Rare variant of TBL1XR1 in West syndrome: A case report

Abstract Background West syndrome (WS) is an epileptic encephalopathy (EE) that begins in children 4–7 months of age (in rare cases older than 2 years). To date, over 30 genes that have been reported to be related to WS. Reports involving the extremely rare pathogenic gene, transducin beta‐like 1‐X‐ linked receptor 1(TBL1XR1) are quite limited. Methods We performed exome sequencing (ES) of family trios for this infant. We also collected and summarized the clinical data for reported heterozygous germline variants of TBL1XR1. Moreover, we reviewed all published cases and summarized the clinical features and genetic variants of TBL1XR1. Results ES revealed a de novo variant in TBL1XR1 [NM_024665.5: exon4: c.187G > A (p.Glu63Lys)]. This variant was classified as likely pathogenic according to the ACMG (American College of Medical Genetics and Genomics) guidelines and was verified by Sanger sequencing. Further conservation analyses revealed a high conservation among several species. There was clinical heterogeneity among all patients with TBL1XR1‐related West syndrome. Conclusion Our results expand the pathogenic variant spectrum of TBL1XR1 and strengthen the pathogenic evidence of TBL1XR1 in West syndrome.


| INTRODUCTION
West syndrome (WS) is an epileptic encephalopathy (EE) that begins in children 4-7 months of age (in rare cases older than 2 years). WS is characterized by infantile spasms (IS), hypsarrhythmia, an interictal electroencephalogram (EEG) pattern with irregular, high-amplitude slow waves on a chaotic epileptic background, and neurodevelopmental delay or regression; the presence of two of these symptoms confirms the diagnosis (Hrachovy & Frost, 2013;Pellock et al., 2010;Salar et al., 2018). Over 30 genes that have been reported to be related to WS (McTague et al., 2016), most of which are extremely rare. Transducin beta-like 1 X-linked receptor 1 (TBL1XR1) is a gene reported to be associated with autistic spectrum disorder (ASD), intellectual disability (ID), and Pierpont syndrome. Some studies have also suggested that diseasecausing variants in TBL1XR1 may contribute to genetic vulnerability to multiple neurodevelopmental psychiatric conditions. However, the evidence relating TBL1XR1 to West syndrome is still quite limited. In this study, we collected data regarding the phenotypic and genetic variants and reviewed all reported West syndrome cases caused by TBL1XR1.

| Genetic sequencing and data analysis
Genomic DNA was extracted from blood samples of the proband and their families. xGen Exome Research Panel probes (IDT, USA) were utilized to capture the exon region following the manufacturer's recommendations, and then the libraries were sequenced on an Illumina NovaSeq 6000 platform. Raw data were mapped to the human reference genome (hg38) by the Burrows-Wheeler Aligner (BWA) (Abuin et al., 2015), variant calling was performed by Genome Analysis Toolkit (GATK), variants were annotated by ANNOVAR, and the pathogenicity of candidate variants was evaluated according to American College of Medical Genetics and Genomics (ACMG) guidelines (https://www.acmg.net/).

