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TBC1D3H Gene

protein-coding   GIFtS: 33
GCID: GC17M034581

TBC1 Domain Family, Member 3H

  See related diseases
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 3H1 2
TBC1 Domain Family Member 3-Like Protein LOC7298372
TBC1 Domain Family Member 3H2

External Ids:    HGNC: 307081   Entrez Gene: 7298772   Ensembl: ENSG000002423847   OMIM: 6108115   UniProtKB: P0C7X13   

Export aliases for TBC1D3H gene to outside databases

Previous GC identifers: GC17M031820 GC17U900808 GC17M033544 GC17M033416 GC17M034745


(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 TBC1D3H Gene:
TBC1D3H (TBC1 domain family, member 3H) is a protein-coding gene. Diseases associated with TBC1D3H include intrahepatic cholangiocarcinoma, and cholangiocarcinoma. An important paralog of this gene is TBC1D3F.

UniProtKB/Swiss-Prot: TBC3H_HUMAN, P0C7X1
Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity)




(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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RefSeq DNA sequence:
NT_187614.1  NC_000017.11  NT_010783.16  NC_018928.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TBC1D3H
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TBC1D3H

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D3H


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

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

TBC1D3H Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D3H gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M034581:  view genomic region     (about GC identifiers)

Start:
34,581,086 bp from pter      End:
34,808,061 bp from pter
Size:
226,976 bases      Orientation:
minus strand

1 alternative location:
Chr17-,NW_003315949 262,104-273,236     

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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: TBC3H_HUMAN, P0C7X1 (See protein sequence)
Recommended Name: TBC1 domain family member 3H  
Size: 549 amino acids; 62203 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: A6NH17 A8MZ78

Explore the universe of human proteins at neXtProt for TBC1D3H: NX_P0C7X1

Explore proteomics data for TBC1D3H at MOPED

Post-translational modifications: 

  • Ubiquitinated by a CUL7-based E3 ligase, which leads to proteasomal degradation (By similarity)1
  • Palmitoylation is required for membrane localization and protects TBC1D3 from ubiquination (By similarity)1
  • Modification sites at neXtProt

  • See TBC1D3H Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001116864.3  
    ENSEMBL proteins: 
     ENSP00000340678   ENSP00000377887   ENSP00000409195   ENSP00000441721   ENSP00000383522  

    TBC1D3H 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 P0C7X1

    ProtoNet protein and cluster: P0C7X1

    UniProtKB/Swiss-Prot: TBC3H_HUMAN, P0C7X1
    Similarity: Contains 1 Rab-GAP TBC domain


    TBC1D3H for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC3H_HUMAN, P0C7X1
    Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    TBC1D3H for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TBC1D3H
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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
    TBC3H_HUMAN, P0C7X1: Cell membrane; Lipid-anchor (By similarity). Note=Associated with lipid rafts (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    cytoskeleton1

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

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

    TBC1D3H for ontologies           About GeneDecksing


    (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 TBC1D3H
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D3H

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

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

    TBC1D3H for ontologies           About GeneDecksing



    (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 TBC1D3H (TBC3H)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TBC1D3H gene: 
    NM_001123392.3  

    Unigene Cluster for TBC1D3H:

    TBC1 domain family, member 3H
    Hs.569742  [show with all ESTs]
    Unigene Representative Sequence: NM_001123392
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000340106 ENST00000394359(uc002hmb.2) ENST00000455054(uc002hmc.3 uc010wcx.1 uc002hmd.3)
    ENST00000588440 ENST00000592088 ENST00000589865 ENST00000535446(uc002hlm.2 uc010wcv.1)
    ENST00000400684
    miRNA
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      Search QuantiTect SYBR Green Assays in human, mouse, rat TBC1D3H
      QuantiFast Probe-based Assays in human, mouse, rat TBC1D3H

    14 DOTS entries:

    DT.92042803  DT.120994583  DT.92048469  DT.120948274  DT.120994560  DT.95298563  DT.97771291  DT.97858652 
    DT.120894916  DT.120948278  DT.120948285  DT.120994618  DT.120994639  DT.212833 

    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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    TBC1D3H expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    TBC1D3H Expression
    About this image

    TBC1D3H Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D3H Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.569742

