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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. 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).

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

Genomics for TBC1D5 Gene

Regulatory Elements for TBC1D5 Gene

Enhancers for TBC1D5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F018422 0.2 ENCODE 13.1 +20.3 20251 5.2 PKNOX1 SIN3A FEZF1 ZNF2 YY1 GLIS2 ZNF263 SP3 JUNB TBX21 SATB1 SATB1-AS1 TBC1D5 GC03P018426 ENSG00000272477
GH03F018420 0.5 Ensembl 12.2 +24.0 24017 0.4 JUND SATB1 SATB1-AS1 TBC1D5 GC03P018426 ENSG00000272477
GH03F018419 1.4 Ensembl 12.2 +25.4 25417 0.4 ZNF692 SCRT2 SATB1 SATB1-AS1 TBC1D5 GC03P018426 ENSG00000272477
GH03F018418 0.5 Ensembl 12 +26.6 26617 0.4 SATB1 SATB1-AS1 TBC1D5 GC03P018426 ENSG00000272477
GH03F018502 0.4 ENCODE 11.8 -57.3 -57307 0.2 ZFHX2 SATB1 SATB1-AS1 TBC1D5 GC03M018512 GC03P018474
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around TBC1D5 on UCSC Golden Path with GeneCards custom track

Promoters for TBC1D5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001404848 317 5000 PKNOX1 ZNF76 ZNF2 RAD21 GLIS2 ZNF366 SCRT2 EGR2 ZNF680 REST

Genomic Location for TBC1D5 Gene

Chromosome:
3
Start:
17,157,162 bp from pter
End:
18,444,817 bp from pter
Size:
1,287,656 bases
Orientation:
Minus strand

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};

    Alternative splice isoforms for TBC1D5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D5 Gene

Post-translational modifications for TBC1D5 Gene

  • Ubiquitination at Lys 456
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TBC1D5 Gene

Domains & Families for TBC1D5 Gene

Protein Domains for TBC1D5 Gene

InterPro:
Blocks:
ProtoNet:

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.
  • Contains 1 Rab-GAP TBC domain.
genes like me logo Genes that share domains with TBC1D5: view

No data available for Gene Families for TBC1D5 Gene

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).

Gene Ontology (GO) - Molecular Function for TBC1D5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA,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

Inhibitory RNA Products

Flow Cytometry 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
Jensen Localization Image for TBC1D5 Gene COMPARTMENTS Subcellular localization image for TBC1D5 gene
Compartment Confidence
endosome 5
vacuole 5
cytosol 3
golgi apparatus 2
nucleus 2
plasma membrane 2
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for TBC1D5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005776 autophagosome IEA,IDA 22354992
GO:0005829 cytosol IEA --
GO:0010008 endosome membrane IEA,IDA 20923837
GO:0016020 membrane IEA --
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 IEA --
GO:0010508 positive regulation of autophagy IDA 22354992
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

Transcripts for TBC1D5 Gene

Unigene Clusters for TBC1D5 Gene

TBC1 domain family, member 5:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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
genes like me logo Genes that share expression patterns with TBC1D5: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.8 (n)
dog
(Canis familiaris)
Mammalia TBC1D5 34 35
  • 91.05 (n)
mouse
(Mus musculus)
Mammalia Tbc1d5 34 16 35
  • 87.55 (n)
cow
(Bos Taurus)
Mammalia TBC1D5 34 35
  • 86.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D5 35
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tbc1d5 34
  • 85.89 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D5 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves TBC1D5 34 35
  • 75.59 (n)
lizard
(Anolis carolinensis)
Reptilia TBC1D5 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d5 34
  • 71.94 (n)
Str.17379 34
zebrafish
(Danio rerio)
Actinopterygii tbc1d5 34 35
  • 66.92 (n)
zgc63624 34
fruit fly
(Drosophila melanogaster)
Insecta CG8449 35
  • 28 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea rbg-3 35
  • 31 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP6 37
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs10049142 -- 17,345,569(+) TACTG(A/G)GTATA intron-variant
rs10049143 -- 17,345,588(+) GGACT(A/C)TAAAT intron-variant
rs10188112 -- 17,615,835(-) GAGCT(C/G)GTTTT intron-variant
rs10212255 -- 17,409,616(+) actca(A/G)aagtg intron-variant
rs10433559 -- 17,724,467(+) ccctg(C/T)atagt 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)

Relevant External Links 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

Relevant External Links for TBC1D5

Genetic Association Database (GAD)
TBC1D5
Human Genome Epidemiology (HuGE) Navigator
TBC1D5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TBC1D5

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 M.N. … Bright N. (J. Cell. Sci. 2009) 2 3 4 64
  2. TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy. (PMID: 24603492) Popovic D. … Dikic I. (EMBO Rep. 2014) 3 4 64
  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. (Mol. Cell. Biol. 2012) 3 4 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. The cargo-selective retromer complex is a recruiting hub for protein complexes that regulate endosomal tubule dynamics. (PMID: 20923837) Harbour M.E. … Seaman M.N. (J. Cell. Sci. 2010) 3 4 64

Products for TBC1D5 Gene

Sources for TBC1D5 Gene

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