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Aliases for TBC1D5 Gene

Aliases for TBC1D5 Gene

  • TBC1 Domain Family Member 5 2 3 5
  • TBC1 Domain Family, Member 5 2
  • KIAA0210 4

External Ids for TBC1D5 Gene

Previous GeneCards Identifiers for TBC1D5 Gene

  • GC03M017129
  • GC03M017174
  • GC03M017198
  • GC03M017133

Summaries for TBC1D5 Gene

GeneCards Summary for TBC1D5 Gene

TBC1D5 (TBC1 Domain Family Member 5) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and AP-2 adaptor complex binding. An important paralog of this gene is TBC1D13.

UniProtKB/Swiss-Prot for TBC1D5 Gene

  • May act as a GTPase-activating protein (GAP) for Rab family protein(s). May act as a GAP for RAB7A. Can displace RAB7A and retromer CSC subcomplex from the endosomal membrane to the cytosol; at least retromer displacement seems to require its catalytic activity (PubMed:19531583, PubMed:20923837). Required for retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN); the function seems to require its catalytic activity. Involved in regulation of autophagy (PubMed:22354992). May act as a molecular switch between endosomal and autophagosomal transport and is involved in reprogramming vesicle trafficking upon autophagy induction. Involved in the trafficking of ATG9A upon activation of autophagy. May regulate the recruitment of ATG9A-AP2-containing vesicles to autophagic membranes (PubMed:24603492).

Additional gene information for TBC1D5 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBC1D5 Gene

Genomics for TBC1D5 Gene

GeneHancer (GH) Regulatory Elements for TBC1D5 Gene

Promoters and enhancers for TBC1D5 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
GH03I017738 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550 +703.5 703466 5.3 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 SP3 SSRP1 ZNF610 LOC105376975 TBC1D5 RNU7-10P PIR60426
GH03I018442 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 550.8 -0.3 -326 4.6 PKNOX1 ZNF76 ZNF2 ZNF335 GLIS2 ZNF366 SCRT2 EGR2 SMARCA5 ZNF174 SATB1 TBC1D5 SATB1-AS1 GC03M018433 GC03M018291
GH03I017700 Promoter 0.6 EPDnew 550 +744.8 744779 0.1 POLR3A TRC-GCA25-1 TBC1D5 RNU7-10P ENSG00000233133
GH03I018421 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 13.2 +20.3 20251 5.2 PKNOX1 SIN3A FEZF1 ZNF2 IRF4 YY1 GLIS2 ATF7 RUNX3 KLF13 SATB1 SATB1-AS1 TBC1D5 GC03P018426 ENSG00000272477 GC03M018291
GH03I018739 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.7 -297.4 -297352 5.1 SMAD1 EBF1 RBBP5 BMI1 BATF KLF5 IRF4 GATA3 NFATC1 ZNF207 SATB1 SATB1-AS1 TBC1D5 LOC105376976 GC03M018291
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBC1D5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBC1D5 gene promoter:

Genomic Locations for TBC1D5 Gene

Genomic Locations for TBC1D5 Gene
chr3:17,157,162-18,444,817
(GRCh38/hg38)
Size:
1,287,656 bases
Orientation:
Minus strand
chr3:17,198,654-18,486,309
(GRCh37/hg19)

Genomic View for TBC1D5 Gene

Genes around TBC1D5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D5 Gene

Proteins for TBC1D5 Gene

  • Protein details for TBC1D5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92609-TBCD5_HUMAN
    Recommended name:
    TBC1 domain family member 5
    Protein Accession:
    Q92609
    Secondary Accessions:
    • A6NP25
    • C9JP52

    Protein attributes for TBC1D5 Gene

    Size:
    795 amino acids
    Molecular mass:
    89004 Da
    Quaternary structure:
    • Interacts with MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1, GABARAPL2. Interacts with VPS29 and VPS35; indicative for an association with retromer CSC subcomplex. MAP1LC3A and VPS29 compete for binding to TBC1D5 (PubMed:20923837, PubMed:22354992). Interacts with AP2M1; indicative for an association with the AP2 complex. Interacts with ULK1 and ATG13 (phosphorylated); indicative for an association with the activated ULK1-ATG13-FIP200 complex. Interacts with ATG9A; the interactions seems to be restricted to the AP2-clathrin-associated fraction of ATG9A (PubMed:24603492).
    SequenceCaution:
    • Sequence=BAA13201.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TBC1D5 Gene

