AP4S1 splice-site mutation in a case of spastic paraplegia type 52 with polymicrogyria

Clinical case presentation

We report the case of a Portuguese 2-year-old boy born to healthy nonconsanguineous parents after a full-term gestation with intrauterine growth restriction after week 37. During the first months of life, the patient presented poor weight gain, hyperammonemia with elevation of glutamine and ornithine, low citrulline, and negative orotic acid. Weight recovery and normalization of amino acid profile were observed after protein restriction and remained normal after reintroduction of normal diet. Genetic study of urea cycle disorders (NAGS, CPS, and OTC) was negative. Around 9 months of age, global developmental delay, hypotonia, and strabismus were evident. Brain MRI with spectroscopy (performed at 10 months) showed delayed myelination/hypomyelination associated with a posterior perisylvian polymicrogyria, thinning of the corpus callosum, dilation and dysmorphia of the ventricles, and enlargement of the subarachnoid frontotemporal space (figure A). Spectroscopy suggested a possible discrete reduction of N-acetylaspartate. EEG showed a slight intermittent lentification in the left temporal region. At 15 months of age, the patient had 1 afebrile episode of status epilepticus. Two previous shorter episodes with fever had also occurred. Levetiracetam was started. No regression of psychomotor development after seizure was observed, and the patient has been evolving gradually with improvement of axial hypotonia. He says a few simple words, responds to his name, and has some nonverbal communication. The most recent neurologic evaluation revealed an alteration of the muscle tone (hypertonia) in the left lower limb and pyramidal signs in both legs.

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Figure Patient's brain imaging, pedigree, and consequences of AP4S1 c.294+1G>T variant

(A) Left image: sagittal T1 weighted image showing thin corpus callosum. Central and right images: axial T2 weighted images showing delayed myelination, bilateral posterior perisylvian polymicrogyria, dysmorphic and enlarged ventricles, and enlargement of subarachnoid space. (B) Family pedigree. The proband presents the splice-site variant chr14:g.31542180G>T NM_001128126.2:c.294+1G>T in the homozygous state, and both parents are heterozygous for the variant. +: c.294+1G>T allele; −: wild-type allele. (C) AP4S1 transcript size of the homozygous patient, both heterozygous parents, and the wild-type individual. A shorter transcript is produced in the presence of the variant. Each band of the marker ladder represents 100 bp (band size from gel bottom to top: 100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 bp). (D) Alignment of the wild-type protein sequence (NP_001121598) to the mutated protein. The alignment was performed with Clustal Omega. The variant leads to the loss of amino acids 76–98. C− = negative control; F = father; M = marker ladder; Mo = mother; mut = mutated protein; P = patient; WT = wild-type.

Exome sequencing of the proband and parents was performed as described in Supplementary Material (links.lww.com/NXG/A86) and revealed the homozygous AP4S1 splice site NM_001128126.2:c.294+1G>T r.619_687del variant in the proband, present in the heterozygous state in the parents (figure B). The variant was located in a 2.4-Mb homozygous region of chromosome 14. This variant is extremely rare in the population, with only 1 heterozygous individual present in the Genome Aggregation Database. In silico analysis predicted the loss of the donor splice site of exon 4. A transcript size analysis and Sanger sequencing of cDNA confirmed the presence of a shorter transcript skipping exon 4 associated with the variant (figure C). As a consequence, the polypeptide of 23 amino acids (76 a.a.–98 a.a.) encoded by exon 4 is lost (figure D).