Is ALPL (alkaline phosphatase, liver/bone/kidney) gene testing reliable for diagnosing hypophosphatasia?

ALPL Gene Testing Reliability for Hypophosphatasia Diagnosis

ALPL gene testing is highly reliable and essential for confirming the diagnosis of hypophosphatasia, but it should not be used in isolation—diagnosis requires integration of clinical features, biochemical markers (particularly low serum alkaline phosphatase), and genetic confirmation. 1, 2

Diagnostic Approach

Initial Biochemical Screening

• Low serum alkaline phosphatase (ALP) is the primary biochemical hallmark that should prompt consideration of hypophosphatasia, with levels typically below age-appropriate reference ranges 1
• Elevated pyridoxal 5-phosphate (PLP) levels provide additional biochemical support for the diagnosis 3
• These biochemical abnormalities must be present before proceeding to genetic testing 1

Role of ALPL Gene Testing

Confirmatory Value:

• ALPL gene sequencing is mandatory for definitive diagnosis and allows identification of the specific pathogenic variants responsible for the disease 1, 2
• Genetic testing confirms the diagnosis when biochemical and clinical data are unclear or ambiguous 2
• Most pathogenic variants (approximately 65+ distinct mutations identified) are missense mutations, which correlates with the wide clinical variability seen in hypophosphatasia 2

Reliability Considerations:

• ALPL testing has high specificity when pathogenic variants are identified, as these mutations directly cause tissue-nonspecific alkaline phosphatase (TNSALP) deficiency 1, 3
• The test reliably detects known pathogenic variants and can identify novel variants that require functional characterization 3, 4
• Genetic testing enables genotype-phenotype correlation, though the same variant may produce different clinical severities in different individuals due to dominant negative effects and environmental factors 5

Critical Limitations and Pitfalls

Cannot Rule Out Disease Completely

• A negative genetic test does not definitively exclude hypophosphatasia if clinical and biochemical features are strongly suggestive 2
• Variants of uncertain significance (VUS) are frequently identified and require functional characterization to determine pathogenicity 4
• Blind spots exist in intron regulatory regions and noncoding sequences that may harbor pathogenic variants not detected by standard sequencing 5

Interpretation Challenges

• Novel or rare variants require in vitro functional studies to confirm their pathogenic nature, including measurement of ALP activity, protein expression, and cellular localization 3, 4, 5
• The presence of compound heterozygous variants complicates interpretation and may require family studies 5
• Dominant negative effects can occur, where mutant protein interferes with wild-type protein function, affecting disease severity 3, 5

Clinical Integration Required

ALPL testing must be interpreted within the complete clinical context:

• Clinical features ranging from severe perinatal forms (stillbirth, unmineralized bone, seizures, hypercalcemia) to mild adult forms (premature tooth loss only) 1
• Radiological findings showing impaired bone mineralization 1
• The diagnosis is schematic: low ALP levels PLUS genetic defect in ALPL gene 1

Genetic Counseling Applications

• ALPL testing enables genetic counseling and prenatal diagnosis in families with severe forms of hypophosphatasia 2
• Testing identifies inheritance patterns (autosomal recessive most common, but dominant transmission occurs) 2
• Family screening can identify asymptomatic carriers 2

Practical Recommendations

For ruling IN hypophosphatasia:

• ALPL testing is highly reliable when a known pathogenic variant is identified in the context of compatible clinical and biochemical findings 1, 2
• Identification of biallelic pathogenic variants (compound heterozygous or homozygous) strongly confirms the diagnosis 5

For ruling OUT hypophosphatasia:

• ALPL testing alone cannot definitively rule out the disease due to possible VUS, undetected variants in regulatory regions, or technical limitations 2, 5
• Normal ALPL sequencing in a patient with persistently low ALP and compatible clinical features should prompt consideration of functional studies or alternative diagnostic approaches 4
• The absence of identified mutations does not exclude hypophosphatasia if biochemical and clinical criteria are met 2