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

Gene ID: 64786, updated on 7-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (71839759..71924313)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (71817237..71901791)
105.20220307 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. p53 destabilizing protein skews asymmetric division and enhances NOTCH activation to direct self-renewal of TICs. Choi HY, et al. Nat Commun, 2020 Jun 17. PMID 32555153, Free PMC Article
  3. TBC1D15 affects glucose uptake by regulating GLUT4 translocation. Wu J, et al. Gene, 2019 Jan 30. PMID 30316925
  4. Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy. Yamano K, et al. Elife, 2014 Feb 25. PMID 24569479, 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 (85) 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)

Genotypes

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 activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

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