Exome sequencing identifies a rare HSPG2 variant associated with familial idiopathic scoliosis

Abstract

Idiopathic scoliosis occurs in 3% of individuals and has an unknown etiology. The objective of this study was to identify rare variants that contribute to the etiology of idiopathic scoliosis by using exome sequencing in a multigenerational family with idiopathic scoliosis. Exome sequencing was completed for three members of this multigenerational family with idiopathic scoliosis, resulting in the identification of a variant in the HSPG2 gene as a potential contributor to the phenotype. The HSPG2 gene was sequenced in a separate cohort of 100 unrelated individuals affected with idiopathic scoliosis and also was examined in an independent idiopathic scoliosis population. The exome sequencing and subsequent bioinformatics filtering resulted in 16 potentially damaging and rare coding variants. One of these variants, p.Asn786Ser, is located in the HSPG2 gene. The variant p.Asn786Ser also is overrepresented in a larger cohort of idiopathic scoliosis cases compared with a control population (P = 0.024). Furthermore, we identified additional rare HSPG2 variants that are predicted to be damaging in two independent cohorts of individuals with idiopathic scoliosis. The HSPG2 gene encodes for a ubiquitous multifunctional protein within the extracellular matrix in which loss of function mutation are known to result in a musculoskeletal phenotype in both mouse and humans. Based on these results, we conclude that rare variants in the HSPG2 gene potentially contribute to the idiopathic scoliosis phenotype in a subset of patients with idiopathic scoliosis. Further studies must be completed to confirm the effect of the HSPG2 gene on the idiopathic scoliosis phenotype.

Keywords: HSPG2; exome sequencing; idiopathic scoliosis; perlecan.

Figure 1

(A) Pedigree for the multigenerational family with IS. Individuals IV:1, IV:6, and II:4 underwent exome sequencing. Sanger sequencing was completed for those three individuals in addition to the affected individuals III:2 and III:6 and unaffected individuals III:1, III:7, and IV:2. Lumbar and thoracic curves are abbreviated with L and T, respectively. Double curves are represented by a slash (right thoracic/left lumbar), and triple curves are represented with three slashes (left high thoracic/right thoracic/left lumbar). CT or TT is the individual genotype at HSPG2 position p.Asn786Ser. A “?” represents individuals that have not been examined, so their scoliosis status is unknown. (B) Chromatograms for Variant p.Asn786Ser. Chromatograms for p.Asn786Ser are shown for two individuals from the multigenerational family (III:6, affected, and III:7, unaffected). The variant p.Asn786Ser, in the HSPG2 gene, is heterozygous in the affected individuals within the family, but not in the unaffected individuals (with the exception of IV:2, as discussed in the section Results).

Figure 2

Rare HSPG2 variants identified in IS patients. Structure of the HSPG2 protein showing the amino acid positions of the rare coding variants identified in the combined IS cohort of 241 individuals. Amino acid positions are based on transcript NM_005529.5. Variant p.Asn786Ser is the original variant identified in this study (combined Denver−St. Louis dataset, P = 0.024, odds ratio 2.4). Also note that variant 22186669 (c.5014+1G > A) is not shown on the diagram because it is a splicing variant and does not have an amino acid position. IS, idiopathic scoliosis.