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Condition report · Metabolic

Phenylketonuria (PKU)

Whole genome sequencing identifies PAH variants that predict BH4 responsiveness, enabling your physician to consider sapropterin therapy that may reduce dietary restriction and improve quality of life.

Updated 16 October 2026

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About this condition

An inherited metabolic disorder caused by variants in the PAH gene, in which the body cannot break down the amino acid phenylalanine. Without a special diet from infancy, phenylalanine builds up and damages the brain.

Phenylketonuria (PKU) is an autosomal recessive disorder of phenylalanine metabolism caused by PAH mutations, which encode phenylalanine hydroxylase, the enzyme that converts phenylalanine to tyrosine. Loss-of-function PAH variants impair this critical amino acid conversion, causing phenylalanine accumulation to toxic levels and tyrosine deficiency. Untreated PKU causes severe intellectual disability, behavioral problems, neurological regression, eczema, light skin pigmentation, and a characteristic musty or mousy body odor. However, early treatment with lifelong phenylalanine-restricted diet prevents all manifestations; treated individuals develop normal intelligence and have normal lifespans.

PKU affects approximately 1 in 10,000 to 1 in 15,000 individuals in European populations, with higher prevalence in some Asian and Middle Eastern populations. Over 1,100 PAH variants have been catalogued, showing wide genetic heterogeneity. PKU has been detected via universal newborn screening in all 50 US states since the 1960s, one of the earliest success stories of genetic disease prevention. Critically, approximately 25-50% of PKU patients carry PAH variants that confer BH4 (tetrahydrobiopterin) responsiveness; these individuals can respond to sapropterin (Kuvan), a synthetic BH4 cofactor that enhances residual PAH enzyme activity and may allow significantly less restrictive diets. Genotype-phenotype correlation is strong: specific variant classes (particularly missense mutations maintaining residual activity) respond to BH4, while null variants and frameshift mutations do not.

A PAH variant diagnosis identified at birth through newborn screening mandates immediate dietary intervention with phenylalanine restriction; this prevents intellectual disability and neurological manifestations entirely. Genotype-phenotype correlation directly informs management: BH4-responsive variants may qualify patients for sapropterin therapy, potentially allowing less restrictive diets and improved quality of life compared to lifelong severe phenylalanine restriction. Early treatment is paramount; even brief periods of elevated phenylalanine during the neonatal period can cause permanent cognitive damage. Genetic diagnosis enables carrier screening of family members and preconception counseling for affected individuals planning pregnancy (maternal PKU requiring strict dietary control during pregnancy to prevent fetal damage).

Approximately 25-50% of PKU patients carry BH4-responsive PAH variants that respond to sapropterin therapy, potentially allowing less restrictive diets and improved quality of life.

The condition we analyse

Phenylketonuria

Autosomal recessive

A disorder of phenylalanine metabolism due to phenylalanine hydroxylase deficiency, causing intellectual disability if untreated.

What a diagnosis changes

Phenylalanine-restricted diet, sapropterin (BH4) therapy for BH4-responsive variants, medical foods, newborn screening

Genes analysed

Also known as

hyperphenylalaninemia, non-PKU mild; PAH deficiency; phenylalanine hydroxylase deficiency; PKU

Includes 4 related subtypes ↓
  • classic phenylketonuria
  • mild phenylketonuria
  • tetrahydrobiopterin-responsive phenylketonuria
  • tetrahydrobiopterin-unresponsive phenylketonuria
MONDO:0009861OMIM 261600Orphanet 716MedGen 19244

Example variants this report looks at

For each condition, a few of the variants ClinVar classifies under it, those with most review stars. Each page describes ClinVar's public record of the variant, never a result.

VariantGeneClinVar classificationReview status
A47VPAHLikely pathogenic3 stars out of 4 reviewed by expert panel
A90Cfs*12PAHPathogenic3 stars out of 4 reviewed by expert panel
A104DPAHPathogenic3 stars out of 4 reviewed by expert panel

616 more variants under Phenylketonuria have a page. Every variant, by gene:

Why whole genome sequencing

PAH variant testing is important for predicting BH4 responsiveness and dietary tolerance. Over 1,100 variants exist with strong genotype-phenotype correlation. WGS complements, but does not replace, newborn screening.

PAH genotype predicts BH4 responsiveness and dietary flexibility

Although PKU is detected through newborn screening (the standard of care for early detection), genetic testing plays a critical role in predicting BH4 responsiveness and dietary tolerance. Approximately 25-50% of PKU patients carry PAH variants that respond to sapropterin (Kuvan), a BH4 cofactor that enhances residual PAH activity. Specific variant classes, particularly missense mutations maintaining residual enzymatic activity, predict BH4 responsiveness, while null variants and frameshift mutations do not. Over 1,100 PAH variants have been catalogued with strong genotype-phenotype correlation. Whole genome sequencing captures all PAH variants and enables accurate prediction of sapropterin response, confirmed through clinical BH4 loading tests.

Identifying BH4 responsiveness can expand dietary flexibility and quality of life

A PAH variant diagnosis combined with BH4 responsiveness testing can substantially improve quality of life in PKU patients. Lifelong severe phenylalanine restriction is challenging and affects nutrition, social integration, and psychological well-being. BH4-responsive patients may qualify for sapropterin therapy, which can partially normalize phenylalanine metabolism and allow less restrictive diets. This enables greater food choices, improved nutritional status, and better quality of life while maintaining safe phenylalanine levels. Even a modest reduction in dietary restriction can have significant psychosocial benefits. Genetic testing identifies which patients can benefit from this approach.

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