A new set of primers for mutation analysis of the human PAX6 gene

Correlation of novel PAX6 gene abnormalities in aniridia and clinical presentation

OBJECTIVE

To describe the clinical presentation and genotype of subjects with aniridia with a particular focus on foveal hypoplasia.

DESIGN

Prospective cohort study.

PARTICIPANTS

Thirty-three Canadian participants with aniridia and of various ethnic backgrounds residing in British Columbia.

METHODS

Full ophthalmic examinations and posterior segment spectral domain-optical coherence tomography (SD-OCT) imaging were performed. Foveal hypoplasia was graded independently by 2 staff ophthalmologists. PAX6 sequencing was performed and chromosomal 11p anomalies investigated. Candidate gene and single-nucleotide polymorphism sequencing in genes functionally related to PAX6 were also studied.

RESULTS

Best corrected visual acuities in the cohort ranged from 0.0 logMAR to no light perception. Total absence of iris tissue was seen in the majority (42 of 66 eyes). In those in whom SD-OCT was possible, foveal hypoplasia was seen in the majority (45 of 56 eyes, 80%). Molecular genetic defects involving PAX6 were identified in 30 participants (91%), including 4 novel PAX6 mutations (Gly18Val; Ser65ProfsX14; Met337ArgfsX18; Ser321CysfsX34) and 4 novel chromosome 11p deletions inclusive of PAX6 or a known PAX6 regulatory region.

CONCLUSIONS

The number of PAX6 mutations associated with aniridia continues to increase. Variable foveal architecture despite nearly identical anterior segment disease in 4 participants with an Ex9 ELP4-Ex4 DCDC1 deletion suggested that molecular cues causing variation in disease in the posterior segment differ from those at play in the anterior segment. Results in 3 patients without identifiable PAX6 mutations and a review of the literature suggest that such cases be described as phenocopies rather than actual cases of the syndrome of aniridia.

Assessment of PAX6 alleles in 66 families with aniridia

We report on PAX6 alleles associated with a clinical diagnosis of classical aniridia in 81 affected individuals representing 66 families. Allelic variants expected to affect PAX6 function were identified in 61 families (76 individuals). Ten cases of sporadic aniridia (10 families) had complete (8 cases) or partial (2 cases) deletion of the PAX6 gene. Sequence changes that introduced a premature termination codon into the open reading frame of PAX6 occurred in 47 families (62 individuals). Three individuals with sporadic aniridia (three families) had sequence changes (one deletion, two run-on mutations) expected to result in a C-terminal extension. An intronic deletion of unknown functional significance was detected in one case of sporadic aniridia (one family), but not in unaffected relatives. Within these 61 families, single nucleotide substitutions accounted for 30/61 (49%), indels for 23/61 (38%), and complete deletion of the PAX6 locus for 8/61 (13%). In five cases of sporadic aniridia (five families), no disease-causing mutation in the coding region was detected. In total, 23 unique variants were identified that have not been reported in the Leiden Open Variation Database (LOVD) database. Within the group assessed, 92% had sequence changes expected to reduce PAX6 function, confirming the primacy of PAX6 haploinsufficiency as causal for aniridia.

A novel PAX6 mutation in Chinese patients with severe congenital aniridia

PURPOSE

We identified a novel mutation in Paired Box gene 6 (PAX6) and characterized its associated clinical features of severe ocular malformation in a Chinese family with congenital aniridia.

METHODS

We studied two patients with aniridia from a Chinese family. All patients and noncarriers in this family underwent full ophthalmologic, general and urinary examinations. Total genomic DNA was isolated from peripheral blood of two aniridia patients. PAX6 levels were determined by PCR and its mutational status was determined by sequencing. Direct sequencing detected variations in PAX6.

RESULTS

Patients had bilateral congenital nystagmus, anterior polar cataract, absence of iris tissue, and foveal hypoplasia with severely reduced visual acuity. A novel heterozygous PAX6 mutation in exon 6 c.662G>A (p.W100X) was identified which created a premature termination codon. This observed sequence alteration was not found in 100 normal controls and has not been previously reported.

