ClinVar Genomic variation as it relates to human health

Variant summary: The PAH c.261C>A (p.Ser87Arg) variant involves the alteration of a non-conserved nucleotide and 2/4 in silico tools (MutationTaster not captured here due to low p-value) predict a damaging outcome. This variant was found in 10/121410 control chromosomes at a frequency of 0.0000824, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). The variant of interest has been reported in affected individuals via publication, predominantly showing a mild HPA phenotype. In addition, a clinical diagnostic laboratory and reputable database classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

The PAH c.261C>A (p.Ser87Arg) missense variant has been reported in a compound heterozygous state in six unrelated individuals with phenylalanine hydroxylase deficiency, including in five with mild hyperphenylalaninemia and in one with mild phenylketonuria (Guldberg et al. 1994; Zekanowski et al. 1999; Desviat et al. 2004; Bueno et al. 2013; Ohlsson et al. 2017). The p.Ser87Arg variant was also identified in at least one additional individual, but the zygosity of the variant was not provided (Zurflüh et al. 2008; Couce et al. 2013). The variant was absent from 220 control chromosomes, but is reported at a frequency of 0.00014 in the European (non-Finnish) population of the Exome Aggregation Consortium. In addition, Couce et al. (2013) report data from the PAHdb which indicates in vitro residual PAH activity at 25-82% of wild type for the variant. Based on the evidence, the p.Ser87Arg variant is classified as pathogenic for phenylalanine hydroxylase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 87 of the PAH protein (p.Ser87Arg). This variant is present in population databases (rs62516151, gnomAD 0.01%). This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 8088845, 10495930). ClinVar contains an entry for this variant (Variation ID: 583). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PAH protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 23500595). For these reasons, this variant has been classified as Pathogenic.

The c.261C>A (p.S87R) alteration is located in coding exon 3 of the PAH gene. This alteration results from a C to A substitution at nucleotide position 261, causing the serine (S) at amino acid position 87 to be replaced by an arginine (R). Based on data from the Genome Aggregation Database (gnomAD), the PAH c.261C>A alteration was not observed, with coverage at this position. The c.261C>A (p.S87R) alteration has been reported in combination with a second pathogenic alteration in multiple unrelated families presenting with hyperphenylalaninemia and mild PKU (Bueno, 2013; Desviat, 2004; Guldberg, 1993; Jeannesson-Thivisol, 2015; Rajabi, 2019). The p.S87 amino acid is not conserved in available vertebrate species. The in silico prediction for the p.S87R alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

The PAH c.261C>A variant is predicted to result in the amino acid substitution p.Ser87Arg. This variant has been reported along with a second causative PAH variant in multiple patients with phenylalanine hydroxylase deficiency (Guldberg et al. 1994. PubMed ID: 8088845; Zekanowski et al. 1999. PubMed ID: 10495930; Desviat et al. 2004. PubMed ID: 15464430; Jeannesson-Thivisol et al. 2015. PubMed ID: 26666653; Table S3, Hillert A et al 2020. PubMed ID: 32668217). This variant has been reported to be associated with mild hyperphenylalaninemia (Table S2, Hillert A et al 2020. PubMed ID: 32668217). Internally, we have observed this variant along with a second causative PAH variant in patients with abnormal newborn screen results suggestive of phenylalanine hydroxylase deficiency. The p.Ser87 amino acid resides in the PAH regulatory domain, and in functional studies the p.Ser87Arg substitution has been reported to reduce activity of the PAH enzyme to between ~25-82% of wild-type (Gjetting et al. 2001. PubMed ID: 11161839; Couce et al. 2013. PubMed ID: 23500595). The p.Ser87Arg substitution has been reported to result in a PAH enzyme that is responsive to tetrahydrobiopterin (BH4) (Zurflüh et al. 2008. PubMed ID: 17935162). A different nucleotide change leading to the same amino acid substitution (c.259A>C, p.Ser87Arg) has also been reported in association with phenylalanine hydroxylase deficiency (Himmelreich et al. 2018. PubMed ID: 30037505). The c.261C>A (p.Ser87Arg) variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Based on these observations, this variant is interpreted as pathogenic.