Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project

Abstract

Hereditary spastic paraplegia (HSP) is a group of heterogeneous inherited degenerative disorders characterized by lower limb spasticity. Fifty percent of HSP patients remain yet genetically undiagnosed. The 100,000 Genomes Project (100KGP) is a large UK-wide initiative to provide genetic diagnosis to previously undiagnosed patients and families with rare conditions. Over 400 HSP families were recruited to the 100KGP. In order to obtain genetic diagnoses, gene-based burden testing was carried out for rare, predicted pathogenic variants using candidate variants from the Exomiser analysis of the genome sequencing data. A significant gene-disease association was identified for UBAP1 and HSP. Three protein truncating variants were identified in 13 patients from 7 families. All patients presented with juvenile form of pure HSP, with median age at onset 10 years, showing autosomal dominant inheritance or de novo occurrence. Additional clinical features included parkinsonism and learning difficulties, but their association with UBAP1 needs to be established.

Fig. 1. Pedigrees, DNA, RNA and protein analysis of UBAP1.

a Pedigrees, b Sanger Sequencing, c Western Blot, d RNA. a Pedigrees of families reported in this study. Squares represent males, circles represent females, shaded shapes represent individuals with HSP, and unshaded shapes represent individuals without HSP. b Electropherograms of Sanger sequencing performed for the validation of variants identified in families 3, 4, and 5. c Western Blot analysis for the proband of family 4 (p.Gln125Ter/WT) and two healthy controls (WT/WT), showing reduced expression of normal size ubiquitin-associated protein 1 (UBAP1) and the presence of a smaller additional band in the proband, indicating the presence of truncated protein. Loading control with β-actin.was performed to confirm that the same amount of the total protein was loaded for all three samples. d Gel electrophoresis of PCR products amplified from cDNA synthesized from RNA of the proband of family 4 (c.373C > T) and a healthy control, showing the presence of amplicons of target sequence in both samples. Sanger sequencing of the same PCR products confirm the result as well as the presence of the variant in the proband, as shown by the respective electropherograms. WT wild type; KDa kilodalton; bp base pairs.

Fig. 2. Schematic representation of UBAP1 with all variants reported in this study and previously.

The table indicates the number of families carrying each variant. Each circle represents one family. Shaded circles represent positive family history, unshaded circles represent de novo occurrence, and half-shaded circles indicate unknown family history. Exons are numbered like in Fard et al. 2019 [4].