Journal: Journal of Neurology
Article Title: SPG7 mutations in amyotrophic lateral sclerosis: a genetic link to hereditary spastic paraplegia
doi: 10.1007/s00415-020-09861-w
Figure Lengend Snippet: Five heterozygous SPG7 mutations were detected in nine patients of a European ALS cohort. a Electropherograms demonstrating four rare heterozygous SPG7 missense variants in DNA from whole blood of eight ALS patients (affected nucleotides are designated by an arrow). All variants were predicted to be deleterious by at least one of two prediction tools, i.e. SIFT according to Alamut Visual Version 2.11, Interactive Biosoftware, Rouen, France or PolyPhen-2. b Missense variants detected in SPG7 affect amino acids highly or very highly conserved in paraplegin orthologs from different species (data taken from Alamut Visual Version 2.11). c Mapping of the amino acid residues affected by the identified SPG7 missense variants on a structural model of the AAA+ domain of human paraplegin (gold) with its substrate adenosine diphosphate (ADP). Close-up views show the mutated residues as obtained after energy minimization using Macromodel of the Schrödinger Suite and the OPLS3 force field [ , ]. Variant p.(G349S) is part of the P-loop and may affect nucleotide binding and hydrolysis. In contrast, p.(R486Q) and p.(A510V) may disturb the structure of the α-helical bundle and thereby oligomerization. p.(R400W) is located in the N-terminal P-loop domain and as part of the hexamer interface may interfere with formation of the supracomplex. Sensor 1 is shown in green, Sensor 2 in blue, and the P-loop (Walker A motif) in cyan. d The rare heterozygous SPG7 splice site variant c.1552 + 1G > T detected in ALS patient MD018 on genomic DNA, its effect on cDNA, and its predicted consequence on the protein level. Given are electropherograms of targeted SPG7 sequencing on genomic DNA and cDNA from whole blood of patient MD018. By cDNA sequencing, an aberrant SPG7 transcript lacking exon 11 was identified. The predicted consequence of the aberrant transcript on the protein level was visualized in a crystal structure model of the functional AAA+ domain of paraplegin composed of the P-loop domain and the α-helical bundle. The skipping of exon 11 is predicted to result in a frameshift, leading to a premature stop codon. This would result in an altered α-helical bundle as indicated by the red color and a truncated peptidase domain
Article Snippet: Variant pathogenicity was predicted using SIFT according to Alamut Visual software, version 2.11 (Interactive Biosoftware, Rouen, France), PolyPhen-2 ( http://genetics.bwh.harvard.edu/pph2/ ), and the American College of Medical Genetics (ACMG) criteria [ ].
Techniques: Variant Assay, Binding Assay, Sequencing, Functional Assay
![Five heterozygous SPG7 mutations were detected in nine patients of a European ALS cohort. a Electropherograms demonstrating four rare heterozygous SPG7 missense variants in DNA from whole blood of eight ALS patients (affected nucleotides are designated by an arrow). All variants were predicted to be deleterious by at least one of two prediction tools, i.e. SIFT according to Alamut Visual Version 2.11, Interactive Biosoftware, Rouen, France or PolyPhen-2. b Missense variants detected in SPG7 affect amino acids highly or very highly conserved in paraplegin orthologs from different species (data taken from Alamut Visual Version 2.11). c Mapping of the amino acid residues affected by the identified SPG7 missense variants on a structural model of the AAA+ domain of human paraplegin (gold) with its substrate adenosine diphosphate (ADP). Close-up views show the mutated residues as obtained after energy minimization using Macromodel of the Schrödinger Suite and the OPLS3 force field [ , ]. Variant p.(G349S) is part of the P-loop and may affect nucleotide binding and hydrolysis. In contrast, p.(R486Q) and p.(A510V) may disturb the structure of the α-helical bundle and thereby oligomerization. p.(R400W) is located in the N-terminal P-loop domain and as part of the hexamer interface may interfere with formation of the supracomplex. Sensor 1 is shown in green, Sensor 2 in blue, and the P-loop (Walker A motif) in cyan. d The rare heterozygous SPG7 splice site variant c.1552 + 1G > T detected in ALS patient MD018 on genomic DNA, its effect on cDNA, and its predicted consequence on the protein level. Given are electropherograms of targeted SPG7 sequencing on genomic DNA and cDNA from whole blood of patient MD018. By cDNA sequencing, an aberrant SPG7 transcript lacking exon 11 was identified. The predicted consequence of the aberrant transcript on the protein level was visualized in a crystal structure model of the functional AAA+ domain of paraplegin composed of the P-loop domain and the α-helical bundle. The skipping of exon 11 is predicted to result in a frameshift, leading to a premature stop codon. This would result in an altered α-helical bundle as indicated by the red color and a truncated peptidase domain](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_9373/pmc07419373/pmc07419373__415_2020_9861_Fig1_HTML.jpg)