Intragenic deletions of ALDH7A1 in pyridoxine-dependent epilepsy caused by Alu - Alu recombination

Abstract

Objective: To investigate the role of intragenic deletions of ALDH7A1 in patients with clinical and biochemical evidence of pyridoxine-dependent epilepsy but only a single identifiable mutation in ALDH7A1.Methods: We designed a custom oligonucleotide array with high-density probe coverage across the ALDH7A1 gene. We performed array comparative genomic hybridization in 6 patients with clinical and biochemical evidence of pyridoxine-dependent epilepsy but only a single detectable mutation in ALDH7A1 by sequence analysis. Results:We found partial deletions of ALDH7A1 in 5 of 6 patients. Breakpoint analysis reveals that the deletions are likely a result of Alu-Alu recombination in all cases. The density of Alu elements within introns of ALDH7A1 suggests susceptibility to recurrent rearrangement. Conclusion:Patients with clinical pyridoxine-dependent epilepsy and a single identifiable mutation in ALDH7A1 warrant further investigation for copy number changes involving the ALHD7A1 gene. Neurology ® 2015;85:756-762 GLOSSARY a-AASA 5 a-aminoadipic semialdehyde; CGH 5 comparative genomic hybridization; PDE 5 pyridoxine-dependent epilepsy.First described in 1954, pyridoxine-dependent epilepsy (PDE) is a metabolic epileptic encephalopathy characterized by pharmacoresistant seizures that typically come under control after initial administration followed by supplementation of pyridoxine at pharmacologic doses. The biochemical and genetic bases of this rare familial epilepsy were solved in 2006 when mutations in ALDH7A1 resulting in dysfunction of the protein antiquitin were discovered. 1 Metabolic changes consistent with PDE can be detected by measuring elevated levels of the biomarker a-aminoadipic semialdehyde (a-AASA) in various body fluids.1,2 As elevations of a-AASA are also present in patients with molybdenum cofactor deficiency and isolated sulfite oxidase deficiency, 3 genotyping of ALDH7A1 is required to confirm the diagnosis. In the vast majority of published cases, homozygous or compound heterozygous mutations of both ALDH7A1 alleles have been detected.We investigated 6 patients with a clinical diagnosis of PDE and positive biomarkers in which only a single, heterozygous mutation in ALDH7A1 could be identified by sequence analysis. We designed a custom oligonucleotide array that included high-density probe coverage of the ALDH7A1 gene to look for intragenic deletions or duplications that would have been missed by conventional sequence analysis. Using this strategy, we found partial deletions of ALDH7A1 in 5 of 6 patients, each of which is likely the result of an Alu-Alu recombination event. Our results suggest that in patients with clinical and biochemical evidence of PDE in the setting of a

Pyridoxine-Dependent Epilepsy: An Expanding Clinical Spectrum

“…If sequencing does not reveal point mutations, molecular testing for insertions, copy number variants, and intronic variants should be performed. 59 To date, more than 80 mutations have been reported within the 18 exons of ALDH7A1 on the Human Gene Mutation Database web site. The missense mutation, p.E399Q in exon 14, occurs in various populations and accounts for about 30% of published alleles.…”

Structural and biochemical consequences of pyridoxine‐dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1

“…2). Approximately 16 cases of patients harboring one of these mutations have been reported in the literature [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29]. All of these patients have biallelic mutations consistent with autosomal recessive inheritance, and the majority is compound heterozygous for one of the mutations studied here.…”

“…Herein, we investigate the biochemical and structural consequences of PDE-associated mutations that affect residues in the substrate AASAL-binding site: N167S [14][15][16][17][18][19][20][21], P169S [22,23], A171V [13,24,25], G174V [24,26,27], and W175G [22,28,29] (Fig. 2).…”

The genotypic spectrum of ALDH7A1 mutations resulting in pyridoxine dependent epilepsy: A common epileptic encephalopathy

“…11,12 A small number of patients were reported to have a single pathogenic variant identified, 10,12 and the majority of these patients were later identified to have an intragenic copy number variations (CNVs) within ALDH7A1. 14 Genetic testing, either through specific gene panels or genomic sequencing, is increasingly accepted as first tier testing for epileptic encephalopathies, even when pathognomonic biomarkers exist. Genetic testing is a powerful diagnostic tool and limits the need for clinical suspicion of PDE and targeted testing.…”