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    TBC1D15 TBC1 domain family member 15 [ Homo sapiens (human) ]

    Gene ID: 64786, updated on 9-Dec-2024

    Summary

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    Official Symbol
    TBC1D15provided by HGNC
    Official Full Name
    TBC1 domain family member 15provided by HGNC
    Primary source
    HGNC:HGNC:25694
    See related
    Ensembl:ENSG00000121749 MIM:612662; AllianceGenome:HGNC:25694
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RAB7-GAP
    Summary
    This gene encodes a member of the Ras-like proteins in brain-GTPase activating protein superfamily that share a conserved Tre-2/Bub2/Cdc16 domain. The encoded protein interacts with Ras-like protein in brain 5A and may function as a regulator of intracellular trafficking. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 10.9), adrenal (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D15 in Genome Data Viewer
    Location:
    12q21.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (71839759..71924313)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (71817237..71901791)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (72233539..72318093)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:72103459-72104658 Neighboring gene uncharacterized LOC107984530 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:72119048-72120247 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:72141645-72141854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6664 Neighboring gene RAB21, member RAS oncogene family Neighboring gene MPRA-validated peak1826 silencer Neighboring gene Sharpr-MPRA regulatory region 15327 Neighboring gene MRS2 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:72332491-72332790 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:72342997-72343855 Neighboring gene NANOG hESC enhancer GRCh37_chr12:72352432-72352933 Neighboring gene Sharpr-MPRA regulatory region 15256 Neighboring gene NANOG hESC enhancer GRCh37_chr12:72431129-72431630 Neighboring gene tryptophan hydroxylase 2 Neighboring gene thyrotropin releasing hormone degrading enzyme Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:72608405-72609204 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:72609205-72610002 Neighboring gene TRHDE antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. IFNB/interferon-β regulates autophagy via a MIR1-TBC1D15-RAB7 pathway. Ejlerskov P, et al. Autophagy, 2020 Apr. PMID 31958036, Free PMC Article
    2. TBC1D15 affects glucose uptake by regulating GLUT4 translocation. Wu J, et al. Gene, 2019 Jan 30. PMID 30316925
    3. Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy. Yamano K, et al. Elife, 2014 Feb 25. PMID 24569479, Free PMC Article
    4. The REEP5/TRAM1 complex binds SARS-CoV-2 NSP3 and promotes virus replication. Li J, et al. J Virol, 2023 Oct 31. PMID 37768083, Free PMC Article
    5. Silencing of TBC1D15 promotes RhoA activation and membrane blebbing. Takahara Y, et al. Mol Cell Biochem, 2014 Apr. PMID 24337944

    See all (107) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NOTCH localizes to mitochondria through the TBC1D15-FIS1 interaction and is stabilized via blockade of E3 ligase and CDK8 recruitment to reprogram tumor-initiating cells.
      Title: NOTCH localizes to mitochondria through the TBC1D15-FIS1 interaction and is stabilized via blockade of E3 ligase and CDK8 recruitment to reprogram tumor-initiating cells.
    2. A conserved, noncanonical insert in FIS1 mediates TBC1D15 and DRP1 recruitment for mitochondrial fission.
      Title: A conserved, noncanonical insert in FIS1 mediates TBC1D15 and DRP1 recruitment for mitochondrial fission.
    3. IFNB/interferon-beta regulates autophagy via a MIR1-TBC1D15-RAB7 pathway.
      Title: IFNB/interferon-β regulates autophagy via a MIR1-TBC1D15-RAB7 pathway.
    4. p53 destabilizing protein skews asymmetric division and enhances NOTCH activation to direct self-renewal of TICs.
      Title: p53 destabilizing protein skews asymmetric division and enhances NOTCH activation to direct self-renewal of TICs.
    5. Here, we demonstrate that this cellular cholesterol imbalance is due to AnxA6 promoting Rab7 inactivation via TBC1D15, a Rab7-GAP.
      Title: Annexin A6 modulates TBC1D15/Rab7/StARD3 axis to control endosomal cholesterol export in NPC1 cells.
    6. Report provides evidence for a new function of TBC1D15 in the control of GLUT4 vesicles translocation through regulating Rab7 activity. Glucose uptake was greatly reduced when TBC1D15 was knocked out.
      Title: TBC1D15 affects glucose uptake by regulating GLUT4 translocation.
    7. Demonstrate that TBC1D15 and TBC1D17 mediate proper autophagic encapsulation of mitochondria by regulating Rab7 activity at the interface between mitochondria and isolation membranes.
      Title: Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy.
    8. TBC1D15 is required for the accumulation of RhoA.
      Title: Silencing of TBC1D15 promotes RhoA activation and membrane blebbing.
    9. Fis1 acts as a mitochondrial recruitment factor for TBC1D15 that is involved in regulation of mitochondrial morphology.
      Title: Fis1 acts as a mitochondrial recruitment factor for TBC1D15 that is involved in regulation of mitochondrial morphology.
    10. although only TBC1D15/Rab7-GAP altered Rab7-GTP levels, both Rab7-GAP and mVps39 regulate lysosomal morphology and play a role in maintaining growth factor dependence
      Title: Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with TBC1 domain family, member 15 (TBC1D15) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12085, FLJ33191, DKFZp686M1379, DKFZp761D0223

