TBC1D3
protein-codingTBC1 domain family member 3
Gene summary
Predicted to enable GTPase activator activity. Predicted to be located in early endosome membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TBC1D3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001123391.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 3 | 0 | 4 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001116863.3 | 13 | MANE Select | |
| Ensembl | ENSP00000478683.1 | 13 | MANE Select | |
| Ensembl | ENSP00000566580.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- TBC/RABGAPs
- Membrane Trafficking
- Rab regulation of trafficking
Biological Process
- intracellular protein transport
- activation of GTPase activity
- regulation of cilium assembly
Molecular Function
- GTPase activator activity
- Rab GTPase binding
Cellular Component
- plasma membrane
- early endosome membrane
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11. {ECO:0000269|PubMed:12359748}.;
Essentials
- Essential (CRISPR)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0279
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |