Table 2

Classification of non-synonymous sequence variants detected by massively parallel DNA sequencing

PatientGeneExonNucleotide changeAmino acid changeComputational pathogenicity predictionFrequency (%) controls*Variant classification
PolyPhen§PmutSIFT**WTVariant
RP179CRB17c.2129ATp.E710VProb DNT99.20.8Known compound heterozygous mutation12
CRB17c.2548GAp.G850SProb DNT1000Known compound heterozygous mutation17
RP148PDE6B13c.1685GAp.G562DPoss DPD1000Known homozygous mutation12
FSCN21c.538C→Tp.R180WProb DPT99.90.1Unclassified variant
RP167CNGB129c.2957ATp.N986IProb DPD1000Novel homozygous mutation
RP75ROM12c.686G→Ap.R229HBNT1000Known polymorphism18
RP141ABCA423c.3352C→Gp.H1118DProb DPD1000Unclassified variant
CA47c.700G→Ap.V234IBNT95.44.6SNP
CNGA12c.95G→Ap.R32QBNT98.11.9SNP
PDE6A16c.1963C→Tp.H655YBNT97.42.6SNP
RP14c.4250T→Cp.L1417PPoss DPT1000Rare polymorphism (no segregation)19
RP14c.1118C→Tp.T373IPoss DPD991SNP (no segregation)19
USH2A15c.3123C→Ap.H1041QProb DNT99.70.3Unclassified variant
  • Thirteen non-synonymous variants were detected by massively parallel DNA sequencing including four mutations (bold text): one known homozygous mutation in PDE6B (patient RP148; p.G562D), two compound heterozygous mutations in CRB1 (patient RP179; p.E710V and p.G850S) and a novel homozygous mutation in CNGB1 (RP167; p.N986I).

  • * The frequency of non-synonymous sequence variants was assessed in 360 population controls (720 chromosomes).

  • Two variants (ROM1: p.R229H; RP1: p.L1417P) were classified as rare polymorphisms, as they were seen in <1% of controls but did not segregate.

  • Variants present in at least 1% of the control population were classified as SNPs.

  • § PolyPhen classification: Prob D (probably damaging: high confidence change affects protein function or structure); Poss D (possibly damaging: may affect protein structure or function); and B (benign: lacks phenotypic effect).

  • PMut classification: N (neutral) and P (pathogenic).

  • ** SIFT classification: T (tolerated) and D (damaging).

  • SNP, single-nucleotide polymorphism; WT, wild-type.