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PAX6 gene analysis in irido-fundal coloboma.

Kumar K, Tanwar M, Naithani P, Insaan R, Garg S, Venkatesh P, Dada R - Mol. Vis. (2011)

Bottom Line: This study expands the SNP spectrum of PAX6, only rare variations which are not causative have been found.Since this is a pilot study in the north Indian population, results should be confirmed in different populations by similar studies.Familial cases are required for determining the underlying genetic loci accounting for this clinical phenotype and may lead to better understanding of disease pathogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India.

ABSTRACT

Purpose: To screen the paired box gene 6 (PAX6) gene in irido-fundal coloboma.

Methods: The entire coding region of PAX6 including intron-exon boundaries was amplified from cases (n=30) and controls (n=30). All sequences were analyzed against the ensemble sequence (ENSG00000007372) for PAX6.

Results: DNA sequence analysis of patients and controls revealed a total of three nucleotide changes (g.31815391Cytosine>Thymine; Glycine72Glycine and g.31812215Thymine>Guanine) of which one was neutral/synonymous change and the remaining two were intronic changes. Of these 3 changes, 2 were novel and one was already reported change. All these changes were non-pathogenic, according to in silico analysis.

Conclusions: In our study no pathogenic PAX6 mutation were identified. This suggests involvement of other coloboma genes. This study expands the SNP spectrum of PAX6, only rare variations which are not causative have been found. Since this is a pilot study in the north Indian population, results should be confirmed in different populations by similar studies. Familial cases are required for determining the underlying genetic loci accounting for this clinical phenotype and may lead to better understanding of disease pathogenesis.

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Related in: MedlinePlus

DNA sequence of PAX6 equivalent to codon 71–75. A: The reference sequence derived from the control shows the heterozygous c.216T>G change which predicts a codon change from GGT>GGG and p.G72G mutation. B: The sequence derived from another patient shows a homozygous p.G72G mutation.
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f5: DNA sequence of PAX6 equivalent to codon 71–75. A: The reference sequence derived from the control shows the heterozygous c.216T>G change which predicts a codon change from GGT>GGG and p.G72G mutation. B: The sequence derived from another patient shows a homozygous p.G72G mutation.

Mentions: In this mutation a single nucleotide T was replaced by guanine (G) at genomic position g.31823250; cDNA position c.216; codon 72 resulted in a codon change GGT>GGG which predicts a synonymous change p.Gly72Gly (p.G72G; Figure 5). This change was present as heterozygous change in 29 cases and 20 controls; and as a homozygous change in one case. This change was novel and registered at GenBank with accession number HQ397714.


PAX6 gene analysis in irido-fundal coloboma.

Kumar K, Tanwar M, Naithani P, Insaan R, Garg S, Venkatesh P, Dada R - Mol. Vis. (2011)

DNA sequence of PAX6 equivalent to codon 71–75. A: The reference sequence derived from the control shows the heterozygous c.216T>G change which predicts a codon change from GGT>GGG and p.G72G mutation. B: The sequence derived from another patient shows a homozygous p.G72G mutation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108901&req=5

f5: DNA sequence of PAX6 equivalent to codon 71–75. A: The reference sequence derived from the control shows the heterozygous c.216T>G change which predicts a codon change from GGT>GGG and p.G72G mutation. B: The sequence derived from another patient shows a homozygous p.G72G mutation.
Mentions: In this mutation a single nucleotide T was replaced by guanine (G) at genomic position g.31823250; cDNA position c.216; codon 72 resulted in a codon change GGT>GGG which predicts a synonymous change p.Gly72Gly (p.G72G; Figure 5). This change was present as heterozygous change in 29 cases and 20 controls; and as a homozygous change in one case. This change was novel and registered at GenBank with accession number HQ397714.

Bottom Line: This study expands the SNP spectrum of PAX6, only rare variations which are not causative have been found.Since this is a pilot study in the north Indian population, results should be confirmed in different populations by similar studies.Familial cases are required for determining the underlying genetic loci accounting for this clinical phenotype and may lead to better understanding of disease pathogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India.

ABSTRACT

Purpose: To screen the paired box gene 6 (PAX6) gene in irido-fundal coloboma.

Methods: The entire coding region of PAX6 including intron-exon boundaries was amplified from cases (n=30) and controls (n=30). All sequences were analyzed against the ensemble sequence (ENSG00000007372) for PAX6.

Results: DNA sequence analysis of patients and controls revealed a total of three nucleotide changes (g.31815391Cytosine>Thymine; Glycine72Glycine and g.31812215Thymine>Guanine) of which one was neutral/synonymous change and the remaining two were intronic changes. Of these 3 changes, 2 were novel and one was already reported change. All these changes were non-pathogenic, according to in silico analysis.

Conclusions: In our study no pathogenic PAX6 mutation were identified. This suggests involvement of other coloboma genes. This study expands the SNP spectrum of PAX6, only rare variations which are not causative have been found. Since this is a pilot study in the north Indian population, results should be confirmed in different populations by similar studies. Familial cases are required for determining the underlying genetic loci accounting for this clinical phenotype and may lead to better understanding of disease pathogenesis.

Show MeSH
Related in: MedlinePlus