GNPTAB c.2404C > T nonsense mutation in a patient with mucolipidosis III alpha/beta: a case report

Mucolipidosis alpha/beta encompasses a phenotypic spectrum of GlcNAc-1-phosphotransferase (EC 2.7.8.17) deficiency caused by pathogenic variants affecting the alpha/beta subunits-encoding GNPTAB gene. Clinical severity and age of onset depend on residual enzyme activity: mucolipidosis type III alpha/beta (MIM 252600) is characterized by significant residual enzyme activity [1], a milder clinical course and a later, childhood, onset compared to the type II (I-cell) disease (MIM 252500), in which minimal enzyme activity causes neonatal disease progressing to childhood death. Despite initial reports of bone marrow transplant successfully delaying cardiopulmonary complications and reversing biochemical or even certain physical abnormalities [2], more extensive case series confirmed the overall poor prognosis and limited reversibility, particularly in the severe form of the disease [3].

At the molecular level, the autosomal recessive disease results from disruptions of the generation of mannose 6-phosphate markers on soluble hydrolases [4], leading to failure of their proper lysosomal targeting and subsequent extracellular loss [5, 6]. These extracellular lysosomal enzymes are nonetheless active and can be detected at elevated levels in the plasma of affected patients [7]. However, due to the missorting of various hydrolases to outside of the lysosomal compartment, there is an accumulation of non-degraded material including oligosaccharides, glycolipids and glycosaminoglycans (GAGs) [8]. These accumulations lead to cellular and organ dysfunction [9, 10], characterized by neuro-developmental, musculoskeletal and cardiopulmonary disorders with lethal complications [7, 11].

In this study, we report a two-year-old boy being diagnosed of mucolipidosis III alpha/beta, with initial presentation of poor weight gain, microcephaly and increased tone at five months of age. Subsequent follow up showed evolving coarse facial features, musculoskeletal abnormalities including craniosynostosis, joint contractures and developmental delay which prompted a series of biochemical investigations. A dried blood spot (DBS) enzyme activity assay found increased activity of multiple lysosomal enzymes, which pointed to mucolipidosis II/III. Targeted genetic study of the GNPTAB gene was performed on the index patient and his parents, confirming the patient as a compound heterozygote with c.2715 + 1G > A and the c.2404C > T (p.Q802*) nonsense mutation, reported shortly after the initial submission of this article [12]. In light of the genetic findings, the clinical history of the patient is reviewed, and the management and future treatment options for this patient are discussed.

In this study, we reported a two-year-old boy confirmed to have mucolipidosis III alpha/beta due to compound heterozygous pathogenic variants in the GNPTAB gene. Cascade screening revealed the parental origin of both mutations, including the common splice site variant c.2715 + 1G > A, accounting for up to 28% of pathogenic variants in a Chinese cohort [20], and the recently reported nonsense variant c.2404C > T (p.Q802*). Clinically, the patient had multiple phenotypic features of mucolipidosis III alpha/beta which mimicked manifestations of MPS, including gradual evolvement of large and small joint contractures, coarse facial features, kypho-lordosis with pectus carinatum, umbilical hernia and developmental delay [21]. A differentiating clinical feature in this case, however, was the presence of microcephaly - which would be atypical of MPS – despite being a common feature of mucolipidosis alpha/beta and even the main presenting sign in some patients [22, 23]. Developmentally, the degree of delay in this patient was relatively mild compared to more commonly seen MPS cases in the region [24], particularly type I and type II MPS in which patients can manifest severe complications early [25]. These clinical features, while not absolute, should nevertheless alert the physician the possibility of mucolipidosis in patients being investigated for suspected MPS. Retrospectively, the subtle dysmorphic features could have been noticed earlier but these insidious clinical features were also partly masked by the baby’s medical history of prematurity. Clinicians’ awareness of the disorder could have been improved, despite the rarity of the disorder. Also, universal newborn screening for lysosomal storage disorders could have helped in early diagnosis [26], although such testing is currently not available in Hong Kong.

The generalized increase in plasma lysosomal enzyme activity provided an important diagnostic clue to establishing the biochemical and genetic diagnosis in this case. While specific patterns of enzyme activity elevation has been reported and applied in simplified, targeted screening strategies [27], it should perhaps be emphasized that only the use of multi-enzyme activity paneling would allow the most sensitive detection simultaneous differentiation from the phenotypically-similar MPSs and other inborn metabolic defects [28]. Of note, the more recently developed tandem mass spectrometry assays have allowed the determination of multiple lysosomal enzyme activity [29, 30] and GAG levels [31] from a DBS sample, which can be transported to a reference laboratory by regular mail. With the increasing inclusion of lysosomal storage diseases in newborn screening programmes [26, 32], it is anticipated that the pre-symptomatic detection, particularly of the childhood-onset mucolipidosis and MPS, will allow proactive management and better prevention of complications, even if specific or curative treatments may not be available.

Unlike MPS, in which enzyme replacement therapies have been made available or undergoing clinical trials for multiple subtypes [33‐36], and bone marrow transplant has shown various degrees of success [37], current treatment options of mucolipidosis alpha/beta remain limited. Management for patients with mucolipidosis alpha/beta, particularly type III (attenuated type) patients who may survive into their thirties [38], still focused on the conservative management of the skeletal, cardiac and pulmonary complications. Understandably, due to the pervasive effect on lysosomal enzyme targeting of the GlcNAc-1-phosphotransferase defect, no single lysosomal hydrolase replacement would be effective in treating the condition. Replacement of the GlcNAc-1-phosphotransferase by gene therapy has yet to make its way into human trials [39]. More recent reports and cohorts on allogeneic hematopoietic stem cell transplantation (HSCT) [3, 40, 41] rarely reproduced the marked clinical improvement in early reports [2, 42]. In the USA cohort, it was found that post-transplant prognosis significantly depends on pre-existing disease status [3]. A major limitation, as in the current study, was that most of these HSCT cases were diagnosed only by lysosomal enzyme activity assay and confirmed by gene sequencing; the severity of pathogenic variants were not confirmed at the expression and protein levels. As actual disease severity correlates with residual GlcNAc-1-phosphotransferase activity and resultant lysosomal function, rather than the variably elevated levels of extracellular enzyme activity (representing a combined effect of mis-targeting and upregulation) it remains unclear whether the HSCT-responsive cases could actually be due to residual GlcNAc-1-phosphotransferase activity compatible with a milder phenotype – and thus other mucolipidosis type III patients, as in our case, may benefit from such.

At the age of 23 months, the patient was formally assessed by the Child Assessment Centre (Department of Health, Hong Kong Special Administrative Region, China) and was commented as having mild global delay. Re-assessment by the authors at age of 34 months showed a gross motor and fine motor development corresponding to normal children of 20–22 months, a cognitive function (non-verbal aspects) corresponding to normal children of 18–20 months and a verbal ability corresponding to Chinese children of about 2.5 years of age (able to speak 3–4 word phrases). The patient’s vision and hearing were normal.