CONCLUSIONS

We identified a novel PAX6 mutation in a family with severe ocular malformation. Our study expands the mutational spectrum of PAX6 and enriches our knowledge of the relationship between genotype and phenotype due to these mutations.

Comparison between aniridia with and without PAX6 mutations: clinical and molecular analysis in 14 Korean patients with aniridia

PURPOSE

To describe clinical and molecular characteristics of Korean patients with aniridia and to compare the clinical phenotype between those having an identifiable PAX6 mutation and those not.

DESIGN

Comparative case series.

PARTICIPANTS

A total of 14 Korean patients from 10 families with aniridia.

METHODS

Complete ophthalmologic examinations were performed for all patients. PAX6 analysis included direct sequencing of all coding regions and multiplex ligation-dependent probe amplification (MLPA) to detect large deletions when the sequencing was negative. If the PAX6 analysis failed to reveal any identifiable mutations, genomic copy number variation analysis via array comparative genomic hybridization (CGH) and candidate gene PITX3 and FOXE3 sequencing were then performed.

MAIN OUTCOME MEASURES

Severity of ocular abnormalities and genetic findings.

RESULTS

Sequencing of PAX6 exhibited 5 different heterozygous mutations in 8 patients from 5 families; 2 (p.Ser43Phe, IVS8-9C>G) were novel, and 3 (p.Arg208Trp, p.Arg317X, and p.X423L) have been previously reported. Among the remaining 6 patients in whom the PAX6 sequencing was negative, MLPA identified large deletions in 2 sporadic patients. However, the array CGH and candidate gene sequencing found no genomic or genetic abnormalities. The mutation detection rate was therefore 70%. Patients harboring an identifiable mutation in PAX6 had either a severe or a mild variant phenotype depending on the type of mutations. Likewise, among patients without an identifiable PAX6 mutation, their phenotypes varied widely from severe to very mild.

CONCLUSIONS

This study adds 2 novel PAX6 mutations to those previously reported, providing further evidence for genetic and phenotypic heterogeneity in aniridic ocular malformation. There was no difference in the clinical phenotype between patients with and without detectable mutations in the PAX6 gene. The wide variability of ocular phenotype regardless of the presence or absence of PAX6 mutations calls for a further appreciation of the complexity in the molecular diagnosis of aniridia and suggests that this ocular malformation may be better regarded as a group of heterogeneous disorders, rather than a single disease entity, associated with mutations in PAX6 and/or other genes located elsewhere in the human genome.

FINANCIAL DISCLOSURE(S)

The authors have no proprietary or commercial interest in any of the materials discussed in this article.

A novel heterozygous deletion within the 3' region of the PAX6 gene causing isolated aniridia in a large family group

Paired box gene 6 (PAX6) is the causative gene of aniridia. It is a dominantly inherited eye abnormality characterized by partial or complete absence of the iris. The PAX6 gene is located on chromosome 11p13 and contains 14 exons. It is expressed mainly in the developing eye and central nervous system. Submicroscopic copy number variations are common in the human genome. Submicroscopic deletions may cause several human diseases, either by disrupting coding sequences or by eliminating regulatory elements essential for expression of the gene in question. Over the past several years, array-based comparative genomic hybridization has become an increasingly useful tool for both identifying normal cytogenetic variations and characterizing chromosomal abnormalities associated with developmental delays and cancer. Our results support the notion that assessing copy number variation of the PAX6 gene itself and also of flanking regions, may contribute to the molecular diagnosis of aniridia.

Paired box 6 (PAX6) regulates glucose metabolism via proinsulin processing mediated by prohormone convertase 1/3 (PC1/3)

AIMS/HYPOTHESIS

Human patients with aniridia caused by heterozygous PAX6 mutations display abnormal glucose metabolism, but the underlying molecular mechanism is largely unknown. Disturbed islet architecture has been proposed as the reason why mice with complete inactivation of paired box 6 (PAX6) in the pancreas develop diabetes. This is not, however, the case in human aniridia patients with heterozygous PAX6 deficiency and no apparent defects in pancreatic development. We investigated the molecular mechanism underlying the development of abnormal glucose metabolism in these patients.

