Identification of a Homozygous PGM2L1 Variant in a Male Patient With Developmental Delay and Seizures

ABSTRACT

Background

PGM2L1 gene variants are associated with developmental delays, seizures, and various neurological and physical symptoms. This study aims to report the clinical features and genetic findings in a male patient with developmental delay, regression, and seizures.

Methods

Whole‐exome sequencing (WES) was performed on the patient to identify the genetic etiology of the patient. Sanger sequencing was used for variant confirmation. Clinical evaluations were conducted, including cerebrospinal fluid analysis, cranial MRI, EEG, and neurological assessments.

Results

The patient is a 1‐year‐old male who presented with psychomotor delays and developed seizures and impaired consciousness at 1 year of age. Cranial MRI revealed bilateral frontotemporal subarachnoid widening. Developmental regression was observed shortly after the onset of seizures. The EEG results showed diffuse slow background activity and epileptiform discharges. WES identified a rare homozygous variant in the PGM2L1 gene (OMIM: 611,610, NM_173582.6: c.1673delC, p.Thr558Ilefs*19), which was inherited from both parents. Sanger sequencing confirmed the presence of the variant, and it was evaluated as a likely pathogenic variant according to American College of Medical Genetics and Genomics (ACMG) guidelines.

Conclusion

Our study was the second report of a PGM2L1 gene variant associated with early‐onset developmental delay and seizures, further expanding the genetic spectrum of this disorder.

A rare homozygous variant in the PGM2L1 gene (NM_173582.6: c.1673delC, p.Thr558Ilefs*19) was identified in a patient presenting with developmental delay, seizures, and bilateral frontotemporal subarachnoid widening.

1. Introduction

The PGM2L1 gene, initially identified in 2007 (Maliekal et al. 2007), encodes a protein sharing approximately 60% sequence identity with PGM2 (phosphoglucomutase 2). It is predominantly expressed in the brain, and its catalytic efficiency is approximately 5–20‐fold higher than that of PGM2 for the synthesis of 1,3‐diphosphoglycerate‐dependent synthesis of glucose 1,6‐bisphosphate. Despite exhibiting low pentose phosphate translocase and glucose phosphate translocase activities (less than 5%), PGM2L1 may play a pivotal role in glucose metabolism, particularly in regulating energy supply and metabolic processes within the brain tissue.

The PGM2L1 gene is located on chromosome 11q13.4 and it encodes 622‐amino acids. Recent studies have identified an association between PGM2L1 gene variants and neurodevelopmental disorders characterized by hypotonia, dysmorphic facies and skin abnormalities (NEDHFS) (Morava et al. 2021). All four patients with the PGM2L1 gene variant exhibited severe developmental and speech delays, dysmorphic facial features, strabismus, hypotonia, and keratosis pilaris. Three of the subjects exhibited early‐onset obesity and epilepsy. The functional experiments conducted on pediatric fibroblasts demonstrated that the variants in the PGM2L1 gene resulted in a notable reduction in the levels of glucose‐1,6‐bisphosphate. However, in the brain, the concentration of glucose‐1,6‐bisphosphate is markedly elevated, exceeding 100 μM by at least an order of magnitude, and is at least 100 times higher than the concentration required for glucose phosphorylase activity (Passonneau et al. 1969; Veiga‐da‐Cunha et al. 2008). These findings highlight the need for further investigation into the precise role and mechanisms of PGM2L1 and glucose 1,6‐bisphosphate in brain metabolism and NEDHFS.

In this study, a male patient presented with significant developmental delays, including delayed motor milestones such as delayed head control, inability to sit or walk independently, and speech delays. Clinical examination revealed hypotonia and additional neurological symptoms, including intermittent convulsive episodes and developmental regression. Whole exome sequencing (WES) identified a PGM2L1 gene variant (NM_173582.6: c.1673delC, p.Thr558Ilefs*19), inherited from both parents. Our study was the second report for the PGM2L1 gene variant, and it highlights the clinical features associated with PGM2L1 variants and expands the genetic spectrum of this gene, contributing valuable insights into its role in NEDHFS.

2. Methods

2.1. Ethical Compliance

All procedures were performed with the informed consent of the patient's legal guardians and in accordance with the ethical standards of the hospital ethics committee.

2.2. WES

The reference genomic DNA sequences used for the Homo sapiens PGM2L1 gene were obtained from the NCBI GenBank database under accession number NM_173582.6. Genomic DNA was extracted from the proband and his parents and used to construct a DNA library. The IDT XGen Exome Research Panel was utilized for target capture, and paired‐end sequencing was performed on the MGI DNBSEQ‐T7 platform, achieving an average depth of > 100× and > 98% coverage at 20× for quality assurance. Sequencing reads were aligned to the GRCh38/hg38 human reference genome using the Burrows‐Wheeler Aligner (BWA) (Li and Durbin 2009). Downstream processing, including re‐alignment, duplicate removal, and variant detection, was conducted with Samtools, Picard, and GATK. Variants were annotated with Annovar (Wang et al. 2010), and their pathogenicity was assessed using prediction tools such as Mutation Taster, PolyPhen‐2, and SIFT. Filtering was performed based on inheritance patterns, allele frequency, clinical features, and data from public databases. Pathogenic variants were identified following the ACMG guidelines (Richards et al. 2015). Finally, Sanger sequencing was conducted on the trio to validate the variants detected through WES.

