A Treatable Cause of Seizures and Hyperphosphatasia: Patients with PGAP2 and PGAP3 Mutations

Abstract

Introduction

Hyperphosphatasia with mental retardation syndrome (HPMRS) is characterized by intellectual impairment, seizures, hypotonia, facial dysmorphism, and elevated serum alkaline phosphatase (ALP) level. HPMRS has been linked to mutations in several genes including PGAP2 and PGAP3. Here, we report 2 patients of HPMRS3 and HPMRS4 and highlight the genetic and phenotypic diversity of this disorder.

Case Reports

Patient 1, a 1-year-old male with developmental delay, generalized tonic-clonic seizures, and dysmorphic facial features, was found to have a pathogenic variant in the PGAP3 gene. Patient 2, a 1-year-old female with seizures, hypotonia, joint hypermobility, and facial dysmorphism, was found to have a pathogenic variant in the PGAP2 gene. Both patients exhibited elevated ALP levels. Brain MRI of patient 1 revealed periventricular hyperintense signal foci, while patient 2 showed cerebral atrophy and basal ganglia diffusion restriction.

Discussion

HPMRS3 and HPMRS4 share clinical features including elevated ALP levels, developmental delay, seizures, and facial dysmorphisms. Although joint hypermobility is not a common feature of HPMRS3, it was observed in our patients. Both patients responded well to high-dose pyridoxine, suggesting a potential therapeutic benefit for seizure management. This report expands the understanding of HPMRS by presenting novel genetic findings and providing insights into the clinical presentation of PGAP2- and PGAP3-related conditions.

Established Facts

• Already known fact 1: mutations in PGAP2 and PGAP3 cause a rare disease, HPMRS. Characteristic features in affected patients include facial dysmorphism, seizures, and elevated alkaline phosphatase levels.

• Already known fact 2: seizures can be controlled with pyridoxine.

Novel Insights

• New information: joint mobility has not been previously reported in HPMRS3.

Introduction

Hyperphosphatasia with mental retardation syndrome (HPMRS), also known as Mabry syndrome, was first described in 1970 [1]. The clinical features of the disease include intellectual impairment, a range of neurological findings such as seizures and hypotonia, facial dysmorphism (such as hypertelorism, a broad nasal bridge and tip, long palpebral fissures, and a thin, tented upper lip), shortened distal phalanges, a condition known as brachytelephalangy. In addition, elevated alkaline phosphatase (ALP) levels have been observed [2]. Several genes, including PIGV, PIGO, PIGW, and PIGY have been shown to cause HPMRS. Additionally, pathogenic variants in PGAP2 and PGAP3 are also associated with HPMRS [2–5]. These genes, which are expressed in the Golgi, are involved in post-GPI attachment to protein (PGAP) pathways and help stabilize the membrane attachment of GPI-anchored proteins (GPI-APs). HPMRS3 is caused by PGAP2 variants [6–9], whereas HPMRS4 is caused by PGAP3 variants [10]. There are certain phenotypic variations in HPMRS, such as differences in the associated congenital malformations, and brachytelephalangy is commonly seen in some subtypes, but not in HPMRS3 and HPMRS4 [10–12]. We present 2 patients with neurological delay and seizures, in whom pathogenic variants were identified in PGAP2 and PGAP3, including a novel variant in PGAP3.

Patient Reports

Patient 1

A 1-year-old male patient presented with developmental delay. The parents were not consanguineous. He was born at term with a weight of 3,000 g and had no history of neonatal intensive care unit admission. Psychomotor retardation and generalized weakness were observed at 6 months of age. At 10 months of age, he had generalized tonic-clonic seizures, which were controlled with adequate antiepileptic treatment. On physical examination, weight and height were at the 69th and 48th percentiles, respectively, while head circumference was at the 90th percentile, which is indicative of relative macrocephaly. Dysmorphic features included a broad nasal bridge, a short prominent nose, and hypertelorism, with no abnormalities in the fingers or toes. The patient also exhibited generalized hypotonia and no eye contact. Laboratory tests revealed normal calcium, magnesium, and phosphate levels; however, a markedly elevated serum ALP level (931 U/L, N: 108–317 U/L) was observed. Metabolic screening, including acylcarnitine profiling, plasma and urine amino acids, urine organic acids, and very long-chain fatty acids, revealed no abnormalities. Brain magnetic resonance imaging revealed periventricular hyperintense signal foci on T2-weighted sequences, which were evaluated as being in favor of leukomalacic areas. Echocardiography revealed a secondary atrial septal defect and atrioventricular septal defect. The neuromotor developmental delay, dysmorphia, and seizures prompted the patient to undergo whole-exome sequencing. A homozygous novel pathogenic variant, c.496-39_498 del, was detected in PGAP3. Pridoxine therapy was initiated, and no seizures were documented during follow-up. A review of his medical records revealed that the ALP activity remained persistently elevated. The clinical and laboratory findings are summarized in Table 1.