METHODS

A human aniridia pedigree with a PAX6 R240Stop mutation was examined for abnormal glucose metabolism using an OGTT. The underlying mechanism was further investigated using Pax6 R266Stop mutant small-eye mice, which also have abnormal glucose metabolism similar to that in PAX6 R240Stop mutation human aniridia patients.

RESULTS

Paired box 6 (PAX6) deficiency, both in aniridia patients with a heterozygous PAX6 R240Stop mutation and in mice with a heterozygous Pax6 R266Stop mutation, causes defective proinsulin processing and abnormal glucose metabolism. PAX6 can bind to the promoter and directly upregulate production of prohormone convertase (PC)1/3, an enzyme essential for conversion of proinsulin to insulin. Pax6 mutations lead to PC1/3 deficiency, resulting in defective proinsulin processing and abnormal glucose metabolism.

CONCLUSIONS/INTERPRETATION

This study indicates a novel function for PAX6 in the regulation of proinsulin processing and glucose metabolism via modulation of PC1/3 production. It also provides an insight into the abnormal glucose metabolism caused by heterozygous PAX6 mutations in humans and mice.

Genetic analysis of chromosome 11p13 and the PAX6 gene in a series of 125 cases referred with aniridia

A series of 125 patients referred primarily with aniridia classified as either sporadic (74), familial (24), or in association with WAGR syndrome (14) or other malformations (13) was analysed for mutations, initially by karyotyping and targeted FISH analysis of chromosome 11p13. These methods identified mutations in a significant proportion of patients, 34/125 (27%). Two cases had chromosome rearrangements involving 11p13, 16 cases had visible deletions, and 16 cases had cryptic deletions identified by FISH. The frequency of cryptic deletions in familial aniridia was 27% and in sporadic isolated aniridia was 22%. Of the 14 cases referred with WAGR syndrome, 10 (71%) had chromosomal deletions, 2 cryptic and 8 visible. Of the 13 cases with aniridia and other malformations, 5 (38%) had a chromosomal rearrangement or deletion. In 37 cases with no karyotypic or cryptic chromosome abnormality, sequence analysis of the PAX6 gene was performed. Mutations were identified in 33 cases; 22 with sporadic aniridia, 10 with familial aniridia and 1 with aniridia and other non-WAGR syndrome associated anomalies. Overall, 67 of 71 cases (94%) undergoing full mutation analysis had a mutation in the PAX6 genomic region.

Pax6 3' deletion results in aniridia, autism and mental retardation

The PAX6 gene is a transcription factor expressed early in development, predominantly in the eye, brain and gut. It is well known that mutations in PAX6 may result in aniridia, Peter's anomaly and kertatisis. Here, we present mutation analysis of a patient with aniridia, autism and mental retardation. We identified and characterized a 1.3 Mb deletion that disrupts PAX6 transcriptional activity and deletes additional genes expressed in the brain. Our findings provide continued evidence for the role of PAX6 in neural phenotypes associated with aniridia.

Variable phenotype related to a novel PAX 6 mutation (IVS4+5G>C) in a family presenting congenital nystagmus and foveal hypoplasia

PURPOSE

Several ocular defects have been identified as a consequence of the PAX6 gene mutations. With regard to the implication of this gene in unusual phenotypes, we report a family presenting with congenital nystagmus, foveal hypoplasia, and iris hypoplasia or atypical coloboma.

DESIGN

Observational case report.

METHODS

The entire transcribed region of the PAX6 gene was submitted to mutation search at the DNA and mRNA levels in five affected members of a French family in test with 82 normal subjects.

RESULTS

A novel heterozygous PAX6 gene splice mutation (IVS4 + 5G>C) was identified. The mutation is located in IVS4 within the consensus donor splice site. A mutant mRNA lacking exon 4 as the sole defect was evidenced. The resultant protein was predicted to contain a cryptic ATG initiation codon in exon 3 and a slightly altered paired-domain in an open reading frame extended by 13 amino acids.

