A novel variant in ALG1 gene associated with congenital disorder of glycosylation: A case report and short literature review

Abstract

BackgroundThe congenital disorder of glycosylation associated with ALG1 (ALG1‐CDG) is a rare autosomal recessive disease. Due to the deficiency of β1,4 mannosyltransferase caused by pathogenic variants in ALG1 gene, the assembly and processing of glycans in the protein glycosylation pathway are impaired, resulting in a broad clinical spectrum with multi‐organ involvement. To raise awareness of clinicians for its manifestations and genotype, we here reported a new patient with a novel variant in ALG1 gene and reviewed the literature to study the genotype–phenotype correlation.MethodClinical characteristics were collected, and clinical exome sequencing was used to identify the causative variants. MutationTaster, PyMol, and FoldX were used to predict the pathogenicity, changes in 3D model molecular structure of protein, and changes of free energy caused by novel variants.ResultsThe proband was a 13‐month‐old Chinese Han male characterized by epileptic seizures, psychomotor development delay, muscular hypotonia, liver and cardiac involvement. Clinical exome sequencing revealed the biallelic compound heterozygosity variants, a previously reported variant c.434G>A (p.G145N, paternal) and a novel variant c.314T>A (p.V105N, maternal). The literature review found that in severe phenotypes, the incidences of clinical manifestations were significantly higher than that in mild phenotypes, including congenital nephrotic syndrome, agammaglobulinemia, and severe hydrops. Homozygous c.773C>T was a strongly pathogenic variant associated with a severe phenotype. When heterozygous for c.773C>T, patients with another variant leading to substitution in amino acids within the strongly conserved regions (c.866A>T, c.1025A>C, c.1182C>G) may cause a more severe phenotype than those within less‐conserved regions (c.434G>A, c.450C>G, c.765G>A, c.1287T>A). c.1129A>G, c.1076C>T, and c.1287T>A were more likely to be associated with a mild phenotype. The assessment of disease phenotypes requires a combination of genotype and clinical manifestations.ConclusionsThe case reported herein adds to the mutations identified in ALG1‐CDG and a review of this literature expands the study of the phenotypic and genotypic spectrum of this disorder.

Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics

“…In all of our five selected variants, amino acid substitution seems to affect protein stability, especially in the ANXA11:p. R230C, CDH23:p.Gly2771Ser, and RYR1:p.R1954H with altered H-bonds which may lead to changing in free energy levels (altered ΔΔG value). However, no modification in H-bonds but altered evolutionary conserved residue (POLG structure with mutated variant) may still decrease the protein stability and pose a negative function for that [55].…”

Normal transferrin glycosylation does not rule out severe ALG1 deficiency

“…ALG1‐CDG (Online Mendelian Inheritance in Man [OMIM] #608540) is one of the most common CDG. 17 Since its discovery in 2004 18 , 19 , 20 more than 40 gene variants have been described. 21 …”

“… 16 , 21 According to recent data, congenital nephrotic syndrome, agammaglobulinemia and hydrops are associated with a severe outcome. 17 …”

“…ALG1-CDG (Online Mendelian Inheritance in Man [OMIM] #608540) is one of the most common CDG. 17 Since its discovery in 2004 [18][19][20] more than 40 gene variants have been described. 21 Most patients suffer from neurological involvement: hypotonia, intellectual disability, seizures and microcephaly.…”

“…22,23 Liver and kidney abnormalities may also occur. 16,17,22,24 Most ALG1-CDG phenotypes are also seen in other CDG, such as in the most common phosphomannomutase 2 (PMM2)-CDG. 22 The severity of the disease presentation varies over a wide spectrum.…”