Compound Heterozygous CHAT Gene Mutations of a Large Deletion and a Missense Variant in a Chinese Patient With Severe Congenital Myasthenic Syndrome With Episodic Apnea

Abstract

Congenital myasthenic syndromes (CMSs) are a group of inherited disorders caused by genetic defects in neuromuscular junctions. Mutations in CHAT, encoding choline acetyltransferase, cause congenital myasthenic syndrome with episodic apnea (CMS-EA), a rare autosomal recessive disease characterized by respiratory insufficiency with cyanosis and apnea after infections, fever, vomiting, or excitement. To date, no studies have reported deletions comprised of multiple exons. Here, using next generation sequencing, we identified compound heterozygous mutations, namely a large maternally inherited deletion, including exons 4, 5, and 6, and a paternally inherited missense variant (c.914T>C [p.Ile305Thr]) in CHAT in a Chinese patient with a severe phenotype of CMS-EA. Furthermore, the large deletion was also validated by real-time fluorescence quantitative polymerase chain reaction. The patient was a 10-month-old boy, who presented with a weak cry and feeding difficulties soon after birth, ptosis at 4 months old, episodic apnea after fever at 9 months old, and respiratory insufficiency with cyanosis and apnea that required intubation after a respiratory tract infection at 10 months old. Unfortunately, he died in the Pediatric Intensive Care Unit soon after hospitalization. The patient's elder sister had similar clinical manifestations, and she died prior to the age of 2 months old without a diagnosis. Genotype-phenotype correlation analysis revealed that loss-of-function mutations in exons 4-6 of CHAT might cause more severe CMS-EA. To our knowledge, this is the first study to show compound heterozygous CHAT mutations consisting of a large deletion and missense mutation in a patient with CMS-EA.

Keywords: CHAT; congenital myasthenic syndromes; episodic apnea; large deletion; severe.

FIGURE 1

Magnetic Resonance Imaging (MRI) of the proband and the two-generation pedigree. (A,B) Brain MRI of the proband at the age of 10 months showed deep sulci in the frontal and parietal lobes and a wide subarachnoid space. (C) The two-generation pedigree of the family with CMS-EA. The parents are unaffected, while the two offspring are affected. The arrow indicates the proband.

FIGURE 2

Targeted sequencing-based identification of pathogenic variants. (A) Workflow for the analysis of targeted sequencing data. (B) The SNVs and InDels identified by targeted sequencing. (C) The number of missense and synonymous SNVs in coding regions.

FIGURE 3

Validation of the missense variant and the large deletion in CHAT. (A) The genotype of the missense variant in three members of the CMS-EA family, as identified by Sanger sequencing. (B) The average read depth for the first 8 exons for the proband was calculated with the targeted sequencing data.

FIGURE 4

Estimated copy number of the exons for the CMS family members. The estimated copy number of the 4th (A), 5th (B), and 6th (C) exons were estimated by qPCR.

FIGURE 5

Schematic diagram for the mutant CHAT proteins. (A) The ChAT protein with c.914T>C (p.Ile305Thr) variant. (B) The ChAT protein with the large deletion from the 4th to 6th exons. The red box indicates the acetyl coenzyme -dependent acyltransferase domain.