CONCLUSIONS

The association of anterior segment anomalies and foveal hypoplasia with one of the slightest alterations of the PAX6 protein described to date confirms the association of variant phenotypes with hypomorphic alleles. Mutation screening of the PAX6 gene could be useful in elucidating the origin of complex ocular malformations.

Three novel PAX6 mutations in patients with aniridia

AIMS

To describe mutations in the PAX6 gene in five patients with aniridia from three unrelated families.

METHODS

The PAX6 gene was analysed using single stranded conformational polymorphism analysis and direct sequencing.

RESULTS

In one family, three individuals from two generations had aniridia, whereas in each of the other families only one member was affected. The first patient had the heterozygous Q221X (1023C --> T) nonsense mutation in exon 8. The same mutation was found in his mother and sister. Another patient had a heterozygous Q297X (1252C --> T) mutation in exon 10. The third patient carried a heterozygous IVS5+2T --> C mutation leading to aberrant splicing of mRNA.

CONCLUSIONS

These findings provide further examples of haploinsufficiency of PAX6 in aniridia.

Missense mutations in the DNA-binding region and termination codon in PAX6

We have identified nine novel intragenic mutations of the PAX6 gene in 30 patients with aniridia. One patient with Wilms' tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR syndrome) had deletion of 11p and had lost the paternal PAX6 allele. Two patients had small deletions: a frameshift that should result in early termination of the PAX6 protein, and a frameshift that leads to a termination-site change and run-on into the 3' untranslated region (UTR). The other 27 patients had single base-pair mutations. Four had splicing defects; three had IVS6+1G>A, which was at a mutation hotspot in the PAX6 gene; 10 had premature termination (four 1024C>T [R203X], also at a mutation hotspot); and six had missense mutations. Missense mutation A321T (1378G>A) was a polymorphic change; the other five missense mutations were L46R, C52R, I56T, G73D, and I87K. These five codons are in the PAX6 paired domain and are highly conserved throughout the entire paired family. Seven patients had a mutation in the normal stop codon (TAA). This change leads to run-on into the 3' UTR and is also at a mutation hotspot. All 30 mutations should result in PAX6 haploinsufficiency. No correlation was observed between mutation sites and phenotypes.

Screening for PAX6 gene mutations is consistent with haploinsufficiency as the main mechanism leading to various ocular defects

PAX6, a paired box transcriptional factor, is considered as the master control gene for morphogenesis of the eye. Human PAX6 mutations have been associated with a range of eye abnormalities, including aniridia, various anterior segment defects and foveal hypoplasia. We carried out a mutational analysis of the PAX6 gene in 54 unrelated patients with aniridia or related syndromes. A deleterious variation was evidenced in 17 sporadic cases (50%) and in 13 (72%) familial cases. Twenty-four different mutations, 17 of which are novel, were found. The spectrum of PAX6 mutations was highly homogeneous: 23 mutations (96%) leading to premature stop codons (eight nonsense and four splice site mutations, 11 insertions and deletions) and only one (4%) missense mutation. Twenty-two mutations were associated with aniridia phenotypes whereas two were associated with atypical phenotypes. These latter encompassed a missense mutation (R19P) in an individual with a microphthalmia-sclerocornea and a splice site mutation (IVS4+5G > C) in a family presenting with a congenital nystagmus. Both represented the most probably hypomorphic alleles. Aniridia cases were associated with nonsense or frameshifting mutations. A careful examination of the phenotypes did not make it possible to recognise significant differences whenever the predicted protein was deprived of one or another of its functional domains. This strongly suggested that most of the truncating mutations generated null alleles by nonsense mediated mRNA decay. Our observations support the concept of dosage effects of the PAX6 mutations as well as presenting evidence for variable expressivity.

Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases

I estimate per nucleotide rates of spontaneous mutations of different kinds in humans directly from the data on per locus mutation rates and on sequences of de novo nonsense nucleotide substitutions, deletions, insertions, and complex events at eight loci causing autosomal dominant diseases and 12 loci causing X-linked diseases. The results are in good agreement with indirect estimates, obtained by comparison of orthologous human and chimpanzee pseudogenes. The average direct estimate of the combined rate of all mutations is 1.8x10(-8) per nucleotide per generation, and the coefficient of variation of this rate across the 20 loci is 0.53. Single nucleotide substitutions are approximately 25 times more common than all other mutations, deletions are approximately three times more common than insertions, complex mutations are very rare, and CpG context increases substitution rates by an order of magnitude. There is only a moderate tendency for loci with high per locus mutation rates to also have higher per nucleotide substitution rates, and per nucleotide rates of deletions and insertions are statistically independent on the per locus mutation rate. Rates of different kinds of mutations are strongly correlated across loci. Mutational hot spots with per nucleotide rates above 5x10(-7) make only a minor contribution to human mutation. In the next decade, direct measurements will produce a rather precise, quantitative description of human spontaneous mutation at the DNA level.

PAX6, paired domain influences sequence recognition by the homeodomain

PAX6 functions as a transcription factor and has two DNA-binding domains, a paired domain (PD) and a homeodomain (HD), joined by a glycine-rich linker and followed by a proline-serine-threonine-rich (PST) transactivation region at the C terminus. The mechanism of PAX6 function is not clearly understood, and few target genes in vertebrates have been identified. In this report we described the functional analyses of patient missense mutations from the paired domain region of PAX6 and a paireddomain-less isoform (PD-less) of Pax6 that lacks the paired domain and part of the glycine-rich linker. The PD-less was expressed in the brain, eyes, and pancreas of mouse. The level of expression of this isoform was relatively higher in brain. The mutation sites PAX6-L46R and -C52R were located in the PD of PAX6 on either end of the 5a-polypeptide insert of the alternatively spliced form of PAX6, PAX6-5a. Another PAX6 mutant V53L described in this report was adjacent to C52R. We created corresponding mutations in PAX6 and PAX6-5a, and evaluated their transcriptional activation and DNA binding properties. The PD mutants of PAX6 (L46R, C52R, and V53L) exhibited lower transactivation activities and variable DNA binding ability than wild-type PAX6 with PD DNA-binding consensus sequences. The mutated amino acids containing PAX6-5a isoforms showed unexpected transactivation properties with a reporter containing HD DNA-binding sequences. PAX6-5a-C52R, and -V53L showed lower transactivation activities, but PAX6-5a-L46R had greater transactivation ability than PAX6-5a. The PD-less isoform of Pax6 lost its transactivational ability but could bind to the HD DNA-binding sequences. Functional analysis of the PD-less isoform of Pax6 as well as findings related to missense mutations in the PD suggest that the PD of PAX6 is required for HD function.

Mutation in the PAX6 gene in twenty patients with aniridia

This is a report on the nature of the mutations in the PAX6 gene in twenty patients with aniridia. Five of the twenty patients had sporadic aniridia with deletions in chromosome 11p13. Three of the five had WAGR syndrome (Wilms tumor, aniridia, genitourinary anomalies, mental retardation), and the other two had deletions whose breakpoints occurred between the PAX6 and the WT1 genes. Allelic losses at PAX6 were of paternal origin. The remaining fifteen patients with aniridia had intragenic mutations in the PAX6 gene, with mutations found from exon 5 to exon 12. Twelve cases of dysfunctional PAX6 were due to premature termination of the protein by nonsense mutations (five cases), splicing defect (one case), deletion (two cases), deletion-insertions (two cases), and tandem repeat insertions (two cases). One patient (P2) had a PAX6 protein with de novo in-frame deletion of alanine, arginine, and proline at codon positions 37, 38, and 39. These codons are in the paired box region, and codon 38 is in contact with the phosphate group of the sugar-phosphate backbone of the target DNA. Another patient (P8) had a single nucleotide transition at c.1182 (nucleotide number, Genbank accession #M93650, used as in Glaser et al. [1992]), which generated both a missense mutation (Q255H) and a splicing defect. A missense mutation was found at G387E in a third patient (P10). All observed mutations support the notion that haploinsufficiency in PAX6 results in aniridia and associated eye anomalies.