ClinVar Genomic variation as it relates to human health

This variant has been previously reported as a homozygous or compound heterozygous change in multiple patients with prolidase deficiency (PMID: 8198124, 17142620). Studies using patient fibroblast lines and recombinant prolidase demonstrated that this variant leads to decreased catalytic efficiency, thermal stability and cofactor binding (PMID: 23516557). Additionally, an in vitro experiment in COS-1 cells demonstrated that this variant reduces prolidase activity to undetectable levels (PMID: 8900231). This variant has been classified as Pathogenic by a clinical diagnostic laboratory in the ClinVar database (Variation ID: 213). It is present in the heterozygous state in the gnomAD population database at a frequency of .003% (5/193670) and thus is presumed to be rare. The c.1342G>A (p.Gly448Arg) variant is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1342G>A (p.Gly448Arg) variant is classified as Pathogenic.

The PEPD c.1342G>A (p.Gly448Arg) missense variant has been reported in four studies in which it is found in a total of eight individuals with prolidase deficiency (PD). The variant was found in five individuals in a homozygous state, including a sibling pair, and in three compound heterozygotes, two of whom were related (Ledoux et al. 1994; Forlino et al. 2002; Lupi et al. 2006; Vestita et al. 2017). Ledoux et al. (1994), Lupi et al. (2006) and Besio et al. (2013) demonstrated that prolidase activity in fibroblasts from patients with PD with the p.Gly448Arg variant was reduced to <2% to 13.1% when compared to controls. In addition, transient expression of the p.Gly448Arg variant in COS1 cells produced an inactive enzyme (Ledoux et al. 1996), and a recombinant PEPD enzyme containing the p.Gly448Arg variant showed very low catalytic efficiency, thermal instability, and changes in protein conformations (Besio et al. 2013). Forlino et al. (2002) also showed that cultured PD patient fibroblasts with the p.Gly448Arg variant exhibited multiple cell structure abnormalities. This variant was absent in 150 control chromosomes and is reported at a frequency of 0.000036 in the European (non-Finnish) population. Based on the collective evidence, the p.Gly448Arg variant is classified as pathogenic for prolidase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The p.Gly448Arg variant in PEPD has been reported in 6 individuals with prolidas e deficiency. Three of these individuals were homozygous and three compound hete rozygous with another pathogenic variant in PEPD (Ledoux 1994, Lupi 2006, Forlin o 2002). This variant has also been identified in 0.027% (2/7412) of European ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs121917724). Although this variant is seen in the general population , its frequency is consistent with a recessive carrier frequency. In addition, i n vitro functional studies provide some evidence that the p.Gly448Arg variant ma y impact protein function (Ledoux 1996, Besio 2013). In summary, this variant me ets our criteria to be classified as pathogenic for prolidase deficiency in an a utosomal recessive manner based upon its co-occurrence in trans with other patho genic variants in patients, low frequency in controls and functional evidence.

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 448 of the PEPD protein (p.Gly448Arg). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with prolidase deficiency (PMID: 8198124, 12384772, 17142620, 25460580). ClinVar contains an entry for this variant (Variation ID: 213). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PEPD function (PMID: 8900231, 23516557). For these reasons, this variant has been classified as Pathogenic.