PRIM1 deficiency causes a distinctive primordial dwarfism syndrome.

David Parry ,Katalin Szakszon,Olga Murina,Andrea Leitch,Paula Carroll,Andrew P Jackson,Brigitta Orlik,Martin A.M Reijns,Philip Greene,Andrea Nagy,Lukas Tamayo-Orrego,Balázs Kovács-Pászthy,Gabriella Merő,Julia Rankin,Carolina Uggenti,Rita Káposzta,Magdolna Riszter,Joseph A Marsh,Alan J Quigley

doi:10.1101/gad.340190.120

Abstract

DNA replication is fundamental for cell proliferation in all organisms. Nonetheless, components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Using a variant classification agnostic approach, biallelic mutations in PRIM1 were identified in five individuals. PRIM1 protein levels were markedly reduced in patient cells, accompanied by replication fork asymmetry, increased interorigin distances, replication stress, and prolonged S-phase duration. Consequently, cell proliferation was markedly impaired, explaining the patients' extreme growth failure. Notably, phenotypic features distinct from those previously reported with DNA polymerase genes were evident, highlighting differing developmental requirements for this core replisome component that warrant future investigation.

Highlights

DNA replication is fundamental for cell proliferation in all organisms
We analyzed whole-genome (WGS) and whole-exome (WES) sequence data from 220 families with microcephalic dwarfism spectrum disorders to find variants enriched in this cohort relative to the general population and inherited in a pattern consistent with recessive inheritance (Materials and Methods; Supplemental Table S3)
Supporting its pathogenicity, the intronic PRIM1 variant was significantly enriched in our microcephalic dwarfism cohort in comparison with the Genome Aggregation Database where just two heterozygotes out of 141,456 individuals were observed (Supplemental Table S4)

Summary

Introduction

DNA replication is fundamental for cell proliferation in all organisms. components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Mutations in genes encoding subunits of the replicative DNA polymerases POLA1, POLD1, POLD2, POLE, and POLE2 have implicated components of the active replisome in primordial dwarfism, often with immune deficiency, and in the case of POLE, adrenal failure (Pachlopnik Schmid et al 2012; Thiffault et al 2015; Frugoni et al 2016; Logan et al 2018; Conde et al 2019; Van Esch et al 2019) Each of these genes has been shown to be essential for cellular survival in large-scale functional screens (Supplemental Table S1; Chen et al 2017) while constraint metrics from the gnomAD consortium suggest that loss of a single copy is unlikely to result in developmental disease (Supplemental Table S2; Karczewski et al 2020). We report the identification of PRIM1 as an MPD gene, and demonstrate that mutations reduce cellular PRIM1 protein levels, impairing DNA replication

Methods

Results

Conclusion