Genetic characteristics of retinitis pigmentosa in 1204 Japanese patients

J Med Genet. 2019 Oct;56(10):662-670. doi: 10.1136/jmedgenet-2018-105691. Epub 2019 Jun 17.

Abstract

Background: The genetic profile of retinitis pigmentosa (RP) in East Asian populations has not been well characterised. Therefore, we conducted a large-scale sequencing study to investigate the genes and variants causing RP in a Japanese population.

Methods: A total of 1209 Japanese patients diagnosed with typical RP were enrolled. We performed deep resequencing of 83 known causative genes of RP using next-generation sequencing. We defined pathogenic variants as those that were putatively deleterious or registered as pathogenic in the Human Gene Mutation Database or ClinVar database and had a minor allele frequency in any ethnic population of ≤0.5% for recessive genes or ≤0.01% for dominant genes as determined using population-based databases.

Results: We successfully sequenced 1204 patients with RP and determined 200 pathogenic variants in 38 genes as the cause of RP in 356 patients (29.6%). Variants in six genes (EYS, USH2A, RP1L1, RHO, RP1 and RPGR) caused RP in 65.4% (233/356) of those patients. Among autosomal recessive genes, two known founder variants in EYS [p.(Ser1653fs) and p.(Tyr2935*)] and four East Asian-specific variants [p.(Gly2752Arg) in USH2A, p.(Arg658*) in RP1L1, p.(Gly2186Glu) in EYS and p.(Ile535Asn) in PDE6B] and p.(Cys934Trp) in USH2A were found in ≥10 patients. Among autosomal dominant genes, four pathogenic variants [p.(Pro347Leu) in RHO, p.(Arg872fs) in RP1, p.(Arg41Trp) in CRX and p.(Gly381fs) in PRPF31] were found in ≥4 patients, while these variants were unreported or extremely rare in both East Asian and non-East Asian population-based databases.

Conclusions: East Asian-specific variants in causative genes were the major causes of RP in the Japanese population.

Keywords: genetic epidemiology; next-generation sequencing; retinitis pigmentosa.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Asian People / genetics*
  • Child
  • Child, Preschool
  • Female
  • Gene Frequency
  • Genetic Variation
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Japan
  • Male
  • Middle Aged
  • Mutation
  • Retinitis Pigmentosa / diagnosis
  • Retinitis Pigmentosa / genetics*
  • Sequence Analysis, DNA
  • Usher Syndromes / diagnosis
  • Usher Syndromes / genetics*
  • Young Adult

Supplementary concepts

  • Usher syndrome, type 2A