Homozygosity mapping and whole-genome sequencing reveals a deep intronic PROM1 mutation causing cone-rod dystrophy by pseudoexon activation

Eur J Hum Genet. 2016 Mar;24(3):459-62. doi: 10.1038/ejhg.2015.144. Epub 2015 Jul 8.


Several genes have been implicated in the autosomal recessive form of cone-rod dystrophy (CRD), but the majority of cases remain unsolved. We identified a homozygous interval comprising two known genes associated with the autosomal recessive form of CRD, namely RAB28 and PROM1, in a consanguineous family with clinical evidence of CRD. Both genes proved to be mutation negative upon sequencing of exons and canonical splice sites but whole-genome sequencing revealed a private variant located deep in intron 18 of PROM1. In silico and functional analyses of this variant using minigenes as splicing reporters revealed the integration of a pseudoexon in the mutant transcript, thereby leading to a premature termination codon and presumably resulting in a functional null allele. This is the first report of a deep intronic variant that acts as a splicing mutation in PROM1. The detection of such variants escapes the exon-focused techniques typically used in genetic analyses. Sequencing the entire genomic regions of known disease genes might identify more causal mutations in the autosomal recessive form of CRD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • AC133 Antigen
  • Amino Acid Sequence
  • Antigens, CD / chemistry
  • Antigens, CD / genetics*
  • Base Sequence
  • DNA Mutational Analysis
  • Exons / genetics*
  • Female
  • Genetic Predisposition to Disease*
  • Genome, Human*
  • Glycoproteins / chemistry
  • Glycoproteins / genetics*
  • HEK293 Cells
  • Homozygote
  • Humans
  • Introns / genetics*
  • Male
  • Molecular Sequence Data
  • Mutation / genetics*
  • Pedigree
  • Peptides / chemistry
  • Peptides / genetics*
  • RNA Splicing / genetics
  • Retinitis Pigmentosa / genetics*


  • AC133 Antigen
  • Antigens, CD
  • Glycoproteins
  • PROM1 protein, human
  • Peptides