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This is the first of three articles exploring the aspects of clinical care for children with rare neurological disorders including uncertainties old and new. The disruptive technologies of genomic sequencing and advanced therapeutics such as gene-based therapies offer parents of children with severe but rare neurological conditions for the first-time unprecedented opportunities for 'precision medicine'. At the same time, the realities of limited genomic diagnostic yields and not infrequent detection of variants of uncertain significance, lack of natural history study data and management guidelines for individually rare neurogenetic conditions, means that high pre-genomic test expectations are all too often replaced by an accumulation of new uncertainties. This can add to the chronic traumatic stress experienced by many families but may also have under-recognised impacts for their clinicians, contributing to 'burn-out' and attendant negative psychosocial impacts. This first article aims to address how clinicians might manage the accumulation of uncertainties to be more helpful to patients and their families. Moreover, it seeks to address how clinicians can move forward providing compassionate care to their patients and a little more consideration for themselves.

Missense and truncating variants in the X-chromosome-linked CLCN4 gene, resulting in reduced or complete loss-of-function (LOF) of the encoded chloride/proton exchanger ClC-4, were recently demonstrated to cause a neurocognitive phenotype in both males and females. Through international clinical matchmaking and interrogation of public variant databases we assembled a database of 90 rare CLCN4 missense variants in 90 families: 41 unique and 18 recurrent variants in 49 families. For 43 families, including 22 males and 33 females, we collated detailed clinical and segregation data. To confirm causality of variants and to obtain insight into disease mechanisms, we investigated the effect on electrophysiological properties of 59 of the variants in Xenopus oocytes using extended voltage and pH ranges. