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

• Sequence analysis. Sequencing of all 18 TCF4 coding exons (exons 2 to 19), splice junctions, and immediate intronic flanking regions detects approximately 70% of pathogenic variants [Whalen et al 2012].
• Deletion/duplication analysis. Approximately 30% of TCF4 pathogenic variants are whole- or partial-genedeletions, varying in size from a single exon to ~12 Mb [Whalen et al 2012]. Of these, at least ten reports describe single-exon or partial-gene deletions, detectable only by deletion/duplication analysis (Table 1) [Brockschmidt et al 2007, Rosenfeld et al 2009, Lehalle et al 2011, Whalen et al 2012].
  • Chromosome microarray analysis (CMA) (also known as array comparative genomic hybridization[aCGH]) detects a deletion in about one third of individuals with PTHS. Note: High-resolution chromosome analysis is required to determine if a translocation is present in these individuals.
  • Cytogenetic testing. Cytogenetically visible deletions or chromosome rearrangements disrupting TCF4have been detected in at least seven individuals with PTHS [Gustavsson et al 1999, Giurgea et al 2008, Kalscheuer et al 2008, Kato et al 2010, Marangi et al 2011]. In addition, the size of a number of the deletions detected by CMA would make them cytogenetically visible [Whalen et al 2012].