    Alternative splice isoforms for TBC1D5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D5 Gene

Post-translational modifications for TBC1D5 Gene

No data available for DME Specific Peptides for TBC1D5 Gene

Domains & Families for TBC1D5 Gene

Gene Families for TBC1D5 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TBC1D5 Gene

Suggested Antigen Peptide Sequences for TBC1D5 Gene

Graphical View of Domain Structure for InterPro Entry

Q92609

UniProtKB/Swiss-Prot:

TBCD5_HUMAN :
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
Domain:
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins. LIR 1 is also implicated in interaction with retromer; LIR 2 is only implicated in interaction with ATG8 family proteins.
genes like me logo Genes that share domains with TBC1D5: view

Function for TBC1D5 Gene

Molecular function for TBC1D5 Gene

UniProtKB/Swiss-Prot Function:
May act as a GTPase-activating protein (GAP) for Rab family protein(s). May act as a GAP for RAB7A. Can displace RAB7A and retromer CSC subcomplex from the endosomal membrane to the cytosol; at least retromer displacement seems to require its catalytic activity (PubMed:19531583, PubMed:20923837). Required for retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN); the function seems to require its catalytic activity. Involved in regulation of autophagy (PubMed:22354992). May act as a molecular switch between endosomal and autophagosomal transport and is involved in reprogramming vesicle trafficking upon autophagy induction. Involved in the trafficking of ATG9A upon activation of autophagy. May regulate the recruitment of ATG9A-AP2-containing vesicles to autophagic membranes (PubMed:24603492).

Phenotypes From GWAS Catalog for TBC1D5 Gene

Gene Ontology (GO) - Molecular Function for TBC1D5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IBA --
GO:0005515 protein binding IPI 16189514
GO:0017137 Rab GTPase binding IBA --
GO:0035612 AP-2 adaptor complex binding IDA 24603492
GO:1905394 retromer complex binding IMP 27385586
genes like me logo Genes that share ontologies with TBC1D5: view
genes like me logo Genes that share phenotypes with TBC1D5: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D5 Gene

Localization for TBC1D5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D5 Gene

Endosome membrane. Cytoplasmic vesicle, autophagosome. Note=During starvation induced autophagy is relocalized from endosomal localization to LC3-positive autophagosomes. {ECO:0000269 PubMed:22354992}.

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 TBC1D5 gene
Compartment Confidence
golgi apparatus 5
endosome 5
cytosol 4
plasma membrane 2
nucleus 2
extracellular 1
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBC1D5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005776 autophagosome IDA,IEA 22354992
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IEA --
GO:0010008 endosome membrane IDA,IEA 20923837
genes like me logo Genes that share ontologies with TBC1D5: view

Pathways & Interactions for TBC1D5 Gene

SuperPathways for TBC1D5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TBC1D5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002092 positive regulation of receptor internalization IMP 22354992
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IBA --
GO:0006914 autophagy IDA 22354992
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with TBC1D5: view

No data available for Pathways by source and SIGNOR curated interactions for TBC1D5 Gene

Drugs & Compounds for TBC1D5 Gene

No Compound Related Data Available

Transcripts for TBC1D5 Gene

mRNA/cDNA for TBC1D5 Gene

(50) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(30) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TBC1D5 Gene

TBC1 domain family, member 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D5 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23
SP1: -
SP2:
SP3: -

Relevant External Links for TBC1D5 Gene

GeneLoc Exon Structure for
TBC1D5
ECgene alternative splicing isoforms for
TBC1D5

Expression for TBC1D5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBC1D5 Gene

Protein differential expression in normal tissues from HIPED for TBC1D5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.4), Lymph node (12.3), Bone (12.0), and Monocytes (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TBC1D5 Gene



Protein tissue co-expression partners for TBC1D5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TBC1D5 Gene:

TBC1D5

SOURCE GeneReport for Unigene cluster for TBC1D5 Gene:

Hs.475629

Evidence on tissue expression from TISSUES for TBC1D5 Gene

  • Blood(4.2)
  • Bone marrow(4.2)
  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with TBC1D5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TBC1D5 Gene

