Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis

Abstract

Whole exome sequencing has become a pivotal methodology for rapid and cost-effective detection of pathogenic variations in Mendelian disorders. A major challenge of this approach is determining the causative mutation from a substantial number of bystander variations that do not play any role in the disease etiology. Current strategies to analyze variations have mainly relied on genetic and functional arguments such as mode of inheritance, conservation, and loss of function prediction. Here, we demonstrate that disease-network analysis provides an additional layer of information to stratify variations even in the presence of incomplete sequencing coverage, a known limitation of exome sequencing. We studied a case of Hereditary Spastic Paraparesis (HSP) in a single inbred Palestinian family. HSP is a group of neuropathological disorders that are characterized by abnormal gait and spasticity of the lower limbs. Forty-five loci have been associated with HSP and lesions in 20 genes have been documented to induce the disorder. We used whole exome sequencing and homozygosity mapping to create a list of possible candidates. After exhausting the genetic and functional arguments, we stratified the remaining candidates according to their similarity to the previously known disease genes. Our analysis implicated the causative mutation in the motor domain of KIF1A, a gene that has not yet associated with HSP, which functions in anterograde axonal transportation. Our strategy can be useful for a large class of disorders that are characterized by locus heterogeneity, particularly when studying disorders in single families.

Figure 1.

Pedigree of the affected family. Sex of the nonaffected individuals was randomized to prevent identification of the family.

Figure 2.

Loss of function prediction: KIF1A scores in all the tools. (Orange) The subset of variations that were predicted as harmful by SIFT. (Pink) Harmful variations by PolyPhen. (Green) Harmful variations by MutationTaster. (Blue) High-quality variations based on SNVmix scores. The HDBLP variation was later proved to be a sequencing error. KIF1A is the only harmful variation.

Figure 3.

Ala255Val is a mutation in the protein motor area of KIF1A. (A) Schematic representation of the KIF1A gene, the exons that encode the motor domain (green), and the location of the mutation. (B) A 3D model of KIF1A motor domain. Ala 255 is highlighted. The nucleotide binding pocket (NBP) and the magnesium stabilizer are found in close proximity to the mutation. (C) The amino acid sequence of KIF1A homologs in the vicinity of Ala255 (yellow). Positions that are labeled with a star are fully conserved between human to fungi.