ACAN-related short stature with an incidental ALPL variant: a case report

Abstract.

Hypophosphatasia (HPP) is a rare inherited metabolic bone disorder caused by pathogenic variants in the ALPL gene, with a wide clinical spectrum ranging from severe pediatric forms to mild adult-onset disease. In contrast, heterozygous variants in ACAN are a recognized cause of autosomal dominant short stature, often associated with advanced bone age and premature growth plate closure. We report a 16-yr-old girl evaluated for severe disproportionate short stature with growth arrest during early adolescence. Her medical history included benign childhood epilepsy, mild intellectual disability, and enamel abnormalities. Biochemical evaluation revealed persistently low serum and bone-specific alkaline phosphatase levels, while calcium–phosphate metabolism was otherwise normal. Genetic testing identified a heterozygous pathogenic ALPL variant (c.1426G>A; p.Glu476Lys), inherited from an asymptomatic father, consistent with autosomal dominant HPP with minimal clinical expression. Additionally, a maternally inherited ACAN variant of uncertain significance (c.511G>C; p.Ala171Pro) was detected. Based on phenotypic correlation and family segregation, the growth phenotype is more plausibly explained by ACAN-related growth plate dysfunction, while the ALPL variant likely represents an incidental or mildly expressed finding. This case highlights the importance of careful genotype–phenotype correlation and cautious interpretation of multiple genetic findings in the evaluation of severe short stature.

Highlights

● Severe short stature with advanced bone age may reflect ACAN-related growth plate dysfunction.

● Pathogenic ALPL variants can present with minimal or no clinical expression in adulthood.

● Careful genotype–phenotype correlation is essential when multiple genetic variants are identified.

Introduction

Hypophosphatasia (HPP) is a rare inherited metabolic bone disorder caused by pathogenic variants in the ALPL gene, located on chromosome 1, which encodes the tissue-nonspecific alkaline phosphatase (TNSALP) enzyme (1, 2). More than 400 ALPL mutations have been identified to date (3). HPP can be inherited in an autosomal recessive or dominant manner, with dominant variants usually associated with milder clinical phenotypes (1, 2).

The hallmark of HPP is deficient TNSALP activity, leading to impaired bone and dental mineralization (1). TNSALP accounts for approximately 95% of total alkaline phosphatase (ALP) activity and is highly expressed in bone, liver, and kidneys (4,5,6). Reduced enzyme activity results in the accumulation of its natural substrates, namely inorganic pyrophosphate (PPi), pyridoxal-5-phosphate (PLP), and phosphoethanolamine (PEA), which serve as important biomarkers for the disease (1). PPi inhibits hydroxyapatite crystal formation, contributing to rickets and osteomalacia (1, 7, 8). PLP, the active form of vitamin B6 and an essential cofactor for neurotransmitter synthesis, may accumulate in plasma due to defective dephosphorylation and reduced transport across the blood-brain barrier, potentially causing neurological manifestations, such as seizures, in severe pediatric forms of the disease (1,2,3,4).

The clinical spectrum of HPP is wide, ranging from lethal perinatal forms to mild adult-onset disease, characterized by muscle weakness, pain, dental abnormalities (such as premature loss of teeth, periodontal disease or enamel hypoplasia), abnormal gait, low-trauma fractures, and pseudofractures (1, 6, 9,10,11,12,13). Short stature is uncommon in adult-onset HPP. (1) The diagnosis is mainly clinical (supported by persistently low age- and sex-adjusted serum ALP levels, once secondary causes of hypophosphatasemia have been excluded), and confirmed by ALPL molecular testing (1,2,3, 6, 14).

In contrast, heterozygous variants in ACAN, encoding aggrecan, a key structural component of the growth plate extracellular matrix, are a well-established cause of autosomal dominant short stature (15,16,17). ACAN-related growth disorders are often associated with advanced bone age, early epiphyseal closure, disproportionate short stature, and variable expressivity within families (15, 18, 19).

Here, we present an adolescent girl with severe short stature in whom genetic evaluation identified two genetic variants with distinct and potentially unequal contributions to the observed growth phenotype.

Case Presentation

A 16-yr-old girl was referred to our multidisciplinary rare bone disease team for evaluation of severe short stature. Her medical history was notable for epilepsy, with onset at 7 yr of age. She was initially treated with valproate and clobazam, later transitioning to levetiracetam. The first electroencephalogram revealed rolandic activity and unilateral continuous spikes and waves during sleep. She is currently seizure-free and has been off antiepileptic medication for approximately two years. Additionally, she presented mild intellectual disability, attention deficit hyperactivity disorder, and short stature previously investigated with reportedly normal laboratory results. No growth hormone stimulation testing was performed. Her prenatal history was unremarkable. Family history was also unremarkable, with no known consanguinity.

She was born at term with a birth weight of 2405 g (Z score –1.56) and length of 45 cm (Z score –1.49). Her weight consistently tracked around the 10th percentile, while her height remained below the 3rd percentile, with growth arrest noted from age 12, as depicted in Fig. 1. Menarche occurred at 11 yr. Radiographic assessment at age 12 revealed bone age advancement of approximately two years. Estimated mid-parental height was 153.5 cm (Z score –1.53), based on a maternal height of 147.5 cm and a paternal height of 162.9 cm. Shedding of deciduous teeth occurred after the age of 5 yr.

