ClinVar Genomic variation as it relates to human health

The c.212G>A (p.Arg71His) variant in PAH has been reported in multiple individual with PAH deficiency with BH4 deficiency excluded (PP4_Moderate; PMID: 10495930, 26503515). This variant is absent in population databases (PM2). This variant was detected in trans with known pathogenic variant p.R408W (PM3). Computational evidence supports a deleterious effect. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3, PP3.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31130284, 38706300, 20140859, 29499199, 26503515, 30747360, 32668217, 32039316, 29390883, 33803550, 10495930)

The PAH c.212G>A variant is predicted to result in the amino acid substitution p.Arg71His. This variant has been reported along with a second known pathogenic PAH variant in individuals with hyperphenylalaninemia (Zekanowski et al. 1999. PubMed ID: 10495930, patient IW in Table 1; Li et al. 2015. PubMed ID: 26503515; Hillert et al 2020. PubMed ID: 32668217). The p.Arg71 residue has been moderately conserved during evolution (Alamut Visual v2.10). It is located in a region of the PAH protein where it is thought to be involved in interdomain interactions in the protein monomer, and it is thought that a change in the amino acids in this region could result in a structural disturbance of the protein (Pey et al. 2007. PubMed ID: 17924342). Other variants that disrupt the same amion acid (e.g., p.Arg71Cys, p.Arg71Pro) have been reported in patients with phenylalanine hydroxylase deficiency (Wang et al. 2007. PubMed ID: 17627389; Hillert et al 2020. PubMed ID: 32668217). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant has been interpreted as likely pathogenic or pathogenic by the majority of submitters to ClinVar, including the ClinGen PAH Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/102633/). Taken together, we classify the c.212G>A (p.Arg71His) variant as pathogenic.

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. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg71 amino acid residue in PAH. Other variant(s) that disrupt this residue have been observed in individuals with PAH-related conditions (PMID: 17627389), which suggests that this may be a clinically significant amino acid residue. ClinVar contains an entry for this variant (Variation ID: 102633). This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 10495930, 29390883, 32668217; BIOPKU http://www.biopku.org). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 71 of the PAH protein (p.Arg71His).

Variant summary: PAH c.212G>A (p.Arg71His) results in a non-conservative amino acid change located in the ACT domain (IPR002912) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251342 control chromosomes. c.212G>A has been reported in the literature in individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (e.g. Zekanowski_1999, Zhang_2018, Monies_2019, Yan_2020). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 26503515, 10495930, 29499199, 30747360, 31130284, 32039316, 29390883). ClinVar contains an entry for this variant (Variation ID: 102633). Based on the evidence outlined above, the variant was classified as likely pathogenic.