| Literature DB >> 28417071 |
Faiqa Imtiaz1, Abeer Al-Mostafa1, Rabab Allam1, Khushnooda Ramzan1, Nada Al-Tassan1, Asma I Tahir1, Nouf S Al-Numair1, Mohamed H Al-Hamed1, Zuhair Al-Hassnan2,3, Mohammad Al-Owain2,3, Hamad Al-Zaidan2, Mohammad Al-Amoudi4, Alya Qari2, Ameera Balobaid2, Moeenaldeen Al-Sayed2,3.
Abstract
Maple syrup urine disease (MSUD), an autosomal recessive inborn error of metabolism due to defects in the branched-chain α-ketoacid dehydrogenase (BCKD) complex, is commonly observed among other inherited metabolic disorders in the kingdom of Saudi Arabia. This report presents the results of mutation analysis of three of the four genes encoding the BCKD complex in 52 biochemically diagnosed MSUD patients originating from Saudi Arabia. The 25 mutations (20 novel) detected spanned across the entire coding regions of the BCKHDA, BCKDHB and DBT genes. There were no mutations found in the DLD gene in this cohort of patients. Prediction effects, conservation and modelling of novel mutations demonstrated that all were predicted to be disease-causing. All mutations presented in a homozygous form and we did not detect the presence of a "founder" mutation in any of three genes. In addition, prenatal molecular genetic testing was successfully carried out on chorionic villus samples or amniocenteses in 10 expectant mothers with affected children with MSUD, molecularly characterized by this study.Entities:
Year: 2017 PMID: 28417071 PMCID: PMC5388912 DOI: 10.1016/j.ymgmr.2017.03.006
Source DB: PubMed Journal: Mol Genet Metab Rep ISSN: 2214-4269
Homozygous mutations in BCKDHA, BCKDHB and DBT in Saudi Arabian patients with MSUD.
| Mutation (nucleotide) | Protein change | Mutationtaster prediction/score | Polyphen-2.0 prediction/score | Number of patients | Number of families | Clinical phenotype | Reference | |
|---|---|---|---|---|---|---|---|---|
| c.347A > G | p.Asp116Gly* | Disease causing (0.99) | Probably damaging (0.997) | 1 | 1 | Classic | This study | |
| c.409G > A | p.Glu137Lys* | Disease causing (0.99) | Probably damaging (1.00) | 1 | 1 | N/A | This study | |
| c.647-1G > C | Splice | − | − | 1 | 1 | N/A | Georgiou et al. | |
| c.660_663delGTAC | p.Y221Qfs*108* | Disease causing (1) | − | 1 | 1 | Classic | This study | |
| c.809G > A | p.Ala270Thr* | Disease causing (0.99) | Probably damaging (1.00) | 2 | 1 | Intermediate | This study | |
| c.896A > C | p.Asp299Ala* | Disease causing (0.99) | Probably damaging (1.00) | 1 | 1 | Classic | This study | |
| c.905A > C | p.Asp302Ala | Disease causing (0.99) | Probably damaging (1.00) | 4 | 3 | Classic | Rodriguez-Pombo et al. | |
| c.940C > T | p.Arg314Ter | Disease causing (1) | − | 1 | 1 | Classic | Nellis et al. | |
| c.1270C > T | p.Gln424Ter* | Disease causing (0.99) | − | 1 | 1 | Classic | This study | |
| c.1A > T | p.Met1?* | Disease causing (1) | − | 3 | 3 | Classic | This study | |
| c.197G > C | p.Gly66Arg* | Disease causing (0.99) | Possibly damaging (0.757) | 3 | 3 | Classic | This study | |
| c.286delGAA | p.E96del* | Disease causing (0.99) | − | 1 | 1 | Classic | This study | |
| c.502C > T | p.Arg168Cys | Disease causing (0.99) | Probably damaging (0.998) | 2 | 2 | Classic | Flaschker et al. | |
| c.574G > A | p.Gly192Arg* | Disease causing (0.99) | Probably damaging (1.00) | 1 | 1 | Classic | This study | |
| c.817A > C | p.Thr273Pro* | Disease causing (0.99) | Probably damaging (1.00) | 8 | 4 | Intermediate | This study | |
| c.853C > T | p.Arg285Ter | Disease causing (1) | − | 2 | 2 | N/A | Rodriguez-Pombo et al. | |
| c.1004G > A | p.Gly335Asp* | Disease causing (0.99) | Possibly damaging (0.843) | 3 | 2 | Classic | This study | |
| c.1006G > A | p.Gly336Ser* | Disease causing (0.99) | Probably damaging (1.00) | 3 | 3 | Classic | This study | |
| c.1145 T > C | p.Cys382Ser* | Disease causing (0.99) | Possibly damaging (0.905) | 1 | 1 | Classic | This study | |
| c.61delC | p.R21Afs*12* | Disease causing (1) | − | 2 | 1 | N/A | This study | |
| c.74delAT | p.C26Wfs*2* | Disease causing (1) | − | 1 | 1 | N/A | This study | |
| c.137A > G | p.Lys46Arg* | Polymorphism (0.99) | Benign (0.001) | 3 | 1 | Classic | This study | |
| c.939-2A > G | Splice* | − | − | 3 | 1 | Classic | This study | |
| c.1195 T > C | p.Ser399Pro* | Disease causing (0.99) | Probably damaging (1.00) | 1 | 1 | Classic | This study | |
| c.1281 + 3A > G | Splice* | − | − | 2 | 1 | N/A | This study |
* = novel mutation; N/A = no clinical information available, − = not calculable.