Fig. 1.

Growth chart (WHO reference 2007) showing the patient’s height trajectory from birth.

At age 16, physical examination (Fig. 2) revealed severe short stature (136.7 cm; Z score –3.83), increased upper-to-lower segment ratio (1.24, normal < 1), increased sitting height/height ratio (0.55; Z score +2), and relative macrocephaly (head circumference 56.5 cm; Z score +1.51). Enamel abnormalities were noted bilaterally (Fig. 3).

Fig. 2.

Proband at 16 yr old.

Fig. 3.

Enamel defects.

Laboratory evaluation (Table 1) revealed low serum ALP (35 U/L; reference 50–117) and bone-specific ALP (6.6 µg/L; reference 19.5–150). Calcium, PTH, vitamin D and urinary calcium and phosphorus/creatinine ratios were within normal ranges. Serum phosphorus was mildly elevated. Bone densitometry was normal, and skeletal survey revealed no significant abnormalities.

Table 1. Main laboratory findings.

Genetic testing with WES-based gene panel for skeletal dysplasias identified a heterozygous pathogenic ALPL variant (c.1426G>A; p.(Glu476Lys)), inherited from her father, who also had low serum ALP levels and is otherwise asymptomatic at 50 yr of age. Additionally, a heterozygous variant of uncertain significance (VUS) was found in ACAN (c.511G>C p.(Ala171Pro)). Segregation analysis using Sanger sequencing for the ACAN variant revealed maternal inheritance. The mother had no symptoms suggestive of osteoarthritis, intervertebral disc disease, or osteochondritis, features typically associated with an ACAN-related phenotype. Her brother, currently aged 22 yr, also carries the same 2 variants, although he has normal height (164 cm, Z score –1.72) and is otherwise asymptomatic, with normal ALP levels. However, due to constraints related to residence and distance, the proband’s brother has not yet undergone reevaluation, and he may present subtle phenotypic features that were not identified during the initial assessment.

The patient remains under multidisciplinary follow-up with orthopedics, endocrinology, neurology, and genetics consultations.

Discussion

This case underscores the complexity of interpreting multiple genetic findings in a patient with severe short stature. Although a pathogenic ALPL variant was identified, the overall clinical presentation is not typical of HPP.

Persistently low serum ALP and bone-specific ALP levels, which may be overlooked during the investigation of short stature, prompted targeted genetic testing and the identification of a heterozygous pathogenic variant in the ALPL gene.

The affected child, father, and sibling carrying the ALPL variant showed little to no clinical features of adult-onset HPP. Despite previous reports in variant databases associating this variant with adult-onset hypophosphatasia, no clinically relevant manifestations have been observed in this family to date, suggesting a minimal phenotypic effect (20).

On the other hand, ACAN mutations have been linked to advanced bone age and early growth plate closure, leading to premature cessation of growth and severe short stature in adulthood, with favorable response to growth hormone treatment (21). ACAN encodes aggrecan, the major proteoglycan of the extracellular matrix in the growth plate and articular cartilage, which explains the effects of a pathogenic variant on joints and growth (18, 21,22,23). The phenotypic compatibility of this variant led to segregation testing, which confirmed maternal inheritance of the ACAN variant. The ACAN variant was classified by the laboratory as a VUS, using PM2. A different amino acid change in the same codon has been described in patients with suspected aggrecanopathy, but PM5 was not activated due to conflicting interpretations in ClinVar (24).

In light of aggrecanopathy variability, a composite diagnosis is possible, involving the maternally inherited ACAN variant as the primary contributor, and a potential effect of the ALPL variant, although it likely represents a coincidental finding with limited clinical impact. In fact, ACAN-associated short stature has been described to show variable expressivity, even among individuals carrying the same variant (19). This variability may be influenced by as-yet unidentified modifier genes or other genetic and environmental factors affecting only the proband, such as copy number variants not detectable by exome sequencing.

This patient reinforces the importance of a multidisciplinary and genetics-informed approach in the evaluation of patients with unexplained growth failure and atypical clinical features. Collaboration within the rare bone disease team was crucial for integrating genetic, endocrine, and orthopedic assessments, ultimately guiding diagnosis and follow-up.

To the best of our knowledge, this is the first reported case of co-occurring ALPL and ACAN variants in a single patient. Complex clinical presentations such as this should prompt consideration of additional or overlapping diagnoses, even in the context of an already established rare disease, as in this case.

Conclusion

This case illustrates the complexity of genetic evaluation in severe short stature and highlights the importance of careful phenotype–genotype correlation. Although a pathogenic ALPL variant was identified, the growth phenotype is more plausibly explained by ACAN-related growth plate dysfunction, with the ALPL variant showing minimal or no clinical expression. This report emphasizes the need to critically assess the contribution of each genetic finding and avoid over-attribution of clinical features to coincidental variants, particularly in the era of broad genomic testing.

Conflict of interests

The authors have nothing to declare.