Identification by exome sequencing and functional characterization of novel deafness-causing mutations in PRPS1

Next-generation sequencing is being widely applied for gene discovery in rare inherited disorders, allowing the study of the genetic basis of previously intractable diseases. We used whole-exome sequencing (WES) to identify causative mutations underlying inherited nonsyndromic sensorineural hearing loss (NSHL), a disease with an extremely high level of genetic heterogeneity. WES of a single Italian proband affected by recessive NSHL led to the identification of a novel missense mutation within PRPS1, segregating with pre-lingual profound deafness in the proband’s family. Defects in this gene, which codes for the ubiquitously expressed phosphoribosylpyrophosphate synthetase 1 (PRS-I) enzyme, determine either X-linked syndromic conditions associated with hearing impairment (e.g. Arts syndrome and Charcot-Marie-Tooth disease-5), or NSHL (DFNX1 locus). A subsequent screening of the entire PRPS1 coding region by Sanger sequencing in 13 additional unrelated probands from NSHL families showing a likely X-linked inheritance pattern led to the discovery of a second missense mutation segregating with pre-lingual hearing impairment. The two novel variants were absent in a cohort of 126 Italian audiologically-tested normal-hearing controls. Both amino-acid substitutions are predicted to cause a destabilization of the enzyme structure and result in a marked reduction (>60%) of PRS-I activity in the patients’ erythrocytes compared to controls, as assessed by functional assays. In conclusion, we provide evidence of the usefulness of WES for the genetic diagnosis of NSHL, and highlight the recurrence of genetic defects in PRPS1, suggesting that it may represent a major locus for X-linked NSHL to be prioritised in genetic screenings.