From the National Institutes of Health Gene Reviews article on Pitt Hopkins Syndrome: http://www.ncbi.nlm.nih.gov/books/NBK100240/ :

Molecular Genetic Testing

Gene. TCF4 is the only in which pathogenic variants are known to cause Pitt-Hopkins syndrome.

Testing Strategy

To confirm/establish the diagnosis of Pitt-Hopkins syndrome in a

1.  Perform TCF4 .  Note: propose a tiered sequencing strategy, beginning with 18, which harbors 25% of pathogenic variants; however, such testing may not be widely available.
2.  If a is not found by , perform -level .
3.  If a or is not found by and a strong clinical suspicion of PTHS remains, perform a to look for an apparently balanced involving the 18q21.2 region (which would not be detected by either or CMA).