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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TBC1D1 Gene

protein-coding   GIFtS: 62
GCID: GC04P037892

TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1

 Explore 5 diseases affiliated with
TBC1D1 via our new
 Human Malady Compendium 
Biological research products
for TBC1D1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
TBC1 (Tre-2/USP6, BUB2, Cdc16) Domain Family, Member 11 2
KIAA11081 3 5
TBC1 2
TBC11 2
TBC1 Domain Family Member 12

External Ids:    HGNC: 115781   Entrez Gene: 232162   Ensembl: ENSG000000658827   OMIM: 6098505   UniProtKB: Q86TI03   

Export aliases for TBC1D1 gene to outside databases

Previous GC identifers: GC04P038018 GC04P038181 GC04P037850 GC04P037789 GC04P037716 GC04P037569 GC04P037217


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TBC1D1:
TBC1D1 is the founding member of a family of proteins sharing a 180- to 200-amino acid TBC domain presumed to have a
role in regulating cell growth and differentiation. These proteins share significant homology with TRE2 (USP6; MIM
604334), yeast Bub2, and CDC16 (MIM 603461) (White et al., 2000 (PubMed 10965142)).(supplied by OMIM, Mar 2008)

UniProtKB/Swiss-Prot: TBCD1_HUMAN, Q86TI0
Function: May act as a GTPase-activating protein for Rab family protein(s). May play a role in the cell cycle and
differentiation of various tissues. Involved in the trafficking and translocation of GLUT4-containing vesicles and
insulin-stimulated glucose uptake into cells (By similarity)

Gene Wiki entry for TBC1D1


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_016297.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TBC1D1 gene promoter:
         AREB6   TBP   TFIID   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D1 promoter sequence
   Search SABiosciences Chromatin IP Primers for TBC1D1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TBC1D1


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

Entrez Gene cytogenetic band: 4p14   Ensembl cytogenetic band:  4p14   HGNC cytogenetic band: 4p14

TBC1D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P037892:  view genomic region     (about GC identifiers)

Start:
37,892,708 bp from pter      End:
38,140,796 bp from pter
Size:
248,089 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TBCD1_HUMAN, Q86TI0 (See protein sequence)
Recommended Name: TBC1 domain family member 1  
Size: 1168 amino acids; 133084 Da
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=BAB55057.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for TBC1D1:
3QYE (3D)    
Secondary accessions: B7Z3D9 E9PGH8 Q96K82 Q9UPP4
Alternative splicing: 2 isoforms:  Q86TI0-1   Q86TI0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TBC1D1: NX_Q86TI0

Post-translational modifications:

  • Insulin-stimulated phosphorylation by AKT family kinases stimulates SLC2A4/GLUT4 translocation (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86TI0

  • TBC1D1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (5 alternative transcripts): 
    NP_001240841.1  NP_001240842.1  NP_001240843.1  NP_001240844.1  NP_055988.2  

    ENSEMBL proteins: 
     ENSP00000423651   ENSP00000261439   ENSP00000383994   ENSP00000396877   ENSP00000421641  
     ENSP00000425655   ENSP00000397640   ENSP00000410167  
    Reactome Protein details: Q86TI0
    Human Recombinant Protein Products: 
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    Novus Biologicals TBC1D1 Protein
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for TBC1D1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--


    TBC1D1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TBC1D1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR021785 DUF3350
     IPR000195 Rab-GTPase-TBC_dom
     IPR006020 PTyr_interaction_dom
     IPR011993 PH_like_dom

