| Literature DB >> 35661454 |
Hoda A Ahmed1, Fatina I Fadel2, Mohamed A Abdel Mawla3, Doaa M Salah2, Mohamed Gamal Fathallah2, Khalda Amr1.
Abstract
BACKGROUND: Primary hyperoxaluria (PH) is a rare heterogeneous, autosomal recessive disorder of glyoxylate metabolism. It is characterized by excessive hepatic production of oxalate resulting in a wide spectrum of clinical, imaging, and functional presentation. The characteristic features of PH comprise of recurrent urolithiasis, renal stones, and/or nephrocalcinosis. Three known types of PH have been identified PH1, PH2, and PH3. Pathogenic variants in AGXT, GRHPR, and HOGA1 cause the phenotypic expression of PH.Entities:
Keywords: zzm321990AGXTzzm321990; NGS; PH; mutations; recessive
Mesh:
Substances:
Year: 2022 PMID: 35661454 PMCID: PMC9356549 DOI: 10.1002/mgg3.1992
Source DB: PubMed Journal: Mol Genet Genomic Med ISSN: 2324-9269 Impact factor: 2.473
Clinical manifestations of the studied Egyptian primary hyperoxaluria (PH) patients
| Family | Patient | Sex | Age of onset | Consanguinity | Family history | Nephrolithiasis | Nephrocalcinosis | Infection | ESRD | Hydronephrosis | On dialysis | Systemic oxalosis | Oxaluria μmol/24 h) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| F1 | P1 | M | 11 m | + | + | + | + | + | + | + | Yes |
Myocardial infiltrations and left ventricular hypertrophy Bone deformities | 821 μmol/24 h |
| F2 | P2 | M | 1 y | + | + | + | − | − | + | + | Yes |
Bone deformities | 750 μmol/24 h |
| F3 | P3 | M | 6 m | + | − | + | + | + | + | − | Yes |
Bone deformities | 876 μmol/24 h |
| F4 | P4 | F | 10 m | − | − | + | − | − | + | − | Yes |
Bone deformities Retinal deposition of oxalates and unilateral loss of vision | 605 μmol/24 h |
| F5 | P5 | M | 1 y 2 m | + | + | + | + | + | + | + | Yes |
Myocardial infiltrations and left ventricular hypertrophy | 798 μmol/24 h |
| F6 | P6 | M | 1 y 5 m | − | + | + | − | − | + | − | Yes |
Bone deformities | 630 μmol/24 h |
| F7 | P7 | F | 11 m | + | − | + | + | + | + | + | Yes |
Myocardial infiltrations and left ventricular hypertrophy Bone deformities | 781 μmol/24 h |
| F8 | P8 | F | 8 m | + | − | + | + | − | + | − | Yes |
Bone deformities | 805 μmol/24 h |
| F9 | P9 | M | 9 m | + | + | − | + | + | + | + | Yes |
Myocardial infiltrations and left ventricular hypertrophy | 642 μmol/24 h |
| F10 | P10 | M | 1 y 6 m | + | + | + | − | + | + | + | Yes | − | 621 μmol/24 h |
| F11 | P11 | F | 5 y 6 m | + | + | − | + | + | − | − | No |
Bone deformities | 532 μmol/24 h |
| F12 | P12 | M | 1 y 4 m | + | − | + | + | + | + | + | Yes |
Bone deformities | 760 μmol/24 h |
| F13 | P13 | M | 2 y | + | + | + | + | _ | + | − | Yes |
Bone deformities | 540 μmol/24 h |
| F14 | P14 | F | 1 y 11 m | + | + | + | + | − | + | − | Yes |
Bone deformities | 679 μmol/24 h |
| F15 | P15 | F | 2 y 3 m | + | − | − | + | + | + | − | yes |
Bone deformities | 549 μmol/24 h |
| F16 | P16 | M | 2 y 7 m | − | − | + | − | + | Yes |
Retinal deposition of oxalates and unilateral loss of vision | 767 μmol/24 h | ||
| F17 | P17 | F | 1 y 2 m | + | + | + | − | − | + | + | Yes |
Myocardial infiltrations and left ventricular hypertrophy | 760 μmol/24 h |
| F18 | P18 | M | 2 y 2 m | + | + | + | − | + | + | yes | − | 578 μmol/24 h | |
