OTOP1
Chr 4otopetrin 1
This gene encodes OTOP1, a proton-selective ion channel that is essential for the formation of otoconia, the calcium carbonate structures in the inner ear that detect gravity and linear acceleration. Mutations cause autosomal recessive benign paroxysmal positional vertigo type 2, characterized by episodic vertigo and balance problems due to absent or malformed otoconia. The gene shows minimal constraint against loss-of-function variants, consistent with its recessive inheritance pattern.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function 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
200 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 | 77 | 0 | 77 |
Likely Pathogenic | 0 | 0 | 4 | 0 | 4 |
VUS | 0 | 110 | 0 | 0 | 110 |
Likely Benign | 0 | 5 | 0 | 0 | 5 |
Benign | 0 | 0 | 2 | 0 | 2 |
| Total | 0 | 115 | 83 | 0 | 198 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
OTOP1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
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