Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing

Natália D Linhares,Meire A Tostes,Piotr Wilk,Elżbieta Wątor,Sergio D J Pena,Manfred S Weiss

doi:10.1590/1678-4685-gmb-2020-0393

Abstract

Prolidase Deficiency (PD) is an autosomal recessive rare disorder caused by loss or reduction of prolidase enzymatic activity due to variants in the PEPD gene. PD clinical features vary among affected individuals: skin ulcerations, recurrent infections, and developmental delay are common. In this study, we describe a 16-year-old boy with a mild PD phenotype comprising chronic eczema, recurrent infections and elevated IgE. Whole exome sequencing analysis revealed three PEPD variants: c.575T>C p.(Leu192Pro) inherited from the mother, and c.692_694del p.(Tyr231del) and c.1409G>A p.(Arg470His), both inherited from the father. The variant p.(Tyr231del) has been previously characterized by high-resolution X-ray structure analysis as altering protein dynamics/flexibility. In order to study the effects of the other two prolidase variants, we performed site directed mutagenesis purification and crystallization studies. A high-resolution X-ray structure could only be obtained for the p.(Arg470His) variant, which showed no significant structural differences in comparison to WT prolidase. On the other hand, the p.(Leu192Pro) variant led to significant protein destabilization. Hence, we conclude that the maternal p.(Leu192Pro) variant was likely causally associated with the proband´s disease, together with the known pathogenic paternal variant p.(Tyr231del). Our results demonstrated the utility of exome sequencing to perform diagnosis in PD cases with mild phenotype.

Highlights

Prolidase deficiency (PD) is a rare disorder caused by homozygous or compound heterozygous variants in the PEPD gene (Peptidase D, OMIM*613230)
Exome sequencing analysis resulted in the identification of three rare heterozygous missense variants in PEPD (NM_000285.3)
The second variant was a deletion of three bases that led to the loss of residue Tyr231 in position c.692_694del p.(Tyr231del) in exon 10 (Chr19:33904527_33904529del); it was previously registered in the dbSNP dataset under the number rs745834191 and has been catalogued as pathogenic/likely pathogenic in the ClinVar database (Accession VCV000328810) (Landrum et al, 2018)

Summary

Introduction

Prolidase deficiency (PD) is a rare disorder caused by homozygous or compound heterozygous variants in the PEPD gene (Peptidase D, OMIM*613230). It is characterized by cutaneous lesions, recurrent infections principally of the skin and respiratory tract, dysmorphic facial features such as proptosis, hypertelorism, prominent forehead and micrognathia, hepatomegaly with elevated liver enzymes and splenomegaly (OMIM#170100). A recent review showed that 75 patients have been reported with a molecular diagnosis of PD (Spodenkiewicz et al, 2020); this number is certainly underestimated due to under-recognition of the disease by physicians. Using high-resolution X-ray crystal structure analysis of the PEPD protein prolidase, eight pathogenic variants have been characterized and possible mechanisms of prolidase enzymatic inactivation have been proposed (Wilk et al, 2017; Wilk et al, 2018)

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