    Graphical View of Domain Structure for InterPro Entry Q86TI0

    ProtoNet protein and cluster: Q86TI0

    2 Blocks protein families:
    IPB000195 RabGAP/TBC domain
    IPB011072 Protein kinase PKN/PRK1


    UniProtKB/Swiss-Prot: TBCD1_HUMAN, Q86TI0
    Similarity: Contains 1 PID domain
    Similarity: Contains 1 Rab-GAP TBC domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: TBCD1_HUMAN, Q86TI0
    Function: May act as a GTPase-activating protein for Rab family protein(s). May play a role in the cell cycle and
    differentiation of various tissues. Involved in the trafficking and translocation of GLUT4-containing vesicles and
    insulin-stimulated glucose uptake into cells (By similarity)

    miRNA
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    hsa-miR-125a-5p hsa-miR-137 hsa-miR-181c hsa-miR-4251 hsa-miR-124 hsa-miR-125b hsa-miR-2276 hsa-miR-3116
    SwitchGear 3'UTR luciferase reporter plasmidTBC1D1 3' UTR sequence
    Inhib. RNA
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    Clone
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--


    TBC1D1 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for TBC1D1:
     Increased cell death HMECs cel  Synthetic lethal with Ras  Synthetic lethal with c-Myc af 

    Animal Models:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Tbc1d1):
     normal 

    TBC1D1 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Membrane Trafficking
    Membrane Trafficking1.00
    Translocation of GLUT4 to the Plasma Membrane0.32
    2Glucose / Energy Metabolism
    Glucose / Energy Metabolism1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for TBC1D1
        Glucose / Energy Metabolism

    2        Reactome Pathways for TBC1D1
        Membrane Trafficking
    Translocation of GLUT4 to the Plasma Membrane



    TBC1D1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for TBC1D1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

    5/17 Interacting proteins for TBC1D1 (Q86TI02, 3 ENSP000002614394) via UniProtKB, MINT, STRING, and/or I2D (see all 17)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YWHAGP619812, 3, ENSP000003063304MINT-50868 I2D: score=3 STRING: ENSP00000306330
    SMAD2Q157962, 3MINT-61619 I2D: score=3 
    YWHAHQ049173, ENSP000002489754I2D: score=1 STRING: ENSP00000248975
    UBE2E2Q96LR53, ENSP000003799314I2D: score=1 STRING: ENSP00000379931
    PRKAA2ENSP000003602904STRING: ENSP00000360290
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032880regulation of protein localization IEA--


    TBC1D1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TBC1D1
    Search CenterWatch for drugs/clinical trials and news about TBC1D1 / TBCD1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TBC1D1 gene (5 alternative transcripts): 
    NM_001253912.1  NM_001253913.1  NM_001253914.1  NM_001253915.1  NM_015173.3  

    Unigene Cluster for TBC1D1:

    TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1
    Hs.176503  [show with all ESTs]
    Unigene Representative Sequence: NM_015173
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000508802 ENST00000261439(uc003gtb.3 uc011byd.2 uc010ifd.3)
    ENST00000402522 ENST00000446803(uc011byf.1) ENST00000491553 ENST00000510573
    ENST00000513936 ENST00000509761 ENST00000443855 ENST00000421339 ENST00000469803
    ENST00000511238 ENST00000401554 ENST00000407365(uc021xnh.1 uc021xni.1 uc003gtd.3)
    ENST00000475531 ENST00000406664 ENST00000405444 ENST00000492180

    miRNA
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    hsa-miR-125a-5p hsa-miR-137 hsa-miR-181c hsa-miR-4251 hsa-miR-124 hsa-miR-125b hsa-miR-2276 hsa-miR-3116
    SwitchGear 3'UTR luciferase reporter plasmidTBC1D1 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB029031.1 AB449881.1 AK027355.1 AK057182.1 AK074954.1 AK295746.1 AK303574.1 BC014529.2 
    BC028196.1 BC029950.1 BC032337.1 BC050321.1 BC053648.1 

    24/28 DOTS entries (see all 28):

    DT.456184  DT.100809970  DT.101970788  DT.100809978  DT.101984031  DT.411256  DT.87014296  DT.92445776 
    DT.92445771  DT.95328117  DT.95213176  DT.95326624  DT.100809971  DT.121250835  DT.91676530  DT.95326619 
    DT.95326622  DT.95326623  DT.95326629  DT.121250938  DT.121251039  DT.210960  DT.40196848  DT.92020137 

