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TBC1D16 TBC1 domain family member 16 [ Homo sapiens (human) ]

Gene ID: 125058, updated on 18-Sep-2024

Summary

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Official Symbol
TBC1D16provided by HGNC
Official Full Name
TBC1 domain family member 16provided by HGNC
Primary source
HGNC:HGNC:28356
See related
Ensembl:ENSG00000167291 MIM:616637; AllianceGenome:HGNC:28356
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables GTPase activator activity. Involved in regulation of receptor recycling. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 12.8), kidney (RPKM 8.0) and 23 other tissues See more
Orthologs
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Genomic context

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See TBC1D16 in Genome Data Viewer
Location:
17q25.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (79932343..80035872, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80830270..80934528, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77906142..78009671, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77809787-77810608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9092 Neighboring gene Sharpr-MPRA regulatory region 202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77811431-77812254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77812255-77813076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77814721-77815544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77815545-77816366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9095 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77824032-77825231 Neighboring gene chromobox 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12924 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77842993-77843520 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77843521-77844050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77862335-77862836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77875585-77876566 Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917109-77917834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917835-77918560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77921171-77921997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922367-77922950 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77923535-77924118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922951-77923534 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77924703-77925286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77925287-77925870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77930057-77930557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77948310-77949214 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77951994-77952173 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9097 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78003463-78004332 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12927 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78018463-78018964 Neighboring gene uncharacterized LOC124904074 Neighboring gene coiled-coil domain 40 molecular ruler complex subunit Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78056255-78056756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78064021-78064580 Neighboring gene microRNA 1268b

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 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication.
    Title: Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication.
  2. TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients.
    Title: TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients.
  3. Findings suggest characteristic DNA methylation changes in TBC1D16 is relatively common tumor-associated epigenetic events in multiple tumor types, which is consistent with a potential role as more general drivers of tumor progression.
    Title: Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types.
  4. TBC1D16 is a predictive marker for favorable prognosis of Epithelial ovarian cancer.
    Title: Expression of TBC1D16 Is Associated with Favorable Prognosis of Epithelial Ovarian Cancer.
  5. Bipolar disorder participants with a history of Suicidal behavior showed less overall methylation in the intron 3 of TRE2/BUB2/CDC16 domain family member 16 (TBC1D16).
    Title: Investigation of correlations between DNA methylation, suicidal behavior and aging.
  6. RAB5C is identified as a new TBC1D16 target and showed that it regulates EGFR in melanoma cells.
    Title: Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.
  7. TBC1D16 is a GTPase activating protein for Rab4A that regulates transferrin receptor recycling and EGFR trafficking and signaling.
    Title: TBC1D16 is a Rab4A GTPase activating protein that regulates receptor recycling and EGF receptor signaling.
  8. TBC1D16 and RAB27A, were identified known drivers of melanoma both are involved in the regulation of vesicular trafficking, which highlights this process as important for proliferation in melanoma.
    Title: An integrated approach to uncover drivers of cancer.
Submit: New GeneRIF Correction

Phenotypes

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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

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

  • FLJ20748, MGC25062, DKFZp451F1311

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
NOT involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of receptor recycling IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
TBC1 domain family member 16
Names
CTD-2529O21.1

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_001271844.2 → NP_001258773.1  TBC1 domain family member 16 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains multiple differences in the 5' UTR and coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC100791, BC062601
    Consensus CDS
    CCDS62353.1
    UniProtKB/Swiss-Prot
    Q8TBP0
    Related
    ENSP00000461522.1, ENST00000576768.5
    Conserved Domains (1) summary
    smart00164
    Location:58 → 277
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  2. NM_001271845.2 → NP_001258774.1  TBC1 domain family member 16 isoform c

    See identical proteins and their annotated locations for NP_001258774.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains multiple differences in the 5' UTR and coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC100791, BC036947, BC062601
    Consensus CDS
    CCDS62351.1
    UniProtKB/Swiss-Prot
    Q8TBP0
    Related
    ENSP00000341517.7, ENST00000340848.11
    Conserved Domains (1) summary
    smart00164
    Location:62 → 290
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. NM_001271846.2 → NP_001258775.1  TBC1 domain family member 16 isoform d

    See identical proteins and their annotated locations for NP_001258775.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains multiple differences in both UTRs and the coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (d) is shorter and has distinct N- and C-termini, compared to isoform a.
    Source sequence(s)
    BC001525, BX092567, CR936670
    Consensus CDS
    CCDS62352.1
    UniProtKB/TrEMBL
    I3L0V9
    Related
    ENSP00000458766.1, ENST00000572862.5
    Conserved Domains (1) summary
    smart00164
    Location:62 → 272
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  4. NM_019020.4 → NP_061893.2  TBC1 domain family member 16 isoform a

    See identical proteins and their annotated locations for NP_061893.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC100791, AC116025, BC028290, BC062601, CN361974
    Consensus CDS
    CCDS11766.1
    UniProtKB/Swiss-Prot
    B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
    Related
    ENSP00000309794.2, ENST00000310924.7
    Conserved Domains (1) summary
    smart00164
    Location:424 → 652
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    79932343..80035872 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435346.1 → XP_047291302.1  TBC1 domain family member 16 isoform X7

  2. XM_024450577.2 → XP_024306345.1  TBC1 domain family member 16 isoform X1

    Conserved Domains (1) summary
    smart00164
    Location:424 → 709
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. XM_024450579.2 → XP_024306347.1  TBC1 domain family member 16 isoform X2

    Conserved Domains (1) summary
    smart00164
    Location:423 → 708
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  4. XM_024450580.2 → XP_024306348.1  TBC1 domain family member 16 isoform X3

    Conserved Domains (1) summary
    smart00164
    Location:419 → 695
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  5. XM_047435356.1 → XP_047291312.1  TBC1 domain family member 16 isoform X19

  6. XM_047435354.1 → XP_047291310.1  TBC1 domain family member 16 isoform X18

  7. XM_047435351.1 → XP_047291307.1  TBC1 domain family member 16 isoform X15

  8. XM_047435350.1 → XP_047291306.1  TBC1 domain family member 16 isoform X14

  9. XM_047435357.1 → XP_047291313.1  TBC1 domain family member 16 isoform X20

  10. XM_047435353.1 → XP_047291309.1  TBC1 domain family member 16 isoform X17

  11. XM_047435359.1 → XP_047291315.1  TBC1 domain family member 16 isoform X22

  12. XM_047435352.1 → XP_047291308.1  TBC1 domain family member 16 isoform X16

  13. XM_047435358.1 → XP_047291314.1  TBC1 domain family member 16 isoform X21

  14. XM_017024187.2 → XP_016879676.1  TBC1 domain family member 16 isoform X12

    Conserved Domains (2) summary
    smart00164
    Location:200 → 428
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    PRK12323
    Location:31 → 188
    PRK12323; DNA polymerase III subunit gamma/tau

  15. XM_047435349.1 → XP_047291305.1  TBC1 domain family member 16 isoform X13

  16. XM_047435348.1 → XP_047291304.1  TBC1 domain family member 16 isoform X11

  17. XM_024450582.2 → XP_024306350.1  TBC1 domain family member 16 isoform X23

    Conserved Domains (1) summary
    smart00164
    Location:53 → 338
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  18. XM_047435344.1 → XP_047291300.1  TBC1 domain family member 16 isoform X5

