Exclusion of positional candidate gene coding region mutations in the common posterior polymorphous corneal dystrophy 1 candidate gene interval

Abstract

Purpose: Posterior polymorphous corneal dystrophy (PPCD) is an autosomal-dominant disorder of the corneal endothelium associated with visually significant corneal edema and glaucoma. Statistical genetic analysis of 4 families with PPCD has demonstrated linkage to a 2.4 cM common support interval on chromosome 20 bordered by the markers D20S182 and D20S139. We sought to identify the genetic basis of PPCD linked to chromosome 20 (PPCD1) by screening the 26 positional candidate genes between these markers in a family previously mapped to the PPCD1 region.

Methods: The coding regions of the 26 positional candidate genes mapped to the common PPCD1 support interval were amplified and sequenced in affected and unaffected individuals from a family previously linked to the PPCD1 locus. Nine other genes positioned just outside of the common PPCD1 support interval but within the autosomal-dominant congenital hereditary endothelial dystrophy interval were also screened.

Results: Four DNA sequence variants in 3 of the positional candidate genes demonstrated complete segregation with the affected phenotype: p.Thr109Thr (rs6111803) in OVOL2, p.Arg56Gln (novel variant-RPSnovel) in RPS19P1, and p.Thr85Thr (rs1053834) and p.Pro99Ser (rs1053839) in C20orf79. Each of these 4 sequence variants demonstrated significant linkage with the affected phenotype in this family (P = 2.5 x 10 for RPSnovel, rs1053834 and rs1053839; P = 8.6 x 10 for rs6111803). However, we also identified each of these 4 sequence variants in > or = affected control individuals. The haplotype on which the disease-causing mutation is segregating was found to have a population frequency of 4.2% in the CEPH HapMap trios. Although a number of other previously described and novel single nucleotide polymorphisms were identified in the 35 positional candidate genes located within the PPCD1 and congenital hereditary endothelial dystrophy intervals, none segregated with the affected phenotype.

Conclusions: We report the absence of a presumed pathogenic coding region mutation in the common PPCD1 support interval. Although minor alleles of 4 single nucleotide polymorphisms were identified that segregated with the affected phenotype, the relatively high frequency of each minor allele in the general population indicates that none is a candidate for the causal variant for PPCD. Instead, the causal variant is most likely a coding region deletion or a variant in a noncoding region of the PPCD1 common support interval.

Figure 1

Ideogram of the pericentromeric region of chromosome 20, showing the reported candidate gene intervals for PPCD1 and CHED1 and the positions of the markers that define each candidate gene region. The region of chromosome 20 that lies within all three regions to which PPCD has been mapped, the common PPCD1 interval, is defined by the markers D20S182 and D20S139. The four DNA sequence variants identified within the 2.4 cM common PPCD1 interval that demonstrated complete segregation with the affected phenotype in a family previously linked to the PPCD1 locus are shown.

Figure 2

European population haplotype frequencies of three associated SNPs genotyped in the CEPH HapMap trios. The rare T-T-T haplotype (rs6111803, rs1053834, rs1053839) that is associated with PPCD has a population frequency of 0.042 (4.2%).

Figure 3

European population linkage disequilibrium (LD) of the three associated SNPs genotyped in the CEPH HapMap trios. LD is given as the R-squared (r²) between SNPs. The SNPs rs1053834 and rs1053839 are in complete LD (r² = 1) in the CEPH HapMap trios. There is no LD between rs6111803 and either rs1053834 or rs1053839 (r² = 0.022 and 0.028, respectively).