2.3. Patient

The patient underwent a series of clinical assessments, including cerebrospinal fluid analysis, cranial magnetic resonance imaging (MRI), electroencephalogram (EEG), and a neurological examination to evaluate central nervous system involvement.

3. Results

3.1. Clinical Report

Before the onset of the disease, the male patient's psychomotor development lagged behind that of normal children of the same age. At 4 months, he could laugh in response to sounds; at 7 months, he began reaching out and grasping objects. By 8 months, he could roll over and make unconscious sounds such as “ba” and “ma.” At 9 months, he could sit alone, although unsteadily. At 12 months, he could stand with support but was unable to stand or walk independently. However, he still could not consciously call “papa” or “mama” at this age.

At 1 year of age, the patient was hospitalized due to “fever, convulsive seizures, and impaired consciousness.” Cerebrospinal fluid examination revealed no abnormalities, while cranial MRI indicated bilateral frontotemporal subarachnoid widening (Figure 1A). Following the onset of the disease, developmental regression became evident. At 1 year and 1 month, he could not raise his head in the prone position, could not turn over voluntarily, and was unable to sit alone. His responses to auditory and visual stimuli were poor, and he could unconsciously produce sounds such as “a” or “o.” Swallowing difficulties also emerged, although these improved with rehabilitation therapy. The EEG performed in July 2024, when the patient was 1 year and 2 months old, showed diffuse slow background activity (3–4 Hz, low to medium amplitude), with occasional low‐amplitude fast waves. Focal epileptiform discharges were observed during both wakefulness and sleep, including multiple low to medium amplitude spikes, sharp waves, spike‐and‐slow wave complexes, and sharp‐and‐slow wave complexes (Figure 1B).

FIGURE 1.

The clinical features for our patient. (A) Brain MRI of the patient shows enlargement of the extracerebral spaces in the bilateral frontal and temporal regions, mild widening of the sulci, and hypoplasia of the bilateral frontal lobes, consistent across T1‐weighted, T2‐weighted, and T2‐FLAIR sequences. (B) EEG reveals diffuse slow wave background activity with multifocal epileptiform discharges, including spikes, sharp waves, and spike‐and‐slow wave complexes during wakefulness and sleep. (C) The curly hair on the top area of the patient's head.

At the current age of 1 year and 7 months, the patient is 86 cm tall and weighs 13 kg. He has curly hair on the top of his head (Figure 1C), no obvious facial deformities, a high arched palate, no strabismus, normal skin, and slightly small hands and feet. Cardiac, pulmonary, and abdominal examinations reveal no abnormalities. Neurological findings include a soft neck, rudimentary head and neck muscle strength (graded as V‐), limb muscle strength graded as IV, reduced muscle tone, and active tendon reflexes. Bilateral Babinski's signs are positive, while other pathological signs and meningeal irritation signs are negative.

The patient continues to experience intermittent convulsive episodes, and rehabilitation progress remains limited and slow. He is able to consume a liquid diet. His movement abilities include clumsy turning over, sitting alone with an arched back, and an inability to crawl on his stomach. Active grasping ability is poor, and he cannot pinch objects with his thumb and forefinger. The patient can produce sounds such as “ma,” “bu,” and “nai.” He is able to laugh, recognize strangers, and interact socially to some extent, but he cannot imitate movements, follow instructions, or express his needs. Facial expressions remain relatively uniform.

3.2. Identification of PGM2L1 Gene Variant in Our Patient

A WES was performed to further explore the etiology of our patient. The homozygous variant in the PGM2L1 gene (NM_173582.6: c.1673delC, p.Thr558Ilefs19) was identified. It was confirmed to have been inherited from his parents through Sanger sequencing (Figure 2A,B). It was rare and not included in the normal population database, such as gnomAD and ExAC. The stop codon resulting from c.1673delC is situated within the final 50 base pairs of the final coding exon and is not anticipated to induce nonsense‐mediated mRNA degradation. The variant causes a 64aa deletion in the protein, accounting for more than 10% of the full‐length protein sequence. The new cca is as follows: “IFKMAVLLPFGQVEQNQR*”. In light of the aforementioned evidence, the c.1673delC variant is classified as a likely pathogenic variant, in accordance with the relevant criteria. The classification is supported by PVS1_Strong+PM2_Supporting+PM3_Supporting. The variant p.Thr555ilefs*19 described here, together with all other currently known PGM2L1 variants (Morava et al. 2021), is summarized in Figure 2C.

FIGURE 2.