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 15
    Names
    GAP for RAB7
    GTPase-activating protein RAB7
    Tre-2-budding uninhibited by benzimidazole-cell division cycle 16 domain, domain family member 15
    Tre2/Bub2/Cdc16 domain family member 15
    NP_001139685.2
    NP_001139686.2
    NP_001372777.1
    NP_001372778.1
    NP_001372779.1
    NP_001372780.1
    NP_001372781.1
    NP_001372782.1
    NP_001372783.1
    NP_073608.4
    XP_006719627.1
    XP_011536981.1
    XP_011536983.1
    XP_047285318.1
    XP_047285319.1
    XP_047285320.1
    XP_047285321.1
    XP_047285322.1
    XP_054228887.1
    XP_054228888.1
    XP_054228889.1
    XP_054228890.1
    XP_054228891.1
    XP_054228892.1
    XP_054228893.1
    XP_054228894.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001146213.3 → NP_001139685.2  TBC1 domain family member 15 isoform 3

      See identical proteins and their annotated locations for NP_001139685.2

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Consensus CDS
      CCDS53814.1
      UniProtKB/Swiss-Prot
      Q8TC07
      Related
      ENSP00000420678.2, ENST00000485960.7
      Conserved Domains (2) summary
      pfam12068
      Location:8 → 224
      DUF3548; Domain of unknown function (DUF3548)
      smart00164
      Location:326 → 561
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. NM_001146214.3 → NP_001139686.2  TBC1 domain family member 15 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Related
      ENSP00000318262.6, ENST00000319106.12
      Conserved Domains (2) summary
      smart00164
      Location:227 → 462
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:24 → 112
      DUF3548; Domain of unknown function (DUF3548)

    3. NM_001385848.1 → NP_001372777.1  TBC1 domain family member 15 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:326 → 559
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:10 → 211
      DUF3548; Domain of unknown function (DUF3548)

    4. NM_001385849.1 → NP_001372778.1  TBC1 domain family member 15 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:315 → 550
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:10 → 211
      DUF3548; Domain of unknown function (DUF3548)

    5. NM_001385850.1 → NP_001372779.1  TBC1 domain family member 15 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:326 → 541
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:10 → 211
      DUF3548; Domain of unknown function (DUF3548)

    6. NM_001385851.1 → NP_001372780.1  TBC1 domain family member 15 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      pfam12068
      Location:10 → 211
      DUF3548; Domain of unknown function (DUF3548)
      cl02495
      Location:326 → 539
      RabGAP-TBC; Rab-GTPase-TBC domain

    7. NM_001385852.1 → NP_001372781.1  TBC1 domain family member 15 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:301 → 536
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:10 → 186
      DUF3548; Domain of unknown function (DUF3548)

