Alu-Alu Recombination Underlying the First Large Genomic Deletion in GlcNAc-Phosphotransferase Alpha/Beta (GNPTAB) Gene in a MLII Alpha/Beta Patient

• Published in: JIMD Reports - Case and Research Reports, 2012/1 Vol. 4; pp. 117 - 124
• Main Authors: Coutinho, Maria Francisca, da Silva Santos, Liliana, Lacerda, Lúcia, Quental, Sofia, Wibrand, Flemming, Lund, Allan M., Johansen, Klaus B., Prata, Maria João, Alves, Sandra
• Format: Book Chapter Journal Article
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 01.01.2012
• Series: JIMD Reports
• Subjects: Abnormal Transcript; Deletion Breakpoint; Large Deletion; Maple Syrup Urine Disease; Splice Site Junction
• ISBN: 9783642257513; 3642257518
• ISSN: 2192-8304; 2192-8312
• DOI: 10.1007/8904_2011_83

Mucolipidosis type II α/β is a severe, autosomal recessive lysosomal storage disorder, caused by a defect in the GNPTAB gene that codes for the α/β subunits of the GlcNAc-phosphotransferase. To date, over 100 different mutations have been identified in MLII α/β patients, but no large deletions have been reported. Here we present the first case of a large homozygous intragenic GNPTAB gene deletion (c.3435-386_3602 + 343del897) encompassing exon 19, identified in a ML II α/β patient. Long-range PCR and sequencing methodologies were used to refine the characterization of this rearrangement, leading to the identification of a 21 bp repetitive motif in introns 18 and 19. Further analysis revealed that both the 5′ and 3′ breakpoints were located within highly homologous Alu elements (Alu-Sz in intron 18 and Alu-Sq2, in intron 19), suggesting that this deletion has probably resulted from Alu–Alu unequal homologous recombination. RT-PCR methods were used to further evaluate the consequences of the alteration for the processing of the mutant pre mRNA GNPTAB, revealing the production of three abnormal transcripts: one without exon 19 (p.Lys1146_Trp1201del); another with an additional loss of exon 20 (p.Arg1145Serfs*2), and a third in which exon 19 was substituted by a pseudoexon inclusion consisting of a 62 bp fragment from intron 18 (p.Arg1145Serfs*16). Interestingly, this 62 bp fragment corresponds to the Alu-Sz element integrated in intron 18. This represents the first description of a large deletion identified in the GNPTAB gene and contributes to enrich the knowledge on the molecular mechanisms underlying causative mutations in ML II.