    UniProtKB/Swiss-Prot: TBC3H_HUMAN, P0C7X1
    Tissue specificity: Expressed in heart

        Custom PCR Arrays for TBC1D3H
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D3H

    (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 TBC1D3H 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
    36(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
    21(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 TBC1D3H (if available)
    TreeFam Gene Tree for TBC1D3H (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D3H gene
    LOC101060321  LOC101060389  TBC1D3C1 2  TBC1D3F1 2  LOC102724862  TBC1D31 2  LOC101060376  TBC1D3B1 2  
    LOC101060351  LOC102723859  TBC1D262  ENSG000002487512  GRTP12  TBC1D10C2  TBC1D10A2  TBC1D3G2  
    TBC1D10B2  USP6NL2  TBC1D282  
    15 SIMAP similar genes for TBC1D3H using alignment to 4 protein entries:     TBC3H_HUMAN (see all proteins):
    TBC1D3F    TBC1D3B    TBC1D3    TBC1D3C    TBC1D3G    USP6-short
    USP6    TRE17    tre    LOC440419    TBC1D26    TBC1D28
    TBC1D29    TBC1D10A    FLJ00050

    TBC1D3H for paralogs           About GeneDecksing


    4 Pseudogenes.org Pseudogenes for TBC1D3H
    PGOHUM00000237208 PGOHUM00000259253 PGOHUM00000246111 PGOHUM00000250202


    (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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    Selected SNPs for TBC1D3H (see all 62)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs774797041,2
    C--34754758(+) TGCTGC/GACAAC 1 -- int10--------
    rs1405889171,2
    --34757013(+) GGCAGA/GCCAGA 1 -- ut510--------
    rs1457113701,2
    C--34757031(+) CAGGTG/TCTAAG 1 -- ut510--------
    rs1894844101,2
    --34757345(+) GGGTGG/TTCCTG 1 -- us2k10--------
    rs767730061,2
    C--34757363(-) CCACCA/GCTATG 1 -- us2k11Minor allele frequency- G:0.00NA 2
    rs21707281,2
    --34757454(-) AAAAGC/TGATAC 1 -- us2k10--------
    rs44383521,2
    C--34757572(-) ATAACA/GTGTCT 1 -- us2k10--------
    rs1493989061,2
    --34757591(+) TGGTTA/CATCTG 1 -- us2k10--------
    rs47951341,2
    C,F--34757698(+) AGTCTG/ATCTGT 1 -- us2k12Minor allele frequency- A:0.50NA 6
    rs620790311,2
    C--34757699(+) GTCTGC/TCTGTG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TBC1D3H (34581086 - 34808061 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for TBC1D3H (see all 16):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv471328CNV Duplication19718026
    esv29998CNV Loss17803354
    dgv122e55CNV Gain17911159
    nsv526727CNV Gain19592680
    nsv471697CNV Gain15918152
    nsv428340CNV Gain18775914
    nsv469796CNV Gain16826518
    dgv3145n71CNV Gain21882294
    esv2751645CNV Gain17911159
    nsv9540CNV Gain+Loss18304495

    Site Specific Mutation Identification with PCR Assays
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    (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: 610811    OMIM disorders: --

    2 diseases for TBC1D3H:    
    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma


    TBC1D3H for disorders           About GeneDecksing


    Export disorders for TBC1D3H 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 TBC1D3H gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TBC1D3H)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. TBC1D3, a hominoid oncoprotein, is encoded by a cluster of paralogues located on chromosome 17q12. (PubMed id 16863688)1, 2, 3 Hodzic D....Stahl P.D. (Genomics 2006)
    2. 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)
    3. Diversity of human copy number variation and multicopy genes. (PubMed id 21030649)2 Sudmant P.H.... Eichler E.E. (Science 2010)
    4. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (Biochem. Biophys. Res. Commun. 2006)
    5. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
    6. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. (PubMed id 10737800)1 Dias Neto E....Simpson A.J.G. (Proc. Natl. Acad. Sci. U.S.A. 2000)

    (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: 729877 HGNC: 30708 Ensembl:ENSG00000242384 euGenes: HUgn729877 ECgene: TBC1D3H
    H-InvDB: TBC1D3H

    (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 TBC1D3H Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TBC1D3H gene:
    Search GeneIP for patents involving TBC1D3H

    GeneCards and IP:
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