ClinVar Genomic variation as it relates to human health

The R229Q variant in the PNPO gene has been reported previously in the homozygous state in two unrelated children with early epileptic encephalopathy and in another individual with an unspecified neurocognitive phenotype (Carvill et al., 2013; Ware et al., 2014; Yavarna et al., 2015). The R229Q variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R229Q variant is a semi-conservative amino acid substitution, which occurs at a position that is conserved across species and lies within a region of the protein necessary for substrate binding and catalysis (Musayev et al., 2009). In silico analysis predicts this variant is probably damaging to the protein structure/function. A different missense substitution at the same position (R229W) has also been published in association with PNPO deficiency (Mills et al., 2005), supporting the functional importance of this region of the protein. We interpret R229Q as a pathogenic variant.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 229 of the PNPO protein (p.Arg229Gln). This variant is present in population databases (rs773450573, gnomAD 0.008%). This missense change has been observed in individual(s) with PNPO related disease (PMID: 23708187, 24266778, 28133863, 28985901). ClinVar contains an entry for this variant (Variation ID: 206452). 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 PNPO protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

This variant has been reported in the homozygous state in multiple families with PNPOD (PMID: 28985901, 24266778). Assessment of experimental evidence suggests this variant results in reduced catalytic efficiency (PMID: 19759001). The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study.

Variant summary: PNPO c.686G>A (p.Arg229Gln) results in a conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251476 control chromosomes (gnomAD). c.686G>A has been reported in the literature in at least two homozygous individuals affected with Pyridoxal 5'-Phosphate-Dependent Epilepsy (e.g. Ware_2013, Carvill_2013, Guerriero_2017, Olson_2017, Kingsmore_2022). These data indicate that the variant is likely to be associated with disease. At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant severely decreased enzymatic activity (both Km and Vmax) compared to the WT (Musayev_2009). The following publications have been ascertained in the context of this evaluation (PMID: 24266778, 23708187, 28985901, 28133863, 36007526, 19759001). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This variant is interpretted as Pathogenic for Pyridoxamine 5'-phosphate oxidase deficiency, Austomal Recessive. PM1 - Located in a mutational hot spot and/or critical and well-established functional domain without benign variation. PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PM5 - Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before (PMID: 24645144). PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease. PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation (PMID: 26077850).

The PNPO c.686G>A variant is predicted to result in the amino acid substitution p.Arg229Gln. This variant has been reported in the homozygous state in multiple individuals with PNPO-related epilepsy (see for example, Carvill et al. 2013. PubMed ID: 23708187; Olson et al. 2017. PubMed ID: 28133863; Guerriero et al. 2017. PubMed ID: 28985901; Maron et al. 2021. PubMed ID: 33587123). This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD. A different missense variant affecting the same amino acid (p.Arg229Trp) has been associated with PNPO-related epilepsy in a family; however, the evidence was indirect (Mills et al. 2005. PubMed ID: 15772097). Taken together, the c.686G>A (p.Arg229Gln) variant is interpreted as pathogenic.