  19. XM_047435342.1 → XP_047291298.1  TBC1 domain family member 16 isoform X4

    UniProtKB/Swiss-Prot
    B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

  20. XM_047435347.1 → XP_047291303.1  TBC1 domain family member 16 isoform X7

  21. XM_047435343.1 → XP_047291299.1  TBC1 domain family member 16 isoform X5

  22. XM_047435345.1 → XP_047291301.1  TBC1 domain family member 16 isoform X6

  23. XM_006721694.4 → XP_006721757.1  TBC1 domain family member 16 isoform X4

    See identical proteins and their annotated locations for XP_006721757.1

    UniProtKB/Swiss-Prot
    B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
    Conserved Domains (1) summary
    smart00164
    Location:424 → 652
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  24. XM_024450578.2 → XP_024306346.1  TBC1 domain family member 16 isoform X1

    Conserved Domains (1) summary
    smart00164
    Location:424 → 709
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  25. XM_017024185.2 → XP_016879674.1  TBC1 domain family member 16 isoform X10

  26. XM_005257052.4 → XP_005257109.1  TBC1 domain family member 16 isoform X9

    Conserved Domains (1) summary
    smart00164
    Location:424 → 634
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  27. XM_024450581.2 → XP_024306349.1  TBC1 domain family member 16 isoform X8

    Conserved Domains (1) summary
    smart00164
    Location:424 → 691
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791802.1 Reference GRCh38.p14 PATCHES

    Range
    33071..58783 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    80830270..80934528 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315058.1 → XP_054171033.1  TBC1 domain family member 16 isoform X7

  2. XM_054315056.1 → XP_054171031.1  TBC1 domain family member 16 isoform X5

  3. XM_054315054.1 → XP_054171029.1  TBC1 domain family member 16 isoform X4

    UniProtKB/Swiss-Prot
    B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

  4. XM_054315050.1 → XP_054171025.1  TBC1 domain family member 16 isoform X1

  5. XM_054315059.1 → XP_054171034.1  TBC1 domain family member 16 isoform X7

  6. XM_054315055.1 → XP_054171030.1  TBC1 domain family member 16 isoform X5

  7. XM_054315051.1 → XP_054171026.1  TBC1 domain family member 16 isoform X2

  8. XM_054315057.1 → XP_054171032.1  TBC1 domain family member 16 isoform X6

  9. XM_054315052.1 → XP_054171027.1  TBC1 domain family member 16 isoform X3

  10. XM_054315053.1 → XP_054171028.1  TBC1 domain family member 16 isoform X4

    UniProtKB/Swiss-Prot
    B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

  11. XM_054315049.1 → XP_054171024.1  TBC1 domain family member 16 isoform X1

  12. XM_054315071.1 → XP_054171046.1  TBC1 domain family member 16 isoform X19

  13. XM_054315070.1 → XP_054171045.1  TBC1 domain family member 16 isoform X18

  14. XM_054315067.1 → XP_054171042.1  TBC1 domain family member 16 isoform X15

  15. XM_054315066.1 → XP_054171041.1  TBC1 domain family member 16 isoform X14

  16. XM_054315072.1 → XP_054171047.1  TBC1 domain family member 16 isoform X20

  17. XM_054315069.1 → XP_054171044.1  TBC1 domain family member 16 isoform X17

  18. XM_054315068.1 → XP_054171043.1  TBC1 domain family member 16 isoform X16

  19. XM_054315074.1 → XP_054171049.1  TBC1 domain family member 16 isoform X22

  20. XM_054315073.1 → XP_054171048.1  TBC1 domain family member 16 isoform X21

  21. XM_054315064.1 → XP_054171039.1  TBC1 domain family member 16 isoform X12

  22. XM_054315063.1 → XP_054171038.1  TBC1 domain family member 16 isoform X11

  23. XM_054315065.1 → XP_054171040.1  TBC1 domain family member 16 isoform X13

  24. XM_054315062.1 → XP_054171037.1  TBC1 domain family member 16 isoform X10

  25. XM_054315061.1 → XP_054171036.1  TBC1 domain family member 16 isoform X9

  26. XM_054315060.1 → XP_054171035.1  TBC1 domain family member 16 isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TBP0.1 GenPept UniProtKB/Swiss-Prot:Q8TBP0

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