| Case report
This report concerns a 28-month-old girl who was born at 38 weeks and 4 days of an uneventful pregnancy to nonconsanguineous healthy parents. Her birth weight was 3700 g. She displayed head control and the ability to roll over at 3 and 4 months of age, respectively. Beyond that, she displayed no social smile or communication at 3 months of age. Upon admission at 4 months of age, she began to develop a series of epileptic seizures occurring 3-4 times a day, shortly thereafter she suffered development regression, she could not control her head and roll over, and she still showed no social smile or eye contact. She did not respond to sound or light with hypotonia of the extremities. Four small café au lait spots were found on her arms and legs that were 0.2-0.3 centimeters in size, without any neurofibromas. Her head circumference was within the normal range. No specific facial features were presented. Investigations of other organs (heart, eye, liver, kidney etc.) were negative. EEG suggested hypsarrhythmia patterns ( Figure 1a). These features were consistent with a clinical diagnosis of West syndrome. Brain magnetic resonance imaging showed mild delayed myelination (Figure 1c,d). She had no dysmorphic features or stereotypical hand movements. Laboratory examination revealed that serum levels of several components were normal including lactic acid, blood ammonia, pyruvate, and βhydroxybutyric acid. Both blood and urine metabolic screening were normal. Neither administration of adrenocorticotropic hormone therapy for 28 days nor high-dose vitamin B6 reduced the frequency of spasms. Therefore, we attempted to control the seizures with topiramate, which also failed. We consequently began a trial of vigabatrin. Finally, she was seizure-free 1 month later on a combination therapy of vigabatrin (100 mg/kg/d) and topiramate (8 mg/kg/d). The child had no other skin problems, giant cell astrocytoma, cortical tubers, or subependymal nodules. Furthermore, we observed no kidney, heart, eye, or lung lesions. By the last follow-up of 28 months old, she had been seizure-free for more than 20 months. She could only sit without support, and she spoke no words. Her Gesell Developmental Scale score was 30. Repeated EEG monitoring showed great improvement in the epileptiform discharge with sporadic sharp and slow wave discharge in the left frontal, central, and occipital regions (Figure 1b).  (Table 1). Further conservation analysis confirmed that this amino acid was highly conserved across species (Figure 2b). We reviewed all published cases and summarized the clinical features and genetic variants of TBL1XR1 (

| DISCUSSION
The TBL1XR1 gene is located at 3q26.32. It encodes the protein transducin-beta-like-1 X-linked receptor  (Zhang et al., 2006). Related phenotypes include intellectual disability, Pierpont syndrome, autism spectrum disorders, and intellectual disability with dysmorphism (O'Roak, Vives, Fu et al., 2012;Pons et al., 2015;Saitsu et al., 2014;Tabet et al., 2014). TBL1XR1 is essential in the activation of Wnt-βcatenin signaling pathways, which is an indispensable factor in the functioning and activity of βcatenin-Tcf-mediated Wnt signaling (Choi et al., 2011;Li & Wang, 2008). TCF4 is an essential mediator of Wnt signaling. Pathogenic variant of TCF4 has been revealed to be related to Pitt-Hopkins Syndrome which is characterized by severe intellectual disability, seizures, and stereotypic movements (Zweier et al., 2007). These findings indicate that the βcatenin-Tcf-mediated Wnt signaling pathway is vital for brain function normalization. Moreover, a 5-year-old Japanese girl with West syndrome features was identified to have .4) in the TBL1XR1 gene, which results in a gly70-to-asp (G70D) substitution at a conserved residue in an F-box-like domain (Saitsu et al., 2014). The interaction of TBL1XR1 and SMRT, a corepressor of nuclear hormone receptors, is influenced by the F-boxlike domain of TBLR1 (TBL1XR1) (Zhang et al., 2006). Therefore, this report implied that the pathogenic TBL1XR1 variant may cause West syndrome features (Saitsu et al., 2014). In addition, there was a second case reporting an individual with West syndrome who had a de novo p.Gly29Asp (NM_024665.4:c.86 G > A) variant in the N-terminal LisH domain of TBL1XR1 (Muir et al., 2019).The LisH domain is required for oligomerization, transcriptional repression, and binding to hypoacetylated H2B and H4 (Yoon et al., 2005). Deletion of the LisH domain decreases the half-life of the TBL1XR1 protein and results in its translocation from the nucleus to the cytoplasm (Gerlitz et al., 2005). This may consequently cause West syndrome.

| CONCLUSION
In this patient, we describe a de novo TBL1XR1 variant that may lead to West syndrome via the Wnt signaling pathway. To the best of our knowledge, our patient is the third patient with TBL1XR1 driving West syndrome. We reviewed the clinical features of the limited examples of West syndrome being driven by the TBL1XR1 variant (Table 1). Our report strengthens the etiology of TBL1XR1 as a West syndrome pathogenic gene.