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

Summary

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, Nov 2024]
Expression: Ubiquitous expression in fat (RPKM 12.8), kidney (RPKM 8.0) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

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_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

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.
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.
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.
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.
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.
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.
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.
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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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 Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH103759 (e-PCR)
- UniSTS:98084

RH120869 (e-PCR)
- UniSTS:12093

SHGC-148131 (e-PCR)
- UniSTS:176217

D17S851E (e-PCR)
- UniSTS:472967

RH46396 (e-PCR)
- UniSTS:43914

SHGC-56719 (e-PCR)
- UniSTS:20168

RH12358 (e-PCR)
- UniSTS:29151

RH94345 (e-PCR)
- UniSTS:87011

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)

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
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
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
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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

79932343..80035872 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047435346.1 → XP_047291302.1 TBC1 domain family member 16 isoform X7
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
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
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
XM_047435356.1 → XP_047291312.1 TBC1 domain family member 16 isoform X19
XM_047435354.1 → XP_047291310.1 TBC1 domain family member 16 isoform X18
XM_047435351.1 → XP_047291307.1 TBC1 domain family member 16 isoform X15
XM_047435350.1 → XP_047291306.1 TBC1 domain family member 16 isoform X14
XM_047435357.1 → XP_047291313.1 TBC1 domain family member 16 isoform X20
XM_047435353.1 → XP_047291309.1 TBC1 domain family member 16 isoform X17
XM_047435359.1 → XP_047291315.1 TBC1 domain family member 16 isoform X22
XM_047435352.1 → XP_047291308.1 TBC1 domain family member 16 isoform X16
XM_047435358.1 → XP_047291314.1 TBC1 domain family member 16 isoform X21
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
XM_047435349.1 → XP_047291305.1 TBC1 domain family member 16 isoform X13
XM_047435348.1 → XP_047291304.1 TBC1 domain family member 16 isoform X11
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
XM_047435344.1 → XP_047291300.1 TBC1 domain family member 16 isoform X5
XM_047435342.1 → XP_047291298.1 TBC1 domain family member 16 isoform X4

UniProtKB/Swiss-Prot

B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
XM_047435347.1 → XP_047291303.1 TBC1 domain family member 16 isoform X7
XM_047435343.1 → XP_047291299.1 TBC1 domain family member 16 isoform X5
XM_047435345.1 → XP_047291301.1 TBC1 domain family member 16 isoform X6
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
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
XM_017024185.2 → XP_016879674.1 TBC1 domain family member 16 isoform X10
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
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

NW_025791802.1 Reference GRCh38.p14 PATCHES

Range

33071..58783 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

80830270..80934528 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054315058.1 → XP_054171033.1 TBC1 domain family member 16 isoform X7
XM_054315056.1 → XP_054171031.1 TBC1 domain family member 16 isoform X5
XM_054315054.1 → XP_054171029.1 TBC1 domain family member 16 isoform X4

UniProtKB/Swiss-Prot

B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
XM_054315050.1 → XP_054171025.1 TBC1 domain family member 16 isoform X1
XM_054315059.1 → XP_054171034.1 TBC1 domain family member 16 isoform X7
XM_054315055.1 → XP_054171030.1 TBC1 domain family member 16 isoform X5
XM_054315051.1 → XP_054171026.1 TBC1 domain family member 16 isoform X2
XM_054315057.1 → XP_054171032.1 TBC1 domain family member 16 isoform X6
XM_054315052.1 → XP_054171027.1 TBC1 domain family member 16 isoform X3
XM_054315053.1 → XP_054171028.1 TBC1 domain family member 16 isoform X4

UniProtKB/Swiss-Prot

B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
XM_054315049.1 → XP_054171024.1 TBC1 domain family member 16 isoform X1
XM_054315071.1 → XP_054171046.1 TBC1 domain family member 16 isoform X19
XM_054315070.1 → XP_054171045.1 TBC1 domain family member 16 isoform X18
XM_054315067.1 → XP_054171042.1 TBC1 domain family member 16 isoform X15
XM_054315066.1 → XP_054171041.1 TBC1 domain family member 16 isoform X14
XM_054315072.1 → XP_054171047.1 TBC1 domain family member 16 isoform X20
XM_054315069.1 → XP_054171044.1 TBC1 domain family member 16 isoform X17
XM_054315068.1 → XP_054171043.1 TBC1 domain family member 16 isoform X16
XM_054315074.1 → XP_054171049.1 TBC1 domain family member 16 isoform X22
XM_054315073.1 → XP_054171048.1 TBC1 domain family member 16 isoform X21
XM_054315064.1 → XP_054171039.1 TBC1 domain family member 16 isoform X12
XM_054315063.1 → XP_054171038.1 TBC1 domain family member 16 isoform X11
XM_054315065.1 → XP_054171040.1 TBC1 domain family member 16 isoform X13
XM_054315062.1 → XP_054171037.1 TBC1 domain family member 16 isoform X10
XM_054315061.1 → XP_054171036.1 TBC1 domain family member 16 isoform X9
XM_054315060.1 → XP_054171035.1 TBC1 domain family member 16 isoform X8