ClinVar Genomic variation as it relates to human health

The c.293T>C (p.Leu98Ser) variant in PAH has been reported as homozygous in a Pakistani patient with mild PKU (BH4 deficiency excluded) (PMID: 8364546, 9634518, 26542770) This variant has an extremely low frequency in gnomAD v2.1.1 (MAF=0.0001307). A deleterious effect is predicted in SIFT, Polyphen-2, MutationTaster, and REVEL=0.846. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3_supporting, PP3.

Variant summary: PAH c.293T>C (p.Leu98Ser) 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 allele was found at a frequency of 1.6e-05 in 251448 control chromosomes (gnomAD). c.293T>C has been reported in the literature in the homozygous state in an individual affected with Hyperphenylalaninemia who has subsequently been cited by others (Guldberg_1993, Bayat_2016, Hillert_2020). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. However, another variant affecting the same amino acid (L98V) has been observed in at least one affected individual and has been classified as likely pathogenic, suggesting Leu98 may be important for protein function. The following publications have been ascertained in the context of this evaluation (PMID: 26542770, 8364546, 32668217). Four submitters, including the ClinGen PAH Variant Curation Expert Panel, have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=1)/likely pathogenic (n=2) and VUS (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic until further clinical and/or functional information becomes available.

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Leu98 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26322415). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 expected to disrupt PAH protein function. This variant has been observed in individual(s) with hyperphenylalaninemia (PMID: 26542770). ClinVar contains an entry for this variant (Variation ID: 627). This sequence change replaces leucine with serine at codon 98 of the PAH protein (p.Leu98Ser). The leucine residue is highly conserved and there is a large physicochemical difference between leucine and serine. This variant is present in population databases (rs62517167, ExAC 0.006%).

The p.Leu98Ser variant in PAH has been reported in at least 4 individuals with phenylalanine hydroxylase deficiency (mild non-PKU hyperphenylalaninemia, mild PKU) who were either homozygous or compound heterozygous with another pathogenic variant (Guldberg 1993 PMID: 8364546, Bayat 2016 PMID: 26542770, Hillert 2020 PMID: 32668217). It has also been identified in 0.02% (1/4822) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has been reported as likely pathogenic by the ClinGen PAH Variant Curation Expert Panel using the ACMG-AMP criteria specific for phenylalanine hydroxylase variants (Zastrow 2018 PMID: 30311390) and is curated in the FDA-recognized human genetic variant ClinVar database (Variation ID 627). Computational prediction tools and conservation analyses suggest the variant may impact the protein this codon (p.Leu98Val) have been identified in individuals with phenylalanine hydroxylase deficiency and is classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic autosomal recessive phenylalanine hydroxylase deficiency. ACMG/AMP Criteria applied: PM3, PM2_Supporting, PP3, PP4_Moderate, PM5.

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 26542770, 8364546, 9634518, 10527663)

The PAH c.293T>C variant is predicted to result in the amino acid substitution p.Leu98Ser. This variant has been reported in the homozygous state in at least one patient with hyperphenylalaninemia (Guldberg et al. 1993. PubMed ID: 8364546; Bayat et al. 2016. PubMed ID: 26542770; Table S3, Hillert et al. 2020. PubMed ID: 32668217). It has also been listed in an unclassified variant in a large study of patients with hyperphenylalaninemia, although no additional evidence that could help determine the pathogenicity of this variant was provided (Guldberg et al. 1998. PubMed ID: 9634518). A different substitution of the same amino acid (p.Leu98Val) has been reported, in the compound heterozygous state with the common p.Arg408Trp pathogenic variant, in a patient with mild phenylketonuria (Tao et al. 2015. PubMed ID: 26322415). Although we suspect that the c.293T>C (p.Leu98Ser) variant could possibly be pathogenic, at this time its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence.