A case of de novo splice site variant in SLC35A2 showing developmental delays, spastic paraplegia, and delayed myelination

• Published in: Molecular genetics & genomic medicine 2019-08, Vol.7 (8), p.e814-n/a
• Main Authors: Miyamoto, Sachiko, Nakashima, Mitsuko, Ohashi, Tsukasa, Hiraide, Takuya, Kurosawa, Kenji, Yamamoto, Toshiyuki, Takanashi, Junichi, Osaka, Hitoshi, Inoue, Ken, Miyazaki, Takehiro, Wada, Yoshinao, Okamoto, Nobuhiko, Saitsu, Hirotomo
• Format: Article
• Language: English
• Subjects: Amino acids; Androgen receptors; Atrophy; Child, Preschool; Chromosomes; Clinical Report; Clinical Reports; Congenital anomalies; Congenital diseases; congenital disorders of glycosylation; Congenital Disorders of Glycosylation - diagnosis; Congenital Disorders of Glycosylation - genetics; Congenital Disorders of Glycosylation - pathology; Convulsions & seizures; Deactivation; Delay; delayed myelination; Deoxyribonucleic acid; Developmental Disabilities - diagnosis; Developmental Disabilities - genetics; Developmental Disabilities - pathology; Disorders; DNA; DNA sequencing; Epilepsy; Exome Sequencing; Female; Galactose; Glycoproteins; Glycosylation; Hereditary spastic paraplegia; Humans; Hypotonia; Inactivation; Insertion; Internal Capsule - diagnostic imaging; Internal Capsule - pathology; Leukocytes; Lipids; Magnetic Resonance Imaging; Medical screening; Monosaccharide Transport Proteins - genetics; Myelin Sheath - pathology; Myelination; NMR; Nuclear magnetic resonance; Paraplegia - diagnosis; Paraplegia - genetics; Paraplegia - pathology; Paraplegics; Patients; Polysaccharides; RNA Splicing; Seizures; Severity of Illness Index; Signs and symptoms; SLC35A2; spastic paraplegia; Spasticity; splice site variant; Splicing; Transferrin; Transferrins; X-chromosome inactivation
• ISSN: 2324-9269; 2324-9269
• DOI: 10.1002/mgg3.814

Background Congenital disorders of glycosylation (CDGs) are genetic diseases caused by pathogenic variants of genes involved in protein or lipid glycosylation. De novo variants in the SLC35A2 gene, which encodes a UDP‐galactose transporter, are responsible for CDGs with an X‐linked dominant manner. Common symptoms related to SLC35A2 variants include epilepsy, psychomotor developmental delay, hypotonia, abnormal facial and skeletal features, and various magnetic resonance imaging (MRI) findings. Methods Whole‐exome sequencing was performed on the patient's DNA, and candidate variants were confirmed by Sanger sequencing. cDNA analysis was performed to assess the effect of the splice site variant using peripheral leukocytes. The X‐chromosome inactivation pattern was studied using the human androgen receptor assay. Results We identified a de novo splice site variant in SLC35A2 (NM_005660.2: c.274+1G>A) in a female patient who showed severe developmental delay, spastic paraplegia, mild cerebral atrophy, and delayed myelination on MRI, but no seizures. The variant led to an aberrant splicing resulting in an in‐frame 33‐bp insertion, which caused an 11‐amino acid insertion in the presumptive cytoplasmic loop. X‐inactivation pattern was random. Partial loss of galactose and sialic acid of the N‐linked glycans of serum transferrin was observed. Conclusion This case would expand the phenotypic spectrum of SLC35A2‐related disorders to delayed myelination with spasticity and no seizures. De novo variants in the solute carrier family 35 member A2 gene (SLC35A2), which encodes a UDP‐galactose transporter, are responsible for CDGs with an X‐linked dominant manner. This is the first report of a splice site variant in SLC35A2 and would expand the clinical spectrum of SLC35A2‐related disorders to delayed myelination with spasticity and no seizures.