find genes that share ontologies with TBC1D3           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TBC1D3
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TBC1D3
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    TBC3A_HUMAN, Q8IZP1: Cell membrane; Lipid-anchor. Note=Associated with lipid rafts
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    cytoskeleton1
    endosome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--

    Find genes that share ontologies with TBC1D3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TBC1D3
    Interactions:

        GeneGlobe Interaction Network for TBC1D3

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for TBC1D3 (ENSP000003466914) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GGA3ENSP000002455414STRING: ENSP00000245541
    YWHAEENSP000002643354STRING: ENSP00000264335
    COL4A3BPENSP000003698624STRING: ENSP00000369862
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ----

    Find genes that share ontologies with TBC1D3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TBC1D3 (TBC3A)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TBC1D3 gene: 
    NM_001123391.3  

    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000518551(uc010wdl.1) ENST00000520599 ENST00000517507(uc002hpq.2)
    ENST00000524102(uc010wdm.1) ENST00000354664(uc002hpp.2 uc010cvj.1)
    ENST00000519496 ENST00000519532(uc002hox.2) ENST00000537432 ENST00000339023

    miRNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat TBC1D3

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TBC1D3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    TBC1D3 Expression
    About this image

    TBC1D3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D3 Protein Expression

    UniProtKB/Swiss-Prot: TBC3A_HUMAN, Q8IZP1
    Tissue specificity: Expressed in liver, skeletal muscle, kidney, pancreas, spleen, testis, ovary, small intestine
    and peripheral blood leukocytes. Overexpressed in prostate cancers

        Custom PCR Arrays for TBC1D3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for TBC1D3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    --
    (see all 9)
    Uncharacterized protein
    (see all 9)
    36(a)
    34(a)
    (see all 9)
    many ↔ many
    many ↔ many
    (see all 9)
    4(35158703-35165770)
    22(89476-95800)
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    32(a)
    1 → many
    5(15411217-15475247)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    37(a)
    1 → many
    1(74862925-74883710)
    zebrafish
    (Danio rerio)
    Actinopterygii TBC1D3G6
    TBC1 domain family, member 3G
    14(a)
    1 → many
    25(16824916-16909191) ENSDARG00000086840
    fruit fly
    (Drosophila melanogaster)
    Insecta RN-tre6
    tre oncogene-related protein
    22(a)
    1 → many
    2R(9872320-9878215)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-176
    Protein TBC-17, isoform d (tbc-17) mRNA, complete ...
    14(a)
    1 → many
    II(12694412-12725483) WBGene00012894


    ENSEMBL Gene Tree for TBC1D3 (if available)
    TreeFam Gene Tree for TBC1D3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D3 gene
    TBC1D3F1 2  LOC101060389  LOC101060376  TBC1D3C1 2  LOC101060321  LOC102724862  LOC101060351  TBC1D3H1 2  
    LOC102723859  TBC1D3B1 2  TBC1D262  ENSG000002487512  GRTP12  TBC1D10C2  TBC1D10A2  TBC1D3G2  
    TBC1D10B2  USP6NL2  TBC1D282  
    16 SIMAP similar genes for TBC1D3 using alignment to 7 protein entries:     TBC3A_HUMAN (see all proteins):
    TBC1D3F    TBC1D3H    TBC1D3B    TBC1D3G    TBC1D3C    USP6-short
    TRE17    tre    USP6    CDH11/USP6 fusion oncogene    LOC440419    TBC1D26
    TBC1D28    TBC1D29    TBC1D10A    FLJ00050

    Find genes that share paralogs with TBC1D3           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for TBC1D3 (see all 18)
    PGOHUM00000256803 PGOHUM00000256804 PGOHUM00000256806 PGOHUM00000256807 PGOHUM00000256808


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    2 SNPs for TBC1D3    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs712701261,2
    C,F--36350582(-) TAATCC/TGAGCA 1 -- us2k12Minor allele frequency- T:0.50NA 4
    rs90781,2,4
    ----see VAR_0630882 mis40--------

    HapMap Linkage Disequilibrium report for TBC1D3 (36337528 - 36358166 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for TBC1D3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv471398CNV Duplication19718026
    nsv820624CNV Duplication20802225
    nsv908172CNV Loss21882294
    nsv833435CNV Gain+Loss17160897
    dgv957e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TBC1D3
    DNA2.0 Custom Variant and Variant Library Synthesis for TBC1D3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607741    OMIM disorders: --

    1 disease for TBC1D3:    
    About MalaCards
    prostate cancer


    Find genes that share disorders with TBC1D3           About GenesLikeMe


    Export disorders for TBC1D3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for TBC1D3 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with TBC1D3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The Tre2 (USP6) oncogene is a hominoid-specific gene. (PubMed id 12604796)1, 2, 3 Paulding C.A.... Haber D.A. (Proc. Natl. Acad. Sci. U.S.A. 2003)
    2. PRC17, a novel oncogene encoding a Rab GTPase-activating protein, is amplified in prostate cancer. (PubMed id 12359748)1, 2, 3 Pei L.... Li J. (Cancer Res. 2002)
    3. Ubiquitination and degradation of the hominoid-specific oncoprotein TBC1D3 is regulated by protein palmitoylation. (PubMed id 23578663)1, 2 Kong C....Stahl P.D. (Biochem. Biophys. Res. Commun. 2013)
    4. TBC1D3, a hominoid oncoprotein, is encoded by a cluster of paralogues located on chromosome 17q12. (PubMed id 16863688)1, 3 Hodzic D....Stahl P.D. (Genomics 2006)
    5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)1, 2 Zody M.C.... Nusbaum C. (Nature 2006)
    6. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (Genome Res. 2001)
    7. Human TRE17 oncogene is generated from a family of homologous polymorphic sequences by single-base changes. (PubMed id 8471161)1, 2 Onno M.... Hill M. (DNA Cell Biol. 1993)
    8. Identification of novel sequences in the repertoire of hypervariable TRE17 genes from immortalized nonmalignant and malignant human keratinocytes. (PubMed id 8406013)1, 2 Onno M.... Hill M. (Gene 1993)
    9. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. (PubMed id 23535730)1 Pharoah P.D....Sellers T.A. (Nat. Genet. 2013)
    10. Ubiquitination and degradation of the hominoid-specific oncoprotein TBC1D3 is mediated by CUL7 E3 ligase. (PubMed id 23029530)1 Kong C....Stahl P.D. (PLoS ONE 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 729873 HGNC: 19031 Ensembl:ENSG00000197681 euGenes: HUgn729873 ECgene: TBC1D3
    H-InvDB: TBC1D3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TBC1D3 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for TBC1D3 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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