Orthologs for TBC1D5 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TBC1D5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TBC1D5 33 34
  • 99.8 (n)
dog
(Canis familiaris)
Mammalia TBC1D5 33 34
  • 91.05 (n)
mouse
(Mus musculus)
Mammalia Tbc1d5 33 16 34
  • 87.55 (n)
cow
(Bos Taurus)
Mammalia TBC1D5 33 34
  • 86.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D5 34
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tbc1d5 33
  • 85.89 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D5 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves TBC1D5 33 34
  • 75.59 (n)
lizard
(Anolis carolinensis)
Reptilia TBC1D5 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d5 33
  • 71.94 (n)
Str.17379 33
zebrafish
(Danio rerio)
Actinopterygii tbc1d5 33 34
  • 66.92 (n)
zgc63624 33
fruit fly
(Drosophila melanogaster)
Insecta CG8449 34
  • 28 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea rbg-3 34
  • 31 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP6 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToOne
Species where no ortholog for TBC1D5 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)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for TBC1D5 Gene

ENSEMBL:
Gene Tree for TBC1D5 (if available)
TreeFam:
Gene Tree for TBC1D5 (if available)

Paralogs for TBC1D5 Gene

Paralogs for TBC1D5 Gene

genes like me logo Genes that share paralogs with TBC1D5: view

Variants for TBC1D5 Gene

Sequence variations from dbSNP and Humsavar for TBC1D5 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000000661 -- 17,342,619(-) C/T intron_variant
rs1000011848 -- 17,409,394(-) C/T intron_variant
rs1000012684 -- 17,554,100(-) AAGA/ genic_upstream_transcript_variant, intron_variant
rs1000015854 -- 17,402,561(-) T/C intron_variant
rs1000017827 -- 17,534,269(-) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TBC1D5 Gene

Variant ID Type Subtype PubMed ID
dgv8248n54 CNV loss 21841781
dgv8249n54 CNV loss 21841781
dgv8250n54 CNV loss 21841781
esv1204331 CNV deletion 17803354
esv22074 CNV loss 19812545
esv2211188 CNV deletion 18987734
esv25343 CNV loss 19812545
esv2583047 CNV deletion 19546169
esv2622635 CNV insertion 19546169
esv2663694 CNV deletion 23128226
esv2669615 CNV deletion 23128226
esv2724980 CNV deletion 23290073
esv2724981 CNV deletion 23290073
esv3388594 CNV duplication 20981092
esv3561541 CNV deletion 23714750
esv3561542 CNV deletion 23714750
esv3561543 CNV deletion 23714750
esv3568633 CNV loss 25503493
esv3595418 CNV loss 21293372
esv3595419 CNV loss 21293372
esv3595420 CNV loss 21293372
esv3595422 CNV loss 21293372
esv3595425 CNV loss 21293372
esv4814 CNV loss 18987735
esv6157 CNV loss 19470904
nsv1008636 CNV gain 25217958
nsv1009700 CNV loss 25217958
nsv1013069 CNV loss 25217958
nsv1072290 CNV deletion 25765185
nsv1110945 OTHER inversion 24896259
nsv1127944 CNV deletion 24896259
nsv1149871 CNV deletion 26484159
nsv3715 CNV deletion 18451855
nsv442855 CNV loss 18776908
nsv470439 CNV loss 18288195
nsv478271 CNV novel sequence insertion 20440878
nsv498992 CNV loss 21111241
nsv514139 CNV gain+loss 21397061
nsv589841 CNV loss 21841781
nsv589844 CNV loss 21841781
nsv589850 CNV loss 21841781
nsv820175 CNV loss 19587683
nsv822026 CNV loss 20364138
nsv956837 CNV deletion 24416366
nsv963550 CNV deletion 23825009
nsv963551 CNV deletion 23825009
nsv966992 CNV duplication 23825009
nsv999594 CNV loss 25217958

Variation tolerance for TBC1D5 Gene

Residual Variation Intolerance Score: 19.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.96; 49.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D5 Gene

Disorders for TBC1D5 Gene

Additional Disease Information for TBC1D5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TBC1D5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TBC1D5 Gene

Publications for TBC1D5 Gene

  1. Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. (PMID: 19531583) Seaman MN … Bright N (Journal of cell science 2009) 2 3 4 58
  2. TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy. (PMID: 24603492) Popovic D … Dikic I (EMBO reports 2014) 3 4 58
  3. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. (PMID: 22354992) Popovic D … Dikic I (Molecular and cellular biology 2012) 3 4 58
  4. 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
  5. The cargo-selective retromer complex is a recruiting hub for protein complexes that regulate endosomal tubule dynamics. (PMID: 20923837) Harbour ME … Seaman MN (Journal of cell science 2010) 3 4 58

Products for TBC1D5 Gene

Sources for TBC1D5 Gene

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