“Missing mutations” in MPS I: Identification of two novel copy number variations by an IDUA‐specific in house MLPA assay

Abstract

Background Mucopolysaccharidosis type I (MPS I) is a rare, recessively inherited lysosomal storage disorder, characterized by progressive multi‐systemic disease. It is caused by a reduced or absent alpha‐l iduronidase (IDUA) enzyme activity secondary to biallelic loss‐of‐function variants in the IDUA. Over 200 causative variants in IDUA have been identified. Nevertheless, there is a fraction of MPS I patients with only a single mutated IDUA allele detectable. Methods As genetic testing of MPS I is usually based on sequencing methods, copy number variations (CNVs) in IDUA can be missed and therefore presumably remain underdiagnosed. The aim of this study was the detection of CNVs using an IDUA‐specific in house multiplex ligation‐dependent probe amplification (MLPA) assay. Results A total of five unrelated MPS I patient samples were re‐analyzed after only a single heterozygous IDUA mutation c.979G>C (p.A327P), c.1469T>C (p.L490P), c.1598C>G (p.P533R), c.1205G>A (p.W402X), c.973‐7C>G (p.?) could be identified. We detected a novel splice site variant c.973‐7C>G (p.?), as well as two novel CNVs, a large deletion of IDUA exon 14 and 3’UTR c.(1828 + 1_1829‐1)_(*1963_?)del, and a large duplication extending from IDUA exon 2 to intron 12 c.(157 + 1_158‐1)_(1727 + 1_1728‐1)dup. Conclusion Together with the CNVs we previously identified, a total of four pathogenic IDUA CNVs have now been reported.

Incorporation of Second-Tier Biomarker Testing Improves the Specificity of Newborn Screening for Mucopolysaccharidosis Type I

“…Numerous pilot and full-population screening programs using measurement of α-l-iduronidase (IDUA) activity have been underway in several countries and US states-many of which have experienced a high false-positive rate due to the overlap of IDUA activity between unaffected and affected patients and a high incidence of pseudodeficiency alleles in IDUA, resulting in overall poor specificity for MPS I [5][6][7]. While several programs have implemented second-tier molecular testing in an attempt to address the poor specificity of enzymatic screening alone, this approach has proved to be problematic due to the discovery of private mutations, variants of unknown significance, identification of carrier status and limitations of utilized methodology [8,9]. In addition, the high incidence of genotypic variants leading to pseudodeficiency of IDUA results in excessive performance of potentially unnecessary molecular genetic testing [10].…”

MPSI Manifestations and Treatment Outcome: Skeletal Focus

“…More than 350 causative variants in the IDUA gene have been identified to date, including missense, nonsense, splice site, and insertions, as well as small deletions and duplications [ 9 ]. Copy number variations have been also reported [ 10 ]. The most common causative variants reported worldwide include c.1205G > A (p.Trp402Ter), c.208C > T (p.Gln70Ter), c.1598C > G (p.Pro533Arg), and c.152G > A (p.Gly51Asp) [ 2 , 11 , 12 ].…”