| F19 | P19 | M | 6 y 7 m | + | + | + | + | − | − | − | No | − | 476 μmol/24 h |
| F19 | P20 | M | 5 y 1 m | + | + | + | + | − | − | − | No | − | 567 μmol/24 h |
| F20 | P21 | M | 11 m | − | − | + | + | − | + | − | Yes |
Bone deformities | 746 μmol/24 h |
| F21 | P22 | M | 6 y | − | − | − | + | − | − | − | No | − | 465 μmol/24 h |
Prediction of the potential pathogenicity of the novel variants
| Name of the variants | gnomAD MAF | ExAC MAF | 1000 Genome | Mutation taster prediction and score | PolyPhen‐2.0 prediction and score | SIFT | PhD‐SNP | Mutation Assessor | PROVEAN | SNPs &GO | MutPred | PROVEAN |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
c.80G > A p.Gly27Glu | N/A | N/A | N/A | Disease causing (prob:0.99) | Probably damaging (1.000) | Damaging (0.001) | Disease (RI = 7) | High (4.05) | Deleterious (−7.27) | Disease (RI = 10) |
Deleterious (0.886) Altered Transmembrane protein (0.9; 0.05) Loss of N‐terminal acetylation at M1 (0.02; 7.0e‐03) | Deleterious (−7.27) |
|
c.766delC p.Gln256Serfs*17 | N/A | N/A | N/A | disease causing (prob: 1) | – | – | – | – | – | – | – | – |
Notes: PHD‐SNP & SNPs & GO: directly predicts disease effect and gives Reliability Index range from 0 to 10. 0 unreliable and 10 reliable; MutationAssessor: predicted functional, that is, high (“H”) or medium (“M”) or predicted nonfunctional, that is, low (“L”) or neutral (“N”). Score cutoffs between “H” and “M,” “M” and “L,” and “L” and “N,” are 3.5, 1.935, and 0.8, respectively; PROVEAN: scores ≤−2.5 is predicted as “Damaging”; otherwise, it is predicted as “Neutral”; REVEL, PolyPhen2, and MutPred: score ranges from 0.0 (tolerated) to 1.0 (deleterious); SIFT: threshold for intolerance is 0.0.
FIGURE 2Bioinformatics analysis of a novel missense mutation (c.80G>A, p.Gly27Glu) on protein structure.
FIGURE 1Sequencing chromatograms of AGXT mutations identified in our cohort. (a–b) Two novel AGXT mutations. (c–d) Previously reported AGXT mutations. Wild‐type sequences are shown above each chromatogram and arrows point toward single base changes.
AGXT (NM_000030.3) variations detected in the studied patients with PH1
| Fam | Patient | Exon | Mutation | Type of mutation | Genotype | Reference |
|---|---|---|---|---|---|---|
| Nucleotide change | ||||||
| Protein changes | ||||||
| F1‐7 | P1‐7 | E1 |
c.33dupC p.Lys12Glnfs*156 | Frameshift/insertion | Homozygous | Pirulli et al. ( |
| F8‐11 | P8‐11 | E1,7,10 |
c.[33dupC];[32C > T;731 T > C;1020A > G] p.[Lys12Glnfs*156]; [Pro11Leu;Ile244Thr;Ile340Met] |
Frameshift/Insertion Missense |
Compound Heterozygous | Purdue et al. ( |
| F12‐18 | P12‐18 | E1 |
c.33delC p.Lys12Argfs*34 | Frameshift/deletion | Homozygous | Pirulli et al. ( |
| F19 | P19‐20 | E1 |
c.80G > A p.Gly27Glu | Missense | Homozygous | Current study |
| F20 | P21 | E7 |
c.766delC p.Gln256Serfs*17 | Frameshift/deletion | Homozygous | Current study |
| F21 | P22 | E1 |
c.[65A > G];[1020A > G] p.[Asn22Ser];[Ile340Met] | Missense | Heterozygous | Williams et al. ( |
Nucleotide changes are based on AGXT (NM_000030.2) reference sequences.
Protein changes are based on AGXT(NP_000021.1) reference sequences.
References refer to the first study to report the respective mutations.