    2 AceView cDNA sequences:

    CB529178 CD365618 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TBC1D1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TCCCAGTGTT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See TBC1D1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TBC1D1

    SOURCE GeneReport for Unigene cluster: Hs.176503
        SABiosciences Custom PCR Arrays for TBC1D1
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D1

    (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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TBC1D1 gene from 6/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TBC1D11 TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member more 73.62(n)
    77.98(a)
      426162  XM_423827.3  XP_423827.3 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D16
    --
    69(a)
    1 ↔ 1
    GL343361.1(430798-535509)
    zebrafish
    (Danio rerio)
    Actinopterygii tbc1d11 TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member more 62.13(n)
    62.13(a)
      561193  XM_684525.5  XP_689617.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta plx3   -- 36(a)   83C1   --
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PAM16
    AT3G024606
    RabGAP/TBC domain-containing protein
    27(a)
    27(a)
    possible ortholog
    possible ortholog
    5(5199711-5202452)
    3(505434-508428)
    rice
    (Oryza sativa)
    Liliopsida --
    TBC domain containing protein, expressed
    27(a)
    possible ortholog
    8(19736918-19741786)


    ENSEMBL Gene Tree for TBC1D1 (if available)
    TreeFam Gene Tree for TBC1D1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TBC1D1 gene
    RABGAP1L2  TBC1D122  TBC1D42  TBC1D142  EVI52  EVI5L2  RABGAP12  
    4 SIMAP similar genes for TBC1D1 using alignment to 11 protein entries:     TBCD1_HUMAN (see all proteins):
    TBC1D4    EVI5    SGSM3    FLJ00288

    TBC1D1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 5 variations for TBC1D1
         4 CNVs: 80253 92048 80252 80255
         1 Indel: 80254
    Human Gene Mutation Database (HGMD): TBC1D1
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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.)
    About This Section

    TBC1D1 for disorders           About GeneDecksing

    OMIM gene information: 609850    OMIM disorders: --

    5 diseases for TBC1D1:    About MalaCards
    tuberculous meningitis    morbid obesity    meningitis    obesity
    tuberculosis

    1 disease from the University of Copenhagen DISEASES database for TBC1D1:
    Morbid obesity
    Human Genome Epidemiology (HuGE) Navigator: TBC1D1 (8 documents)

    Export disorders for TBC1D1 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)
    About This Section

    PubMed articles for TBC1D1 gene, integrated from 9 sources (see all 33):
    (articles sorted by number of sources associating them with TBC1D1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The gene encoding TBC1D1 with homology to the tre-2/USP6 oncogene, BUB2, and cdc16 maps to mouse chromosome 5 and human chromosome 4. (PubMed id 10965142)1, 3, 9 White R.A....Zon L.I. (2000)
    2. Crystal structures of human TBC1D1 and TBC1D4 (AS160) RabGTPase- activating protein (RabGAP) domains reveal critical elements for GLUT4 translocation. (PubMed id 21454505)1, 2 Park S.Y.... Shoelson S.E. (2011)
    3. R125W coding variant in TBC1D1 confers risk for familial obesity and contributes to linkage on chromosome 4p14 in the French population. (PubMed id 18325908)1, 2 Meyre D....Froguel P. (2008)
    4. TBC1D1 is a candidate for a severe obesity gene and evidence for a gene/gene interaction in obesity predisposition. (PubMed id 16893906)1, 2 Stone S.... Shattuck D. (2006)
    5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    8. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PubMed id 12168954)1, 2 Nakajima D.... Nagase T. (2002)
    9. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10470851)1, 2 Kikuno R....Ohara O. (1999)
    10. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23216 HGNC: 11578 AceView: TBC1D1.29 Ensembl:ENSG00000065882 euGenes: HUgn23216
    ECgene: TBC1D1 H-InvDB: TBC1D1

    (According to HUGE)
    About This Section
    HUGE: KIAA1108

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for TBC1D1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for TBC1D1 Genetics and Cytogenetics in Oncology and Haematology

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