Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort

Linda A.J. Hendricks, Nicoline Hoogerbrugge, PTEN Study Group, Hanka Venselaar, Stefan Aretz, Isabel Spier, Eric Legius, Hilde Brems, Robin de Putter, Kathleen B.M. Claes, D. Gareth Evans, Emma R. Woodward, Maurizio Genuardi, Fulvia Brugnoletti, Yvette van Ierland, Kim Dijke, Emma Tham, Bianca Tesi, Janneke H.M. Schuurs-Hoeijmakers, Maud BranchaudHector Salvador, Arne Jahn, Simon Schnaiter, Violetta Christophidou Anastasiadou, Joan Brunet, Carla Oliveira, Laura Roht, Ana Blatnik, Arvids Irmejs, Arjen R. Mensenkamp, Janet R. Vos*

*Corresponding author for this work

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Abstract

Background: Pathogenic PTEN germline variants cause PTEN Hamartoma Tumor Syndrome (PHTS), a rare disease with a variable genotype and phenotype. Knowledge about these spectra and genotype-phenotype associations could help diagnostics and potentially lead to personalized care. Therefore, we assessed the PHTS genotype and phenotype spectrum in a large cohort study. Methods: Information was collected of 510 index patients with pathogenic or likely pathogenic (LP/P) PTEN variants (n = 467) or variants of uncertain significance. Genotype-phenotype associations were assessed using logistic regression analyses adjusted for sex and age. Results: At time of genetic testing, the majority of children (n = 229) had macrocephaly (81%) or developmental delay (DD, 61%), and about half of the adults (n = 238) had cancer (51%), macrocephaly (61%), or cutaneous pathology (49%). Across PTEN, 268 LP/P variants were identified, with exon 5 as hotspot. Missense variants (n = 161) were mainly located in the phosphatase domain (PD, 90%) and truncating variants (n = 306) across all domains. A trend towards 2 times more often truncating variants was observed in adults (OR = 2.3, 95%CI = 1.5–3.4) and patients with cutaneous pathology (OR = 1.6, 95%CI = 1.1–2.5) or benign thyroid pathology (OR = 2.0, 95%CI = 1.1–3.5), with trends up to 2–4 times more variants in PD. Whereas patients with DD (OR = 0.5, 95%CI = 0.3–0.9) or macrocephaly (OR = 0.6, 95%CI = 0.4–0.9) had about 2 times less often truncating variants compared to missense variants. In DD patients these missense variants were often located in domain C2. Conclusion: The PHTS phenotypic diversity may partly be explained by the PTEN variant coding effect and the combination of coding effect and domain. PHTS patients with early-onset disease often had missense variants, and those with later-onset disease often truncating variants.

Original languageEnglish
Article number104632
JournalEuropean Journal of Medical Genetics
Volume65
Issue number12
DOIs
Publication statusPublished - Dec 2022

Bibliographical note

Funding Information:
This work (L.A.J.H. and J.R.V.) was financially supported by the PTEN Research Foundation . E.R.W. and D.G.E. are supported by the NIHR Manchester Biomedical Research Centre (Grant Reference Number 1215–200074 ). E.T. is supported by Region Stockholm (Grant ID, 2020-500306 DS ). L.R. is supported by the Estonian Research Council (Grant ID PRG471 ).

Publisher Copyright: © 2022 The Authors

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