Hyperphenylalaninemia Panel

Hyperphenylalaninemia can be caused by defects in any one of six proteins, and is often detected by newborn screening programs in early infancy (Regier and Greene. 2017. PubMed ID: 20301677). Correct and early diagnosis is important to ensure that the proper treatment is administered, leading to the best possible outcome for the patient (Leuzzi et al. 2010. PubMed ID: 20059486; Regier and Greene. 2017. PubMed ID: 20301677).

The primary genetic cause of hyperphenylalaninemia is a defect in the phenylalanine hydroxylase (PAH) enzyme, which is responsible for the enzymatic conversion of phenylalanine to tyrosine and accounts for ~98% of hyperphenylalaninemia cases (Regier and Greene. 2017. PubMed ID: 20301677). Individuals with PAH deficiency range from those with only mildly increased phenylalanine levels, who are generally clinically asymptomatic, to those with markedly increased phenylalanine levels and a diagnosis of classical phenylketonuria (PKU) (Camp et al. 2014. PubMed ID: 24667081). In untreated individuals with mild, moderate or classic PKU, the high levels of phenylalanine interfere with normal brain development and can lead to profound mental retardation, microcephaly, epilepsy and behavioral problems (Regier and Greene. 2017. PubMed ID: 20301677).

Secondary hyperphenylalaninemia can arise due to defects in genes encoding enzymes involved in the biosynthesis or regeneration of tetrahydrobiopterin (BH4) (Blau et al. 2014). The phenylalanine, tyrosine, and tryptophan hydroxylases all require BH4 as a cofactor, and lack of this cofactor results in secondary hyperphenylalaninemia and, in some disorders, depletion of the neurotransmitters dopamine and serotonin (Blau et al. 2014). Urinary pterin profiles and CSF neurotransmitter levels may be helpful in determining which gene in the tetrahydrobiopterin biosynthetic pathway has been disrupted (Blau et al. 2014). Patients with defects in these genes may be only mildly or transiently affected (as in pterin-4 α-carbinolamine dehydratase (PCD) deficiency) or may be quite severely affected (as in dihydropteridine reductase (DHPR) deficiency). In the more severely affected patients, symptoms are mainly neurologic and can include progressive hypotonia, EEG abnormalities, psychomotor retardation, delayed development, tonal abnormalities, seizures, dystonia, microcephaly, abnormal thermogenesis and swallowing difficulties (Blau et al. 2014). More recently, the DNAJC12 protein, a member of a heat shock co-chaperone family, was shown to interact with the phenylalanine, tyrosine and tryptophan hydroxylases (Anikster et al. 2017. PubMed ID: 28132689). Defects in this protein have also been shown to lead to hyperphenylalaninemia. Clinically, patients with hyperphenylalaninemia due to DNAJC12 defects have presented with a movement disorder and additional biochemical disturbances, including deficiencies of dopamin and serotonin in the cerebrospinal fluid and and elevated homovanillic acid/5-hydroxyindoleacetic acid (HVA/HIAA) ratio (Anikster et al. 2017. PubMed ID: 28132689).

More detail about these disorders can be found on the individual gene test pages for the DNAJC12, GCH1, PAH, PCBD1, PTS and QDPR genes. The SPR gene is also involved in BH4 biosynthesis, but patients with SPR defects do not present with hyperphenylalaninemia and thus the SPR gene is not included in this sequencing panel.

All of the hyperphenylalaninemias are inherited in an autosomal recessive manner, and are caused by defects in the DNAJC12, GCH1, PAH, PCBD1, PTS or QDPR genes. Defects in the GCH1 gene can also lead to DOPA-Responsive Dystonia (DRD), although this is an autosomal dominant disorder. See individual gene test descriptions for information on molecular biology of the gene products and mutation spectra.

The vast majority (~98%) of cases of hyperphenylalaninemia are caused by defects in the PAH gene, and only ~2% are due to defects in tetrahydrobiopterin deficiency caused by pathogenic variants in the GCH1, PCBD1, PTS or QDPR genes (Regier and Greene. 2017. PubMed ID: 20301677). The hyperphenylalaninemias caused by tetrahydrobiopterin deficiency are mainly a result of defects in the PTS gene (~65%), followed by QDPR (~25%), GCH1 and PCBD1 (~3% each) (BioDEF database, located at http://www.biopku.org/home/home.asp). Nearly all reported variants in these five genes are detectable via direct sequencing. It is difficult to estimate the proportion of hyperphenylalaninemia cases caused by defects in DNAJC12 as only a small number of patients have been reported.

Defects in the PAH gene are reported to account for ~98% of hyperphenylalaninemia cases, and gross deletions or duplications may account for up to ~3% of pathogenic variants in the PAH gene (Gable et al. 2003. PubMed ID: 12655547; Kozak et al. 2006. PubMed ID: 16931086). Many large deletions or duplications have been reported in the GCH1 gene, but to date, none of them have been associated with hyperphenylalaninemia (Human Gene Mutation Database). Gross deletions appear to be a somewhat common cause of hyperphenylalaninemia due to defects in DNAJC12. Thus far, no pathogenic gross deletions or duplications have been reported in the PCBD1 or QDPR genes. A few gross deletions affecting PTS have been reported, though large copy number variants in PTS appear to be relatively uncommon.

This panel typically provides 100% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

In addition to the regions described above, this testing includes coverage of the following variants that reside in untranslated or deep intronic regions: In PAH c.169-13T>G, c.509+15_509+18del, c.1065+39G>T, c.1066-11G>A, c.1066-13T>G, c.1066-14C>G, c.1199+17G>A, c.1199+20G>C, and c.*144A>G; in GCH1 c.-22C>T; in PTS c.84-323A>T, c.84-291A>G, c.163+696_163+750del, and c.164-716A>T; and in QDPR c.436+2552A>G.