Human glycine decarboxylase gene ( GLDC) and its highly conserved processed pseudogene ( ψ GLDC) : their structure and expression, and the identification of a large deletion in a family with nonketotic hyperglycinemia

Abstract

Mutations in the glycine decarboxylase gene (GLDC) cause nonketotic hyperglycinemia (NKH), an in-born error of metabolism characterized by severe neurological disturbance. We have determined the structure of GLDC and of its pseudogene (psiGLDC) and studied their expression for a molecular analysis of NKH. The GLDC gene spans at least 135 kb and consists of 25 exons. All donor and acceptor sites adhere to the canonical GT-AG rule, except for the donor site of intron 21, where a variant form GC is used instead of GT. The transcription initiation site has been assigned to a residue 163 bp upstream from the translation initiation triplet by primer extension analysis. The psiGLDC gene has no intron and shares 97.5% homology with the coding region of functional GLDC, suggesting that psiGLDC is a processed pseudogene that arose from the GLDC transcript about 4-8 million years ago. RNA blotting analysis has revealed that GLDC is expressed in human liver, kidney, brain, and placenta. We have also examined a patient with NKH with no detectable GLDC mRNA in his lymphoblasts. Exons 1-3 of the functional GLDC gene from this patient are not amplified by polymerase chain reaction (PCR), whereas those from control subjects are. These results suggest a large homozygous deletion (at least 30 kb) in the patient. Furthermore, we have devised a semi-quantitative PCR to estimate the number of GLDC alleles by using psiGLDC as an internal control and have confirmed the homozygosity and heterozygosity of the deletion in the patient and his parents, respectively. Structural information of GLDC and psiGLDC should facilitate the molecular analysis of NKH.

Pitfalls in the diagnosis of glycine encephalopathy (non‐ketotic hyperglycinemia)

“…40 Furthermore, mutation analysis of the P-protein gene, the most commonly affected gene in NKH, is complicated by the existence of a processed pseudogene for the P protein (ϕGLDC) with 97.5% sequence homology to cDNA of GLDC. [41][42] Due to these practical limitations, the diagnosis of NKH, at least in the initial stage if not ultimately, is usually based solely on the determination of plasma and CSF glycine concentrations. In neonatal-onset NKH, with the classical clinical phenotype and marked elevations of glycine levels and C:PGR, the diagnosis may seem clear cut.…”

Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia

“…In 14 of 36 patients, GLDC mutations were identified in only one allele, suggesting that some mutations are not detected by the exon-sequencing method. We have reported several patients with deletion of GLDC exon 1, 22 and Sellner et al 20 have reported a patient with deletion of the GLDC exons 2-15. These studies suggest that a considerable number of deletions may remain unidentified in GLDC.…”

A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among patients with glycine encephalopathy in Jerusalem

“…We have amplified 25 exons of the GLDC gene by PCR, as described (Takayanagi et al 2000), as well as nine exons of the AMT gene and five exons of the GCSH gene. Exon Amplicons were subjected to 2.5% agarose gel electrophoresis, and bands with the expected size were cut out for DNA purification.…”