PAX6 mutations: genotype-phenotype correlations

Abstract

Background: The PAX6 protein is a highly conserved transcriptional regulator that is important for normal ocular and neural development. In humans, heterozygous mutations of the PAX6 gene cause aniridia (absence of the iris) and related developmental eye diseases. PAX6 mutations are archived in the Human PAX6 Allelic Variant Database, which currently contains 309 records, 286 of which are mutations in patients with eye malformations.

Results: We examined the records in the Human PAX6 Allelic Variant Database and documented the frequency of different mutation types, the phenotypes associated with different mutation types, the contribution of CpG transitions to the PAX6 mutation spectrum, and the distribution of chain-terminating mutations in the open reading frame. Mutations that introduce a premature termination codon into the open reading frame are predominantly associated with aniridia; in contrast, non-aniridia phenotypes are typically associated with missense mutations. Four CpG dinucleotides in exons 8, 9, 10 and 11 are major mutation hotspots, and transitions at these CpG's account for over half of all nonsense mutations in the database. Truncating mutations are distributed throughout the PAX6 coding region, except for the last half of exon 12 and the coding part of exon 13, where they are completely absent. The absence of truncating mutations in the 3' part of the coding region is statistically significant and is consistent with the idea that nonsense-mediated decay acts on PAX6 mutant alleles.

Conclusion: The PAX6 Allelic Variant Database is a valuable resource for studying genotype-phenotype correlations. The consistent association of truncating mutations with the aniridia phenotype, and the distribution of truncating mutations in the PAX6 open reading frame, suggests that nonsense-mediated decay acts on PAX6 mutant alleles.

Figure 1

The PAX6 cDNA and protein. Top: the PAX6 cDNA is represented as a horizontal rectangle with the different coding regions indicated: PB, paired box, LNK, linker region, HB, homeobox, PST, proline/serine/threonine-rich region. Exon boundaries are indicated by vertical black lines. 5a is alternatively spliced exon in the paired box. Thick horizontal lines indicate untranslated regions (not to scale). Bottom: cartoon of the PAX6 protein showing the different functional domains. N, N-terminus of protein; C, C-terminus; PB(N), N-terminal subdomain of paired domain; PB(C), C-terminal subdomain of paired domain; HD, homeodomain; PST, PSTdomain.

Figure 2

Distribution of different mutation types in the PAX6 Allelic Variant Database. (a) All disease-associated mutations in the database; (b) mutations causing aniridia; (c) mutations causing non-aniridia phenotypes. Mutation definitions are given in Table 1.

Figure 3

Distribution of CpG dinucleotides in the PAX6 open reading frame. The PAX6 cDNA is represented as a horizontal rectangle with the different coding regions indicated: PB, paired box, LNK, linker region, HB, homeobox, PST, proline/serine/threonine-rich region. Exon boundaries are indicated by vertical black lines. Exon numbers are shown beneath the cDNA, with the number of CpG's in brackets. Above the cDNA, each of the forty-five CpG dinucleotides in the PAX6 ORF is indicated by an arrow. Red arrows indicate the ten CpG's at which a nucleotide transition has occurred. Single-headed arrows indicate that the CpG deamination has occurred only on the forward strand (CpG > TpG). Double-headed arrows indicate that deamination has occurred both on the forward strand (CpG > TpG) and the reverse strand (CpG > CpA). Elongated red arrows indicate those CpG's that have been hit more than once on the forward strand; the resultant mutation is shown together with the number (in brackets) of independent records in the database.

Figure 4

Absence of nonsense mutations at the 3' end of the PAX6 coding region. The PAX6 open reading frame is represented as a horizontal rectangle; the untranslated regions are shown as thick black lines (not to scale). Exon boundaries are shown as vertical lines. PB, paired box; LNK, linker region; HB, homeobox; PST, PST region. Above the cDNA, thick double-headed arrows divide the coding region into two parts. Between bases 363–1495, nonsense-mediated decay is predicted to act on truncating mutations. The region from bases 1496–1628 is predicted to escape nonsense-mediated decay. The number of potential and observed nonsense mutations in the different zones of the coding region is shown in the lower part of the figure. No nonsense mutations have been observed in the region that escapes NMD, even though 14 codons could potentially give rise to nonsense mutations.