TBC1D5
Chr 3TBC1 domain family member 5
TBC1D5 encodes a GTPase-activating protein that regulates retrograde transport from endosomes to the Golgi and controls autophagy by modulating vesicle trafficking. Biallelic mutations cause early-onset neurodevelopmental disorder with intellectual disability, seizures, and movement abnormalities, following autosomal recessive inheritance. The gene shows low constraint against loss-of-function variants, consistent with the recessive inheritance pattern observed in affected patients.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
162 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 23 | 0 | 23 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 97 | 7 | 0 | 104 |
Likely Benign | 1 | 6 | 2 | 0 | 9 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 1 | 103 | 33 | 0 | 137 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
TBC1D5 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools