TBC1D17
protein-codingTBC1 domain family member 17, the group of MicroRNA protein coding host genes
Gene summary
Predicted to enable GTPase activator activity. Involved in retrograde transport, endosome to Golgi. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.1 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 TBC1D17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024682.3. 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 | 1 | 1 | ||||
| missense | 136 | 3 | 139 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 140 | 3 | 0 | 143 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078958.2 | 17 | MANE Select | |
| Ensembl | ENSP00000221543.4 | 17 | MANE Select | |
| RefSeq | NP_001161694.1 | 16 | Standard | |
| Ensembl | ENSP00000446323.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mitophagy - animal - Homo sapiens (human)
- Vesicle-mediated transport
- TBC/RABGAPs
- Membrane Trafficking
- Rab regulation of trafficking
Biological Process
- intracellular protein transport
- autophagy
- retrograde transport, endosome to Golgi
- activation of GTPase activity
- regulation of cilium assembly
Molecular Function
- GTPase activator activity
- protein binding
- Rab GTPase binding
Cellular Component
- autophagosome
- cytosol
- recycling endosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221543
- Coding exons
- 17
- Length
- 11324
- Individuals with no LoFs
- 125632
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 116
- Defined
- 125748
- p
- 0.000461
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.152 | 402 | 411 | 0.979 | 0.0000269 | 4160 |
| Missense (PolyPhen) | 178 | 176.35 | 1.0094 | 1916 | ||
| Synonymous | -1.33 | 197 | 175 | 1.13 | 0.0000119 | 1313 |
| Loss of Function | 0.549 | 33 | 36.6 | 0.902 | 0.00000193 | 367 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00051 | 0.00049 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00053 | 0.00052 | rare |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable GTPase-activating protein for Rab8; its transient association with Rab8 is mediated by OPTN. Inhibits Rab8-mediated endocytic trafficking, such as of transferrin receptor (TfR) and reduces Rab8 recruitnment to tubules emanating from the endocytic recycling compartment (ERC). Involved in regulation of autophagy. Mediates inhibition of autophagy caused by the OPTN variant GLC1E LYS-50; the function requires its catalytic activity, however, the involved Rab is not known. {ECO:0000269|PubMed:22854040, ECO:0000269|PubMed:24752605}.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- RVIS EVS
- -0.8
- RVIS percentile EVS
- 12.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |