POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies

Kelly Smallwood, Kristin E.N. Watt, Satoru Ide, Kristina Baltrunaite, Chad Brunswick, Katherine Inskeep, Corrine Capannari, Margaret P. Adam, Amber Begtrup, Debora R. Bertola, Laurie Demmer, Erin Demo, Orrin Devinsky, Emily R. Gallagher, Maria J. Guillen Sacoto, Robert Jech, Boris Keren, Jennifer Kussmann, Roger Ladda, Lisa A. LansdonSebastian Lunke, Anne Mardy, Kirsty McWalters, Richard Person, Laura Raiti, Noriko Saitoh, Carol J. Saunders, Rhonda Schnur, Matej Skorvanek, Susan L. Sell, Anne Slavotinek, Bonnie R. Sullivan, Zornitza Stark, Joseph D. Symonds, Tara Wenger, Sacha Weber, Sandra Whalen, Susan M. White, Juliane Winkelmann, Michael Zech, Shimriet Zeidler, Kazuhiro Maeshima, Rolf W. Stottmann, Paul A. Trainor, K. Nicole Weaver*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)


Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.

Original languageEnglish
Pages (from-to)809-825
Number of pages17
JournalAmerican Journal of Human Genetics
Issue number5
Early online date18 Apr 2023
Publication statusPublished - May 2023

Bibliographical note

Funding Information:
This work was funded by the National Institutes of Health National Heart Lung and Blood Institute K08 HL143177-01A1 (K.N.W.), the National Institute of Child Health and Human Development K12 HD028827 (K.N.W.), Cincinnati Children's Research Foundation Center for Pediatric Genomics Pilot Proposal (K.N.W.), the Cleft Palate Foundation's Paul W. Black Grant for Emerging Researchers (K.N.W.), the National Institute of Dental and Craniofacial Research K99 (K.E.N.W.), and the Stowers Institute for Medical Research 1008 (P.A.T.). Operational Program Integrated Infrastructure, funded by the ERDF (ITMS2014+:313011V455) was provided to M.S. and M.Z. receives research support from the German Research Foundation (DFG 458949627; ZE 1213/2-1). The Acute Care Genomics study is funded by grants from the Australian Government's Medical Research Futures Fund (GHFM76747) and the Royal Children's Hospital Foundation (2020-1259). In vitro work was funded by the Japan Society for the Promotion of Science (JSPS) grants (22H05606, 21H02535 to S.I.; 19H05273, 20H05936 to K. Maeshima), JST CREST (JPMJCR15G2 to K. Maeshima), the Takeda Science Foundation (K. Maeshima), and the Uehara Memorial Foundation (K. Maeshima). A.B. M.J.G.S. K. McWalters, R.P. and R.S. are employees of GeneDx.

Publisher Copyright:
© 2023 American Society of Human Genetics


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