Autism-Associated PTCHD1 Missense Variants Bind to the SNARE-Associated Protein SNAPIN but Exhibit Impaired Subcellular Trafficking

Background

PTCHD1 is a susceptibility gene for autism spectrum disorder and intellectual disability. Its function in brain development and neurotransmission remains elusive. Studies have sought to characterize PTCHD1 function by elucidating its neural network of interacting proteins. However, given the current paucity of functional information, many PTCHD1 missense variants in clinical databases are classified as variants of uncertain significance (VUSs), severely limiting the health care resources available to patients and families.

Methods

A yeast 2-hybrid assay was used to identify synaptic PTCHD1-interacting proteins. Candidate binding partners were validated by cloning; transient overexpression in human embryonic kidney (HEK) 293T cells, followed by co-immunoprecipitation and immunoblotting; and immunocytochemistry in differentiated P19 cells. Site-directed mutagenesis was used to evaluate the pathogenicity of clinical missense variants, followed by transient overexpression and immunocytochemistry in non-neuronal (HEK293T) and neuronal (Neuro-2a cells) systems.

Results

A novel interaction was identified between the first lumenal loop of PTCHD1 and the SNARE-associated protein SNAPIN, which is implicated in synaptic vesicle exocytosis. Clinically associated missense variants within this region did not disrupt SNAPIN binding, indicating that the pathoetiology of these variants is unrelated to this interaction. However, 6 of the 12 missense variants tested exhibited pronounced retention within the endoplasmic reticulum and impaired neuronal and non-neuronal trafficking to the plasma membrane.

Conclusions

These data yield insights into the role of PTCHD1 in neurodevelopment and neurotransmission and suggest a neuropathological mechanism for missense variants. These findings provide a platform for diagnostic assay and VUS interpretation, allowing for clinical reclassification of these variants.