Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities

Abstract

MN1 was originally identified as a tumor-suppressor gene. Knockout mouse studies have suggested that Mn1 is associated with craniofacial development. However, no MN1-related phenotypes have been established in humans. Here, we report on three individuals who have de novo MN1 variants that lead to a protein lacking the carboxyl (C) terminus and who presented with severe developmental delay, craniofacial abnormalities with specific facial features, and structural abnormalities in the brain. An in vitro study revealed that the deletion of the C-terminal region led to increased protein stability, an inhibitory effect on cell proliferation, and enhanced MN1 aggregation in nuclei compared to what occurred in the wild type, suggesting that a gain-of-function mechanism is involved in this disease. Considering that C-terminal deletion increases the fraction of intrinsically disordered regions of MN1, it is possible that altered phase separation could be involved in the mechanism underlying the disease. Our data indicate that MN1 participates in transcriptional regulation of target genes through interaction with the transcription factors PBX1, PKNOX1, and ZBTB24 and that mutant MN1 impairs the binding with ZBTB24 and RING1, which is an E3 ubiquitin ligase. On the basis of our findings, we propose the model that C-terminal deletion interferes with MN1's interaction molecules related to the ubiquitin-mediated proteasome pathway, including RING1, and increases the amount of the mutant protein; this increase leads to the dysregulation of MN1 target genes by inhibiting rapid MN1 protein turnover.

A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis

“…Lastly, the diagnosis of individual U036 was confirmed through international collaboration for new syndrome discovery: MN1 C-terminal truncation syndrome, where 23 individuals who harbor truncating variants at C-terminal of MN1 gene were found to share strikingly similar neurodevelopmental and craniofacial features 51 . It is postulated that these C-terminal truncating variants have escaped nonsense-mediated mRNA decay, thus creating a gain-of-function effect that increased protein stability, diminished cell proliferation, and enhanced MN1 aggregation 51 , 52 .…”

Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations

“…Truncations of IDRs could also affect protein stability (Babu et al, 2011), which would result in lower protein concentrations. IDR truncations may also disrupt specific protein-protein interactions that affect protein partitioning into condensates (Miyake et al, 2020) and alter protein-protein interactions that change normal threshold concentrations for phase separation (Riback et al, 2020). Missense mutations in IDRs can change the strength of the underlying physicochemical interactions (Box 1) that give rise to material properties of a condensate, varying from a dynamic liquid (readily assembling and disassembling) to an aberrant gelled or fibrillar state in disease (Molliex et al, 2015;Murakami et al, 2015;Patel et al, 2015).…”

OTUD5 Variants Associated With X-Linked Intellectual Disability and Congenital Malformation

“…For Individuals 1 and 2, WES was performed using an illumina platform as previously described ( Miyake et al, 2020 ). The mean read depth of the RefSeq coding region was 98.3 and 113.6 reads (corresponding to 96.1%- and 96.4%-, respectively, covered by >20 reads), respectively.…”