Two novel mutations in ALDH18A1 and SPG11 gene found by whole-exome sequencing in spastic paraplegia disease patients in Iran

Abstract

Hereditary spastic paraplegia is a not common inherited neurological disorder with heterogeneous clinical expressions. ALDH18A1 (located on 10q24.1) gene-related spastic paraplegias (SPG9A and SPG9B) are rare metabolic disorders caused by dominant and recessive mutations that have been found recently. Autosomal recessive hereditary spastic paraplegia is a common and clinical type of familial spastic paraplegia linked to the SPG11 locus (locates on 15q21.1). There are different symptoms of spastic paraplegia, such as muscle atrophy, moderate MR, short stature, balance problem, and lower limb weakness. Our first proband involves a 45 years old man and our second proband involves a 20 years old woman both are affected by spastic paraplegia disease. Genomic DNA was extracted from the peripheral blood of the patients, their parents, and their siblings using a filter-based methodology and quantified and used for molecular analysis and sequencing. Sequencing libraries were generated using Agilent SureSelect Human All ExonV7 kit, and the qualified libraries are fed into NovaSeq 6000 Illumina sequencers. Sanger sequencing was performed by an ABI prism 3730 sequencer. Here, for the first time, we report two cases, the first one which contains likely pathogenic NM_002860: c.475C>T: p.R159X mutation of the ALDH18A1 and the second one has likely pathogenic NM_001160227.2: c.5454dupA: p.Glu1819Argfs Ter11 mutation of the SPG11 gene and also was identified by the whole-exome sequencing and confirmed by Sanger sequencing. Our aim with this study was to confirm that these two novel variants are direct causes of spastic paraplegia.

Keywords: metabolism; mutation; neurological disorder; polyneuropathy; spastic paraplegia; whole-exome sequencing.

Fig. 1.

(A) Pedigree of the first proband. (B) Pedigree of the second proband.

Fig. 2.

Confirmation sequences of the proband’s sisters, father, mother, and the proband itself. (A) There are both forward strand sequence named sibing 1 (F), and reverse strand sequence named sibing 1 (R). (B) There are both forward strand sequence named sibing 2 (F), and reverse strand sequence named sibing 2 (R). (C) There are proband’s mother forward strand sequence named Mother F, and proband’s father forward strand sequence named Father F. (D) There is proband’s forward strand sequence named Proband F. Sanger sequencing confirmed heterozygosity of the proband 1 in NM_001323412: c.142C>T: p.R159X variant as a novel de novo mutation of the ALDH18A1 gene.

Fig. 3.

Confirmation sequences of the proband’s sisters, father, mother, and the proband itself. (A) There are both forward strand sequence named sibing 1 (F), and reverse strand sequence named sibing 1 (R). (B) There are both forward strand sequence named sibing 2 (F), and reverse strand sequence named sibing 2 (R). (C) There are proband’s father forward strand sequence named Father F, and proband’s mother forward strand sequence named Mother F. (D) There is proband’s forward strand sequence named Proband F. Sanger sequencing confirmed homozygosity of the proband 2, homozygosity of her sister (A), heterozygosity of her brother (B) and heterozygosity of her father and mother (C) in NM_001160227.2: c.5454dupA: p.Glu1819Argfs Ter11 mutation of the SPG11 gene.

Fig. 4.

Mutated truncated protein models of the first proband are visible in three forms: balls and sticks (A), ribbon (B), and molecular surface (C), and the second proband protein model is shown in ribbon form (D). Models A, B, and C were created template-free by web based I-tasser software using protein sequence from Protein Data Bank [23], and model D, the mutated truncated protein model was made template free by web based SWISS-MODEL software using protein sequence from Protein Data Bank [24].