Table 1.

Summary of clinical features and laboratory findings of patients

​	Patient 1 (PGAP3 variant)	Patient 2 (PGAP2 variant)
Current age/sex	2 years/male	2 years/female
Age of admission	1 year	1 year
First seizure (age)	10 months	6 months
Parental consanguinity	No	Yes (first-degree cousins)
Developmental delay	+	+
Dysmorphic features	Broad nasal bridge, short prominent nose, hypertelorism	Broad nasal bridge, wide palpebral fissures, arched eyebrows, hypertelorism
Macrocephaly	+	​
Microcephaly	​	+
Other systemic findings	Cardiac defects (ASD, AVSD)	Hepatosplenomegaly
		Joint hypermobility
ALP level, U/L	931	2,858
Calcium, mg/dL	10.8	10
Phosphate, mg/dL	5.3	4.8

ALP, alkaline phosphatase; ASD, atrial septal defect; AVSD, atrioventricular septal defect.

Patient 2

A 1-year-old female patient presented with seizures. Their parents were first-degree relatives with a history of sibling death. She was born at 36 weeks of gestation with a birth weight of 3,500 g, and did not require admission to the neonatal intensive care unit. The patient’s developmental milestones were also delayed. She had her first seizure at 6 months of age. Anthropometric measurements revealed weight at the 63rd percentile, height at the 34th percentile, and a head circumference below the 3rd percentile. Upon examination, the patient was hypotonic, lacked eye contact, and showed no deep tendon reflexes, although babbling was present. Generalized joint hypermobility was also observed. Dysmorphic features include a broad nasal bridge, wide palpebral fissures, arched eyebrows, and hypertelorism, with no detectable anomalies in the hands or feet. Hepatosplenomegaly was also observed. While the serum calcium, magnesium, and phosphate levels were within normal limits, a markedly elevated ALP (2,858 U/L, N: 108–317 U/L) level was observed. Comprehensive metabolic investigations, including acylcarnitine profiling, plasma and urine amino acids, urine organic acids, and very long-chain fatty acids, revealed no abnormalities. Brain MRI revealed cerebral atrophy and diffusion restriction in the basal ganglia. Whole-exome sequencing performed after an unremarkable metabolic evaluation identified known homozygous pathogenic variant c.479A>G in PGAP2. Pyridoxine was then added to the antiepileptic regimen. The patient did not experience any seizures during the 8-month follow-up. The clinical and laboratory findings are summarized in Table 1.

Discussion

Hyperphosphatasia with mental retardation syndrome (HPMRS) is clinically characterized by profound intellectual disability, a range of neurological impairments such as seizures and hypotonia, distinct facial dysmorphism (including hypertelorism, a broad nasal bridge and tip, elongated palpebral fissures, and a tented thin upper lip), shortened distal phalanges, a feature referred to as brachytelephalangy, and elevated serum ALP [13, 14]. In HPMRS3 of HPMRS4, brachytelephalangy was not expected, unlike in other forms and HPMRS. Interestingly, brachytelephalangy has been previously reported in a patient with HPMRS4. However, in both our patients, brachytelephalangy was absent, which is consistent with the literature. The milestones of development in both patients were significantly delayed, and they exhibited hypotonia, a history of seizures, and dysmorphic facial features. While our HPMRS3 patient was microcephalic, our HPMRS4 patient had macrocephaly. Although most patients in the literature are normocephalic, microcephaly has been reported in patients with HPMRS3 and macrocephaly in patients with HPMRS4 [8]. Cleft palate has been previously reported in HPMRS4 [11]. However, our patient did not have cleft palate. In patient 2, who was diagnosed with HPMRS3, joint hypermobility was a striking finding. Joint mobility is not a characteristic feature of HPMRS3 but has been reported in congenital glycosylation defects [15].

Seizures are commonly observed throughout the progression of the disease and present in various forms, including absence seizures, epileptic spasms, tonic-clonic seizures, myoclonic seizures, and febrile seizures [8, 9, 16]. The seizures in both of our patients were generalized tonic-clonic and, similar to previously reported patients in the literature, were not drug-resistant [11].