    8. NM_001385853.1 → NP_001372782.1  TBC1 domain family member 15 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:326 → 522
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:10 → 211
      DUF3548; Domain of unknown function (DUF3548)

    9. NM_001385854.1 → NP_001372783.1  TBC1 domain family member 15 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Conserved Domains (2) summary
      smart00164
      Location:268 → 503
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      pfam12068
      Location:4 → 153
      DUF3548; Domain of unknown function (DUF3548)

    10. NM_022771.6 → NP_073608.4  TBC1 domain family member 15 isoform 1

      See identical proteins and their annotated locations for NP_073608.4

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109
      Consensus CDS
      CCDS31858.1
      UniProtKB/Swiss-Prot
      B4DMT9, B9A6L6, J3KNI9, Q8TC07, Q9HA83
      Related
      ENSP00000448182.1, ENST00000550746.5
      Conserved Domains (2) summary
      pfam12068
      Location:8 → 219
      DUF3548; Domain of unknown function (DUF3548)
      smart00164
      Location:343 → 578
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    RNA

    1. NR_027449.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    2. NR_169765.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    3. NR_169766.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    4. NR_169767.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    5. NR_169768.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    6. NR_169769.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    7. NR_169770.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    8. NR_169771.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    9. NR_169772.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    10. NR_169773.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    11. NR_169774.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    12. NR_169775.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    13. NR_169776.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    14. NR_169777.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    15. NR_169778.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    16. NR_169779.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    17. NR_169780.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    18. NR_169781.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    19. NR_169782.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    20. NR_169783.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    21. NR_169784.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    22. NR_169785.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    23. NR_169786.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    24. NR_169787.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    25. NR_169788.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    26. NR_169789.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC089984, AC090109

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      71839759..71924313
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538679.1 → XP_011536981.1  TBC1 domain family member 15 isoform X4

      See identical proteins and their annotated locations for XP_011536981.1

      Conserved Domains (2) summary
      pfam12068
      Location:1 → 120
      DUF3548; Domain of unknown function (DUF3548)
      smart00164
      Location:244 → 479
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. XM_047429362.1 → XP_047285318.1  TBC1 domain family member 15 isoform X2

    3. XM_047429363.1 → XP_047285319.1  TBC1 domain family member 15 isoform X3

    4. XM_047429364.1 → XP_047285320.1  TBC1 domain family member 15 isoform X4

    5. XM_011538681.4 → XP_011536983.1  TBC1 domain family member 15 isoform X5

      Conserved Domains (2) summary
      pfam12068
      Location:8 → 219
      DUF3548; Domain of unknown function (DUF3548)
      smart00164
      Location:343 → 453
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    6. XM_047429365.1 → XP_047285321.1  TBC1 domain family member 15 isoform X6

    7. XM_006719564.3 → XP_006719627.1  TBC1 domain family member 15 isoform X1

      Conserved Domains (2) summary
      pfam12068
      Location:19 → 227
      DUF3548; Domain of unknown function (DUF3548)
      smart00164
      Location:351 → 586
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    8. XM_047429366.1 → XP_047285322.1  TBC1 domain family member 15 isoform X7

      UniProtKB/TrEMBL
      A8K8E1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      71817237..71901791
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372916.1 → XP_054228891.1  TBC1 domain family member 15 isoform X4

    2. XM_054372913.1 → XP_054228888.1  TBC1 domain family member 15 isoform X2

    3. XM_054372914.1 → XP_054228889.1  TBC1 domain family member 15 isoform X3

    4. XM_054372915.1 → XP_054228890.1  TBC1 domain family member 15 isoform X4

    5. XM_054372917.1 → XP_054228892.1  TBC1 domain family member 15 isoform X5

    6. XM_054372918.1 → XP_054228893.1  TBC1 domain family member 15 isoform X6

    7. XM_054372912.1 → XP_054228887.1  TBC1 domain family member 15 isoform X1

    8. XM_054372919.1 → XP_054228894.1  TBC1 domain family member 15 isoform X7

      UniProtKB/TrEMBL
      A8K8E1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TC07.2 GenPept UniProtKB/Swiss-Prot:Q8TC07

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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