De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder

Abstract

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

Severe neurodevelopmental disease caused by a homozygous TLK2 variant

“…We report a homozygous missense variant in TLK2 in a patient with a neurodevelopmental disorder with severe motor and language delay, West syndrome, pontocerebellar hypoplasia, behavioural problems, facial dysmorphism and gastro-intestinal symptoms. The clinical presentation fits what has been described by Reijnders et al [3] for heterozygous TLK2 patients and the dysmorphic features were remarkably similar. Our index case, however, presented with more severe symptoms, with profound ID, spastic tetraparesis and a structural brain anomaly.…”

“…All nine missense variants identified in the 38 families described by Reijnders et al [3] were located either in the catalytic domain or in the coiled-coil motifs of the protein. Our variant is located at the N -terminus in a region where no functional domains are known (Fig.…”

“…3 Schematic representation of the TLK2 missense variants identified. In black, the p.(Lys55Glu) reported here; in grey, the nine variants previously reported by Reijnders et al [3]. Annotation is according to NM_006852.3…”

Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling

“…TLK inhibitors could therefore represent a novel rational targeted therapy to render ALT+ or CIN high cancers more vulnerable to the induction of cell death and provide a window of opportunity to reset chromatin state, enhance existing therapies and provoke tumor regression. Moreover, the newly uncovered role of TLK activity in the suppression of innate immune mediated inflammation may be highly relevant to the etiology of intellectual disability/autism spectrum disorder in patients with germline TLK2 mutations (Lelieveld et al, 2016;Reijnders et al, 2018).…”

Mutations in the Neuronal Vesicular SNARE VAMP2 Affect Synaptic Membrane Fusion and Impair Human Neurodevelopment

“…The present work adds to the evidence that neurodevelopmental disorders (NDDs) have a strong genetic component and encompass a range of frequently co-existing conditions, including ID, developmental delay (DD), and autism spectrum disorders (ASDs). 27 , 28 Neurodevelopmental impairment, epilepsy, and movement disorders also frequently co-exist. 29 , 30 Rare variants in genes that encode a number of presynaptic proteins involved in Ca 2+ -regulated neurotransmitter release have been identified in individuals affected by a spectrum of neurological disorders.…”