Identification of partial SLC20A2 deletions in primary brain calcification using whole-exome sequencing

Abstract

Primary brain calcification (PBC) is a dominantly inherited calcifying disorder of the brain. SLC20A2 loss-of-function variants account for the majority of families. Only one genomic deletion encompassing SLC20A2 and six other genes has been reported. We performed whole-exome sequencing (WES) in 24 unrelated French patients with PBC, negatively screened for sequence variant in the known genes SLC20A2, PDGFB, PDGFRB and XPR1. We used the CANOES tool to detect copy number variations (CNVs). We detected two deletions of exon 2 of SLC20A2 in two unrelated patients, which segregated with PBC in one family. We then reanalyzed the same series using a QMPSF assay including one amplicon in each exon of SLC20A2 and detected two supplemental partial deletions in two patients: one deletion of exon 4 and one deletion of exons 4 and 5. These deletions were missed by the first screening step of CANOES but could finally be detected after readjustment of bioinformatic parameters and use of a genotyping step of CANOES. This study reports the first partial deletions of SLC20A2 and strengthens its position as the major PBC-causative gene. It is possible to detect short CNVs from WES data, although the sensitivity of such tools should be evaluated in comparison with other methods.

Primary familial brain calcification linked to deletion of 5’ noncoding region of SLC20A2

“…A partial deletion of PDGFB was subsequently described by Nicolas et al . Recently, smaller exonic deletions of SLC20A2 were reported in four patients . We identified a ~578 kb deletion in a Finnish family with PFBC using both WGS and a SNP array.…”

“…The exonic deletions reported by David et al. presumably lead to loss of function by removing the translation initiation codon (exon 2 deletion), causing a frameshift (exon 4 deletion) or removing two transmembrane domains (deletion of exons 4 and 5) . The deletion reported here starts between the first two exons of SLC20A2 removing the noncoding exon 1, 5’ UTR, and the putative promoter region upstream of the transcription start site.…”

“…Two studies have broadened the mutational spectrum of SLC20A2 : In 2014, a large deletion encompassing the entire coding region of SLC20A2 was reported . In a recent study by David and coworkers, smaller deletions covering exon 2, exon 4, and exons 4 and 5 of SLC20A2 were found in four patients in a cohort of 24 patients with PFBC . Thus, analysis of copy number variations (CNVs) is emerging as a crucial step in molecular genetic diagnostics of PFBC.…”

Estimation of minimal disease prevalence from population genomic data: Application to primary familial brain calcification

“…In PDGFB and SLC20A2 , variants previously reported as pathogenic or likely pathogenic in PFBC patients are: PTV (canonical splice sites, nonsense, and frameshift), genomic deletions, and missense variants with enough genetic and/or functional evidence in the literature (Baker et al, ; David et al, ; Hsu et al, ; Lemos et al, ; Nicolas G, Pottier C, Maltete et al, ; Nicolas, Rovelet‐Lecrux, et al, ). In PDGFRB and XPR1 , no PTV or genomic deletion has ever been reported in PFBC patients although functional studies demonstrated that the pathogenic missense variants caused PFBC through a loss of protein function mechanism (Anheim et al, ; Arts et al, ; Legati et al, ; Sanchez‐Contreras et al, ; Vanlandewijck et al, ).…”

Fahr’s disease

“…У частини хворих з ювенільною формою зберігається мислення. Часто мають місце прояви гіпер-або гіпотиреозу: позитивні симптоми хвостека і Труссо, тетанічні спазми кінцівок, локальні судоми [23].…”