PTCH2
Chr 1patched 2
Also known as: PTC2, SLC65B2
The protein functions as a transmembrane receptor in the hedgehog signaling pathway and acts as a tumor suppressor. Mutations cause somatic basal cell carcinoma and medulloblastoma through a gain-of-function mechanism. The gene has also been associated with nevoid basal cell carcinoma syndrome and congenital macrostomia susceptibility.
Limited evidence — not for standalone diagnostic reporting
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 (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
700 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 | 1 | 2 | 0 | 3 |
Likely Pathogenic | 1 | 0 | 2 | 0 | 3 |
VUS | 44 | 340 | 23 | 3 | 410 |
Likely Benign | 0 | 3 | 91 | 151 | 245 |
Benign | 0 | 0 | 19 | 4 | 23 |
Conflicting | — | 6 | |||
| Total | 45 | 344 | 137 | 158 | 690 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PTCH2 · 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