Pitt-Hopkins Syndrome via the TCF4 Gene

Pitt-Hopkins syndrome is a rare disorder characterized by extensive developmental delay, severe intellectual disability, intermittent hyperventilation followed by apnea, tendency to epilepsy, absence of speech, stereotypic hand movements, postnatal microcephaly, ocular anomalies and distinctive facial dysmorphism (cupid’s bow mouth, fleshy lips, broad and beaked nasal bridge). To date, no major congenital malformations have been described. Onset of this disease occurs in infancy and childhood (Zweier et al 2007; Peippo and Ignatius 2012; Sweatt 2013). It has been suggested that this disorder may be underdiagnosed. Pitt-Hopkins syndrome overlaps with features from other disorders such as Rett syndrome, Angelman syndrome, Joubert syndrome, Mowat-Wilson syndrome, and ARX, NRXN1 or CNTNAP2 related intellectual disability disorders.

Pitt-Hopkins syndrome is inherited in an autosomal dominant manner and is caused by defects in the TCF4 gene encoding the transcription factor-4, a member of class I basic helix-loop-helix family. TCF4 is the only gene in which pathogenic variants are known to cause Pitt-Hopkins syndrome. The human TCF4 gene consists of 20 exons (exons 2 through 19 are coding exons) and spans 360 kb. It is transcribed into isoforms with 18 different N-terminals, as well as several isoforms with alternative splicing of internal exons (Sweatt 2013). The transcription factor-4 (TCF4) shares homology with several other basic helix-loop-helix transcription factors (Zweier et al. 2007). It is ubiquitously expressed during embryo development, particularly in the brain and retina. It is continuously expressed in adult brain and other organs (Sepp et al 2011). TCF4 forms a homodimer or heterodimers with other proteins, in order to bind DNA and regulate gene expression. Depending on the binding partner, TCF4 may be either a transcription activator or suppressor. Upstream and downstream effectors of the TCF4 signaling pathway are largely unknown (Sweatt 2013).

Haploinsufficiency of the TCF4 gene causes Pitt-Hopkins syndrome, while over-expression of the TCF4 gene in the brain is a risk factor to schizophrenia. Pathogenic variants in TCF4 gene include frameshift, nonsense, splice site, and missense, as well as large deletions. Most cases are caused by de novo pathogenic variants (Amiel et al. 2007; Zweier et al. 2007). The missense variants are generally within the basic helix-loop-helix domain, a hotspot for pathogenic variants (Sweatt 2013). DNA sequence analysis detects ~70% of TCF4 pathologic variants. However, ~30% of TCF4 pathologic variants are due to whole or partial gene deletions, which are generally not detectable by sequencing (Whalen et al. 2012).

Pathogenic variants in TCF4 were confirmed by molecular analysis in 13 of 36 patients (~36%) who were either clinically diagnosed with Pitt-Hopkins syndrome (25 patients), or with Rett/Angelman syndrome, but had negative findings in MECP2 and UBE3A (10 patients), or with Mowat-Wilson syndrome, but had negative findings in ZFHX1B (de Pontual et al 2009).

This test provides full coverage of all coding exons of the TCF4 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.