How to diagnose an amino acid deficiency?

How to Diagnose Amino Acid Deficiency

Quantitative plasma amino acid analysis is the gold standard diagnostic test for amino acid deficiencies, and should be performed as a comprehensive profile rather than measuring individual amino acids in isolation. 1

Primary Diagnostic Testing

Plasma Amino Acid Analysis

• Order a complete quantitative plasma amino acid profile that measures all amino acids simultaneously, not just suspected deficiencies 1
• Collect samples in the fasting state when possible, as this improves diagnostic sensitivity for most disorders 2
• The complete profile is essential because amino acid synthesis defects often present with low or even normal levels of the deficient amino acid, making them easy to miss if only measuring individual metabolites 3
• Interpretation must focus on the overall pattern of amino acid abnormalities rather than isolated findings, as amino acid ratios (such as PHE:TYR) provide critical diagnostic information 1

Critical Timing Considerations

• Diagnostic sensitivity varies dramatically based on the patient's metabolic state (fed vs. fasting, acute illness vs. baseline) 1
• Some amino acid synthesis defects only become apparent during catabolic stress or may be completely missed during asymptomatic periods 1, 3
• Repeat testing during different metabolic states may be necessary if initial results are normal but clinical suspicion remains high 1

Complementary Diagnostic Studies

Urine Organic Acid Analysis

• Obtain urine organic acid analysis to identify secondary metabolites that accumulate when amino acid metabolism is disrupted 1
• This test is particularly valuable for detecting disorders where plasma amino acids may appear normal but downstream metabolic products are elevated 1
• The American College of Medical Genetics and Genomics emphasizes that organic acid interpretation requires board-certified laboratory director review due to complexity 1, 4
• Look for patterns such as N-acetyl amino acids (aminoacylase 1 deficiency), vanilpyruvic acid (aromatic amino acid decarboxylase deficiency), or other specific metabolite signatures 1

Additional Biochemical Testing

• Measure plasma ammonia if urea cycle involvement is suspected, as hyperammonemia >200 µmol/L indicates severe metabolic decompensation 5
• Check plasma glutamine levels, which accumulate as the end product of ammonia detoxification in urea cycle disorders 5
• Obtain comprehensive metabolic panel including liver function tests to assess for hepatobiliary involvement 6

Interpretation Pitfalls and Key Principles

Common Diagnostic Challenges

• Amino acid synthesis defects are particularly difficult to diagnose because they present with low or normal amino acid levels rather than elevations 7, 3
• Serine, glutamine, proline, and asparagine synthesis defects all share this characteristic of subtle or absent biochemical abnormalities 7, 3
• The absence of elevated metabolites does not exclude amino acid deficiency—clinical context and complete amino acid profiling are essential 3

Pattern Recognition Requirements

• Individual amino acid abnormalities should never be interpreted in isolation 1, 5, 4
• The pattern must include assessment of related amino acids, ratios, and downstream metabolites 1
• For example, in phenylalanine hydroxylase deficiency, both elevated PHE and the PHE:TYR ratio >3 are diagnostic, not PHE elevation alone 1

Compartmentation Effects

• Plasma amino acid concentrations do not necessarily reflect levels in target organs like the brain or within specific cellular compartments 2
• This is especially problematic in disorders affecting nonessential amino acids or those with tissue-specific expression 2
• Clinical response to treatment may not correlate with plasma levels due to these compartmentation effects 2

When to Pursue Genetic Testing

Molecular Confirmation

• Obtain genetic testing for definitive diagnosis once biochemical abnormalities are identified 1
• Genotyping provides prognostic information, guides treatment intensity, and predicts response to cofactor supplementation 1
• Submit results to appropriate mutation databases to contribute to genotype-phenotype correlation knowledge 1

Next-Generation Sequencing Indications

• Consider exome or genome sequencing when clinical suspicion is high but biochemical testing is normal or equivocal 3
• This approach has dramatically expanded the recognized phenotypes of amino acid synthesis defects 3

Clinical Presentations Requiring Amino Acid Testing

Neonatal/Pediatric Presentations

• Congenital microcephaly, early-onset seizures, and developmental delay suggest serine or glutamine synthesis defects 7, 3
• Hypomyelination with brain volume loss on MRI is seen across multiple amino acid synthesis disorders 3
• Skin abnormalities (cutis laxa, collodion-like skin, ichthyosis, necrolytic erythema) accompanying neurological symptoms 3

Adult Presentations

• Spastic paraplegia or polyneuropathy with or without intellectual disability may represent late-presenting serine or proline synthesis defects 3