Dataset Information

Frequency Determination of ?-1,3 Glucosyltransferase p.Y131H and p.F304S Polymorphisms in the Croatian Population Revealed Five Novel Single Nucleotide Polymorphisms in the hALG6 Gene.

ABSTRACT: The congenital disorder of glycosylation (CDG)-Ic (ALG6-CDG, CDG-Ic) is caused by mutations in the hALG6 gene that encodes the N-glycosylation pathway enzyme, ?-1,3-glucosyltransferase (NP_037471.2). The aim of our study was to estimate the frequencies of ALG6-CDG related p.Y131H and p.F304S polymorphisms in the Croatian population. Genomic DNA was isolated from blood samples collected from 600 healthy individuals. Functional single-nucleotide polymorphisms rs35383149 and rs17856039 causing p.Y131H and p.F304S, respectively, were genotyped by the TaqMan method and direct sequencing. The frequency of p.F304S polymorphism in the studied cohort was shown to be similar to the frequencies found in other tested populations (27%), whereas the frequency of p.Y131H was found to be three times higher (6.7%). Five novel base substitutions in the hALG6 gene were also found: three in exon 5 (c.383T>C, c.390G>A, and c.429G>C) and two in a downstream intervening sequence (IVS5+17C/T and IVS5+34G/A).

SUBMITTER: Goreta SS

PROVIDER: S-EPMC3265770 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Frequency Determination of α-1,3 Glucosyltransferase p.Y131H and p.F304S Polymorphisms in the Croatian Population Revealed Five Novel Single Nucleotide Polymorphisms in the hALG6 Gene.

Goreta Sandra Supraha SS Dabelic Sanja S Pavlinic Dinko D Lauc Gordan G Dumic Jerka J

Genetic testing and molecular biomarkers 20110907 1

The congenital disorder of glycosylation (CDG)-Ic (ALG6-CDG, CDG-Ic) is caused by mutations in the hALG6 gene that encodes the N-glycosylation pathway enzyme, α-1,3-glucosyltransferase (NP_037471.2). The aim of our study was to estimate the frequencies of ALG6-CDG related p.Y131H and p.F304S polymorphisms in the Croatian population. Genomic DNA was isolated from blood samples collected from 600 healthy individuals. Functional single-nucleotide polymorphisms rs35383149 and rs17856039 causing p.Y1 ...[more]

PMID: 21899441

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Project description:BackgroundSingle-nucleotide polymorphisms (SNPs) have a crucial function in affecting the susceptibility of individuals to diseases and also determine how an individual responds to different treatment options. The present study aimed to predict and characterize deleterious missense nonsynonymous SNPs (nsSNPs) of lysozyme C (LYZ C) gene using different computational methods. Lyz C is an important antimicrobial peptide capable of damaging the peptidoglycan layer of bacteria leading to osmotic shock and cell death. The nsSNPs were first analyzed by SIFT and PolyPhen v2 tools. The nsSNPs predicted as deleterious were then assessed by other in silico tools - SNAP, PROVEAN, PhD-SNP, and SNPs & GO. These SNPs were further examined by I-Mutant 3.0 and ConSurf. GeneMANIA and STRING tools were used to study the interaction network of the LYZ C gene. NetSurfP 2.0 was used to predict the secondary structure of Lyz C protein. The impact of variations on the structural characteristics of the protein was studied by HOPE analysis. The structures of wild type and variants were predicted by SWISS-MODEL web server, and energy minimization was carried out using XenoPlot software. TM-align tool was used to predict root-mean-square deviation (RMSD) and template modeling (TM) scores.ResultsEight missense nsSNPs (T88N, I74T, F75I, D67H, W82R, D85H, R80C, and R116S) were found to be potentially deleterious. I-Mutant 3.0 determined that the variants decreased the stability of the protein. ConSurf predicted rs121913547, rs121913549, and rs387906536 nsSNPs to be conserved. Interaction network tools showed that LYZ C protein interacted with lactoferrin (LTF). HOPE tool analyzed differences in physicochemical properties between wild type and variants. TM-align tool predicted the alignment score, and the protein folding was found to be identical. PyMOL was used to visualize the superimposition of variants over wild type.ConclusionThis study ascertained the deleterious missense nsSNPs of the LYZ C gene and could be used in further experimental analysis. These high-risk nsSNPs could be used as molecular targets for diagnostic and therapeutic interventions.

Dataset Information

Frequency Determination of ?-1,3 Glucosyltransferase p.Y131H and p.F304S Polymorphisms in the Croatian Population Revealed Five Novel Single Nucleotide Polymorphisms in the hALG6 Gene.

Publications

Frequency Determination of α-1,3 Glucosyltransferase p.Y131H and p.F304S Polymorphisms in the Croatian Population Revealed Five Novel Single Nucleotide Polymorphisms in the hALG6 Gene.

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