Human Gene TBC1D4 (uc001vjl.1)
  Description: Homo sapiens TBC1 domain family, member 4 (TBC1D4), mRNA.
RefSeq Summary (NM_014832): This gene is a member of the Tre-2/BUB2/CDC16 domain family. The protein encoded by this gene is a Rab-GTPase-activating protein, and contains two phopshotyrosine-binding domains (PTB1 and PTB2), a calmodulin-binding domain (CBD), a Rab-GTPase domain, and multiple AKT phosphomotifs. This protein is thought to play an important role in glucose homeostasis by regulating the insulin-dependent trafficking of the glucose transporter 4 (GLUT4), important for removing glucose from the bloodstream into skeletal muscle and fat tissues. Reduced expression of this gene results in an increase in GLUT4 levels at the plasma membrane, suggesting that this protein is important in intracellular retention of GLUT4 under basal conditions. When exposed to insulin, this protein is phosphorylated, dissociates from GLUT4 vesicles, resulting in increased GLUT4 at the cell surface, and enhanced glucose transport. Phosphorylation of this protein by AKT is required for proper translocation of GLUT4 to the cell surface. Individuals homozygous for a mutation in this gene are at higher risk for type 2 diabetes and have higher levels of circulating glucose and insulin levels after glucose ingestion. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015].
Transcript (Including UTRs)
   Position: hg19 chr13:75,858,809-76,056,250 Size: 197,442 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr13:75,860,928-76,055,903 Size: 194,976 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:75,858,809-76,056,250)mRNA (may differ from genome)Protein (1298 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TBCD4_HUMAN
DESCRIPTION: RecName: Full=TBC1 domain family member 4; AltName: Full=Akt substrate of 160 kDa; Short=AS160;
FUNCTION: May act as a GTPase-activating protein for RAB2A, RAB8A, RAB10 and RAB14. Isoform 2 promotes insulin-induced glucose transporter SLC2A4/GLUT4 translocation at the plasma membrane, thus increasing glucose uptake.
SUBCELLULAR LOCATION: Cytoplasm. Note=Isoform 2 shows a cytoplasmic perinuclear localization in a myoblastic cell line in resting and insulin-stimulated cells.
TISSUE SPECIFICITY: Widely expressed. Isoform 2 is the highest overexpressed in most tissues. Isoform 1 is highly expressed in skeletal muscle and heart, but was not detectable in the liver nor in adipose tissue. Isoform 2 is strongly expressed in adrenal and thyroid gland, and also in lung, kidney, colon, brain and adipose tissue. Isoform 2 is moderately expressed in skeletal muscle. Expressed in pancreatic Langerhans islets, including beta cells (at protein level). Expression is decreased by twofold in pancreatic islets in type 2 diabetes patients compared to control subjects. Up-regulated in T-cells from patients with atopic dermatitis.
PTM: Phosphorylated by AKT1; insulin-induced. Also phosphorylated by AMPK in response to insulin. Insulin-stimulated phosphorylation is required for SLC2A4/GLUT4 translocation. Has no effect on SLC2A4/GLUT4 internalization. Physiological hyperinsulinemia increases phosphorylation in skeletal muscle. Insulin-stimulated phosphorylation is reduced by 39% in type 2 diabetic patients.
SIMILARITY: Contains 2 PID domains.
SIMILARITY: Contains 1 Rab-GAP TBC domain.
SEQUENCE CAUTION: Sequence=BAA25529.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TBC1D4
CDC HuGE Published Literature: TBC1D4
Positive Disease Associations: Blood Pressure , Blood Pressure Determination , Carotid Stenosis
Related Studies:
  1. Blood Pressure
    , , . [PubMed 0]
  2. Blood Pressure
    , , . [PubMed 0]
  3. Blood Pressure
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TBC1D4
Diseases sorted by gene-association score: diabetes mellitus, noninsulin-dependent, 5* (950)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 53.66 RPKM in Adrenal Gland
Total median expression: 430.75 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -186.10347-0.536 Picture PostScript Text
3' UTR -567.402119-0.268 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR021785 - DUF3350
IPR011993 - PH_like_dom
IPR006020 - PTyr_interaction_dom
IPR000195 - Rab-GTPase-TBC_dom

Pfam Domains:
PF00566 - Rab-GTPase-TBC domain
PF00640 - Phosphotyrosine interaction domain (PTB/PID)
PF11830 - Domain of unknown function (DUF3350)