Hyperphosphatasia is a key clinical characteristic of HPMRS and is observed in all patients. Most patients with PGAP3 variants had significantly higher serum ALP levels than the age-adjusted normal range (1.1–3.6 times the upper limit) [17–20]. However, over 50% of individuals with PGAP2 mutations displayed extremely elevated ALP levels (more than 3.6 times the normal upper limit). These variations in serum ALP levels might be linked to specific genetic variants [18]. In line with the literature, ALP levels in our PGAP3 patient increased 1–3 times, whereas in our PGAP2 patient, they were approximately 9 times higher than normal.

Although brain abnormalities are considered relatively rare, MRI findings similar to those observed in our patient have been previously reported. In the brain MRI images of HPMRS3 and HPMRS4 patients, a thin and hypoplastic corpus callosum, slightly enlarged lateral ventricles, atrophy, increased gyration, mild white matter reduction, and normal MRI findings have also been reported [6, 8, 16, 21, 22]. Brain atrophy was observed in patient 2, along with periventricular hyperintense signal foci in patient 1.

HPMRS is classified as a congenital disorder of glycosylation; however, no simple or universally applicable metabolic test is currently available to facilitate differential diagnosis in suspected patients. Isoelectric focusing of serum transferrin, commonly used for congenital disorder of glycosylation screening, is typically normal in patients with HPMRS, which limits its diagnostic utility in this subgroup [9, 23]. Although elevated ALP is a hallmark of HPMRS, it remains a nonspecific biochemical marker. It may also be observed in other metabolic, hepatic, and bone-related disorders, thus limiting its diagnostic specificity. This could be a reason for the diagnostic delay in all known patients before next-generation sequencing became available. We also reached a diagnosis with the help of whole-exome sequencing and identified the pathogenic missense variant c.479A>G in PGAP2 for HPMRS3. Additionally, a novel pathogenic variant c.496-39_498 del was found in PGAP3, linked to HPMRS4. This variant comprises a deletion of 42 bases, including the first three bases of exon 5 and the canonical splice site of intron 4. In silico splicing prediction tools, notably SpliceAI (score: 0.97), strongly suggest that normal mRNA splicing is disrupted. This variant is extremely rare in population databases (gnomAD MAF: 0.000001239) and, to our knowledge, has not previously been reported in the literature. Considering its predicted impact on splicing, rarity, and phenotypic correlation with HPMRS4, we have classified the variant as pathogenic in accordance with the ACMG and ClinGen criteria.

Currently, there are no specific treatment options for HPMRS. In some patients, seizures can be controlled with antiepileptic drugs, ketogenic diet, combination therapy, or pyridoxine and folinic acid [8, 9]. Studies have shown that pyridoxine and folinic acid supplementation may effectively correct low PLP and 5-MTHFR levels in the cerebrospinal fluid of HPMRS patients and could be beneficial in managing refractory seizures [16, 22]. Pyridoxine was started in addition to antiepileptic drugs for both patients, and no seizures were observed in the last 6 months. Further studies are required to clearly define the benefits of pyridoxine treatment.

Conclusion

In conclusion, we report 2 genetically confirmed patients of HPMRS3 and HPMRS4 with shared clinical features, including elevated ALP, developmental delay, seizures, and facial dysmorphisms. Joint hypermobility observed in 1 HPMRS3 patient expands the known phenotypic spectrum. Both responded well to high-dose pyridoxine, suggesting a potential therapeutic benefit. Further studies are needed to clarify the pathogenesis and guide standardized treatment strategies for these rare disorders.

Acknowledgments

The authors thank patients and their parents involved in this study. This case report was prepared in compliance with the CARE guidelines, and the completed CARE checklist is provided as online supplementary material (for all online suppl. material, see https://doi.org/10.1159/000547293).

Statement of Ethics

The local Institutional Review Board deemed the study exempt from review. Written informed consent was obtained from the parents of the participants for the publication of details regarding their medical case.

Conflict of Interest Statement

The authors declare no conflicts of interest.

Funding Sources

This work was not supported by any funding.

Author Contributions

Ezgi Burgaç designed, managed, and wrote the paper the study; Merve Yoldas Celik collected the data. Burcu Köseci and Habibe Koc Ucar contributed significantly to the data analysis. All the authors have read, edited, and approved the final version of the manuscript.

Funding Statement

This work was not supported by any funding.

Data Availability Statement

No additional data are available.