Mutational survivorship bias: The case of PNKP

Abstract

The molecular function of a protein relies on its structure. Understanding how variants alter structure and function in multidomain proteins is key to elucidate the generation of a pathological phenotype. However, one may fall into the logical bias of assessing protein damage only based on the variants that are visible (survivorship bias), which can lead to partial conclusions. This is the case of PNKP, an important nuclear and mitochondrial DNA repair enzyme with both kinase and phosphatase function. Most variants in PNKP are confined to the kinase domain, leading to a pathological spectrum of three apparently distinct clinical entities. Since proteins and domains may have a different tolerability to variation, we evaluated whether variants in PNKP are under survivorship bias. Here, we provide the evidence that supports a higher tolerance in the kinase domain even when all variants reported are deleterious. Instead, the phosphatase domain is less tolerant due to its lower variant rates, a higher degree of sequence conservation, lower dN/dS ratios, and the presence of more disease-propensity hotspots. Together, our results support previous experimental evidence that demonstrated that the phosphatase domain is functionally more necessary and relevant for DNA repair, especially in the context of the development of the central nervous system. Finally, we propose the term "Wald’s domain" for future studies analyzing the possible survivorship bias in multidomain proteins.

Zika virus induces mitotic catastrophe in human neural progenitors by triggering unscheduled mitotic entry in the presence of DNA damage while functionally depleting nuclear PNKP

“…The most severe of these disorders produces early onset primary microcephaly with seizures and developmental delay (MCSZ, MIM 613402), also known as developmental and epileptic encephalopathy-10, DEE10) (31,97) It is not entirely clear how different PNKP mutations contribute to either neurodevelopmental or neurodegenerative pathologies, but recent data indicate that residual levels of phosphatase or kinase activity may play a role. In-silico genetic variant analysis (103) shows that the phosphatase domain has lower tolerability to variation. This domain has lower variant rates, higher degree of sequence conservation, lower dN/dS ratio, and more disease-propensity hotspots than the kinase domain (103).…”

“…In-silico genetic variant analysis (103) shows that the phosphatase domain has lower tolerability to variation. This domain has lower variant rates, higher degree of sequence conservation, lower dN/dS ratio, and more disease-propensity hotspots than the kinase domain (103). The phosphatase domain pathogenic variants were predicted to be rare and to produce more severe clinical outcomes, a model supported by studies with patient-isolated fibroblasts.…”

Prenatal phenotype of PNKP-related primary microcephaly associated with variants in the FHA and Phosphatase domain

“…Analysis of disease-associated missense variants in the linear protein representation, clustering analysis in 3D and structural modelling of missense variants using the crystal structure 2BRF (23) was performed as described previously (11,13,19) and is detailed in the Supplementary notes.…”

“…To date, exclusively postnatal observations are covered in literature. Most pathogenic PNKP variants described so far are either truncating or located in the Cterminal Kinase domain (11). While genotype-phenotype correlations have been attempted and C-terminal variants have been implied to cause the milder adult-onset diseases, no clear relation could yet be established.…”

CDKs-mediated phosphorylation of PNKP is required for end-processing of single-strand DNA gaps on Okazaki Fragments and genome stability

“…Meanwhile, PNKP mutations are associated with the human inherited disease microcephaly and seizures (MCSZ) (Shen et al, 2010), ataxia oculomotor apraxia 4 (AOA4) (Bras et al, 2015) and Charcot-Marie-Tooth disease (CMT2B2) (Pedroso et al, 2015). These mutations are mostly sited in phosphatase or kinase domains and attenuated phosphatase and kinase activity (Bermudez-Guzman et al, 2020; Kalasova et al, 2020; Reynolds et al, 2012).…”