SCOP Domains:
47923 - Ypt/Rab-GAP domain of gyp1p
50729 - PH domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3QYB - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O60343
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0017137 Rab GTPase binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0016192 vesicle-mediated transport
GO:0031338 regulation of vesicle fusion
GO:0031339 negative regulation of vesicle fusion
GO:0032869 cellular response to insulin stimulus
GO:0090630 activation of GTPase activity

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0012505 endomembrane system
GO:0031982 vesicle


-  Descriptions from all associated GenBank mRNAs
  LF385018 - JP 2014500723-A/192521: Polycomb-Associated Non-Coding RNAs.
CR749622 - Homo sapiens mRNA; cDNA DKFZp779C0666 (from clone DKFZp779C0666).
BC151239 - Homo sapiens TBC1 domain family, member 4, mRNA (cDNA clone MGC:167833 IMAGE:8860512), complete cds.
AB011175 - Homo sapiens KIAA0603 mRNA for KIAA0603 protein.
AK300468 - Homo sapiens cDNA FLJ50736 complete cds, highly similar to TBC1 domain family member 4.
AK304091 - Homo sapiens cDNA FLJ50361 complete cds, highly similar to TBC1 domain family member 4.
AB449885 - Homo sapiens TBC1D4 mRNA for TBC1 domain family, member 4, complete cds.
FM207106 - Homo sapiens mRNA for TBC1 domain family, member 4 (TBC1D4 gene), splice variant AS160_tv2.
FM207107 - Homo sapiens mRNA for TBC1 domain family, member 4 (TBC1D4 gene), splice variant AS160_tv3.
BC146300 - Synthetic construct Homo sapiens clone IMAGE:100015231, MGC:180255 TBC1 domain family, member 4 (TBC1D4) mRNA, encodes complete protein.
AB463305 - Synthetic construct DNA, clone: pF1KA0603, Homo sapiens TBC1D4 gene for TBC1 domain family, member 4, without stop codon, in Flexi system.
AY211910 - Homo sapiens sarcoma antigen NY-SAR-10 mRNA, partial sequence.
AK307493 - Homo sapiens cDNA, FLJ97441.
MA620595 - JP 2018138019-A/192521: Polycomb-Associated Non-Coding RNAs.
JD530819 - Sequence 511843 from Patent EP1572962.
JD349161 - Sequence 330185 from Patent EP1572962.
JD281142 - Sequence 262166 from Patent EP1572962.
JD544468 - Sequence 525492 from Patent EP1572962.
JD163931 - Sequence 144955 from Patent EP1572962.
JD244157 - Sequence 225181 from Patent EP1572962.
JD229936 - Sequence 210960 from Patent EP1572962.
JD479540 - Sequence 460564 from Patent EP1572962.
JD083559 - Sequence 64583 from Patent EP1572962.
JD093999 - Sequence 75023 from Patent EP1572962.
JD242246 - Sequence 223270 from Patent EP1572962.
JD225672 - Sequence 206696 from Patent EP1572962.
JD394251 - Sequence 375275 from Patent EP1572962.
JD444255 - Sequence 425279 from Patent EP1572962.
JD466069 - Sequence 447093 from Patent EP1572962.
JD081505 - Sequence 62529 from Patent EP1572962.
JD019635 - Sequence 659 from Patent EP1572962.
JD035619 - Sequence 16643 from Patent EP1572962.
JD026344 - Sequence 7368 from Patent EP1572962.
JD028561 - Sequence 9585 from Patent EP1572962.
JD261121 - Sequence 242145 from Patent EP1572962.
JD475207 - Sequence 456231 from Patent EP1572962.
JD356130 - Sequence 337154 from Patent EP1572962.
JD458677 - Sequence 439701 from Patent EP1572962.
JD129016 - Sequence 110040 from Patent EP1572962.
JD128875 - Sequence 109899 from Patent EP1572962.
JD078683 - Sequence 59707 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O60343 (Reactome details) participates in the following event(s):

R-HSA-1445149 14-3-3 binds p-5S,T642-AS160 (TBC1D4)
R-HSA-1445148 Translocation of GLUT4 to the plasma membrane
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: A7E2X8, AS160, B4DU25, B4E235, B6ETN8, B6ETN9, KIAA0603, NM_014832, NP_055647, O60343, Q5W0B9, Q68D14, TBCD4_HUMAN
UCSC ID: uc001vjl.1
RefSeq Accession: NM_014832
Protein: O60343 (aka TBCD4_HUMAN or TBC4_HUMAN)
CCDS: CCDS41901.1, CCDS66563.1, CCDS66564.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014832.2
exon count: 21CDS single in 3' UTR: no RNA size: 6363
ORF size: 3897CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7964.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.