Fig. 1Schematic representation of known and novel mutations across BCKDHA, BCKDHB, and DBT genes identified in Saudi Arabian patients with MSUD. Novel mutations are highlighted with an asterisk (*) and closed colored circles represent all mutations and their incidence in the cohort of 52 patients.
Prediction effects of the novel missense mutations.
| Mutation | No. of PDB analyzed | Location of residue | Effect of mutation | Conservation |
|---|---|---|---|---|
| p.Asp116Gly | 24 | α-helix | Instability (destabilizing) | Highly conserved |
| p.Glu137Lys | 26 | Coil | Instability (destabilizing) | Highly conserved |
| p.Ala270Thr | 24 | Coil | Interface-damaging | Fully conserved residue |
| p.Asp299Ala | 25 | β-sheet | Instability (destabilizing) | Fully conserved residue |
| p.Gly66Arg | 24 | Coil | Fold-preventing | Fully conserved residue |
| p.Gly192Arg | 25 | Coil | Instability (destabilizing) | Fully conserved residue |
| p.Thr273Pro | 24 | β-sheet | Instability (destabilizing) | Fully conserved residue |
| p.Gly335Asp | 25 | Coil | Instability (destabilizing) | Fully conserved residue |
| p.Gly336Ser | 26 | Coil | Instability (destabilizing) | Fully conserved residue |
| p.Cys382Ser | 27 | α-helix | Instability (destabilizing) | Fully conserved residue |
| p.Lys46Arg | There is no PDB structure to perform the analysis | Conserved | ||
| p.Ser399Pro | There is no PDB structure to perform the analysis | Fully conserved residue | ||
Causing an internal void ≥ 275 Å to open in the protein owing to the substitution with a smaller residue is considered damaging.
Interfaces are defined by a difference in solvent accessibility between a complex and the individual chain in the crystal structure. A difference of > 10% is taken as indicative of an interface residue. Interfaces may be with another protein chain or a ligand. Affecting residues in the interface with a different protein chain or ligand more likely reflect biologically relevant interactions by a change in solvent-accessibility.
Hydrophobicity values < 0 are hydrophilic.
99% of sidechains in real proteins have an energy less than 34.33 kcal/mol. Consequently energies > 34.33 kcal/mol and < 50 kcal/mol can be considered mild clashes, 50–100 kcal/mol medium clashes, > 100 kcal/mol severe clashes. Note that clash energies can be extremely high (>>100000 kcal/mol).
A “fully conserved residue” indicates positions which have a single, fully conserved residue. A “highly conserved residue” indicates positions with conservation between groups of strongly similar properties. “Conserved” indicates positions with conservation between groups of weakly similar properties.
Results of prenatal genetic testing of targeted mutation analysis of expectant mothers with affected children with MSUD identified by this study.
| Fetus | Sample type | Gene | Target mutation | Amino acid change | Genotype status of fetus |
|---|---|---|---|---|---|
| 1 | CVS | c.660_663delGTAC | p.Y221Qfs*108 | Heterozygous carrier | |
| 2 | Amniotic fluid | c.905A > C | p.Asp302Ala | Normal wild-type | |
| 3 | Amniotic fluid | c.905A > C | p.Asp302Ala | Heterozygous carrier | |
| 4 | Amniotic fluid | c.905A > C | p.Asp302Ala | Heterozygous carrier | |
| 5 | CVS | c.1A > T | p.Met1? | Normal wild-type | |
| 6 | CVS | c.1A > T | p.Met1? | Homozygous affected | |
| 7 | CVS | c.574G > A | p.Gly192Arg | Homozygous affected | |
| 8 | CVS | c.817A > C | p.Thr273Pro | Normal wild-type | |
| 9 | CVS | c.1006G > A | p.Gly336Ser* | Heterozygous carrier | |
| 10 | CVS | c.137A > G | p.Lys46Arg | Heterozygous carrier |
Fig. 2Normal protein structures where the colored spheres show missense and stop codon mutation locations (a) BCKDHA (b) BCKDHB and (c) DBT mutant residues.