The variant in the PGM2L1 gene was successfully identified. (A) The pedigree of the patient under examination. The individual identified as the proband is indicated by a filled shape with an arrow. (B) Sanger sequencing of the trio family. The homozygous variant was identified through sequencing. (C) Schematic representation of the variants identified in the PGM2L1 gene in patients. The variant identified in the patient is highlighted in red text. The domain in PGM2L1 protein: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I‐ III (PGM_PMM_I—III). PGM2L1: NM_173582.6.

4. Discussion

PGM2L1 was first identified in 2007 as a protein coding gene, belonging to the α‐D‐Phosphohexomutase Family. It is expressed at significantly higher levels in brain tissue compared to other tissues, indicating its importance in the nervous system. PGM2L1 and PGM2 co‐catalyze the synthesis of glucose‐1,6‐bisphosphate, which is a key metabolic intermediate involved in glycolysis and energy metabolism (Morava et al. 2021). The product of this gene, hexose bisphosphates (glucose‐, N‐acetyl‐glucosamine‐, and mannose‐1,6‐bisphosphate), serves as cofactors for sugar‐phosphate translocase, facilitating normal sugar metabolism within cells (Najjar and Pullman 1954; Ray Jr. and Roscelli 1964; Pirard et al. 1999). Additionally, PGM2L1 shows varied expression patterns in different cancers (Xue et al. 2022), and some studies suggest it could serve as a potential biomarker for early cancer diagnosis and therapeutic targeting (Xue et al. 2022). Moreover, PGM2L1 is implicated in immune responses, with regulated expression in dendritic cells that may influence immune cell function and inflammatory reactions (Jin et al. 2023).

PGM2L1‐related NEDHFS were first reported in 2021 (Morava et al. 2021). In the study, four children (aged 2–7.5 years) with biallelic inactivating mutations in the PGM2L1 gene were identified. All patients presented with severe developmental and language delays, facial dysmorphia (including ear abnormalities, high arched and narrow palate, and exotropia), hypotonia, skin issues (such as keratosis pilaris), and neurological symptoms, with three developing early‐onset obesity and seizures. These findings suggest a strong association between PGM2L1 deficiency and NEDHFS.

In our patient, developmental delay and hypotonia were present. At 1 year of age, the patient experienced “fever, seizures, and altered consciousness” followed by developmental regression, consistent with the clinical presentation of one previously reported patient. Additionally, our patient exhibited hair abnormalities; although, in contrast to prior reports, he had curly hair on the top of his head but did not exhibit excessive hair growth on his arms and back. Cranial MRI revealed bilateral frontotemporal subarachnoid widening, a feature observed to vary among patients with PGM2L1 mutations. Genetic testing of our patient revealed a homozygous PGM2L1 mutation (p.Thr558Ilefs*19), leading to a 64aa deletion in the protein, accounting for more than 10% of the full‐length protein sequence, similar to other reported variants (see Figure 2C for a short summary). These are truncating mutations, suggesting a significant impact on protein function.

Functional studies further demonstrated that PGM2L1 deficiency caused a marked reduction in glucose‐1,6‐bisphosphate (approximately 90%) in fibroblasts, while NDP‐sugars level remained unaffected, indicating that glycosylation precursor molecules were not impaired. Immunoblot analysis also showed that the glycosylation pattern of LAMP2 in PGM2L1‐deficient cells was similar to the control group, refuting the notion of a glycosylation defect. These findings suggest that although PGM2L1 deficiency decreases glucose‐1,6‐bisphosphate levels, it does not significantly disrupt the overall glycosylation process. As a byproduct of glycolysis, glucose‐1,6‐bisphosphate plays a crucial role in regulating energy balance and glycolytic flux in neurons, though its precise function remains unclear (Safari et al. 2024). In murine models, PGM2L1 knockdown resulted in reduced neuronal survival after ischemia, emphasizing its essential role in neuronal survival and function (Safari et al. 2024). The changes in glucose‐1,6‐bisphosphate levels are closely linked to PGM2L1 activity, affecting mitochondrial pyruvate uptake and oxygen consumption rates.

In conclusion, we report the first Chinese case of a patient with a PGM2L1 gene variant. The patient's clinical phenotype is consistent with previously described cases, and timely genetic testing facilitated an early diagnosis. His curly hair is unique and may be associated with hair abnormalities caused by variants in this gene. Our study expands the genetic spectrum of PGM2L1 variants, and further functional studies are needed to elucidate its role in neurodevelopment.

Author Contributions

Mengmeng Niu: performed data analysis and drafted the manuscript. Dong Wang: provided clinical data, contributed to data interpretation, and assisted with manuscript preparation. Shanshan Jia: designed the study, supervised the research process, and revised the manuscript critically for intellectual content.

Funding

This work was supported by Shaanxi Provincial Key Research and Development Program, 2023‐ZDLSF‐19, 2017SF‐292.

Ethics Statement

The patient and his family were well informed and provided written informed consent. This research was approved by the ethics committee of the Xi'an Children's Hospital.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.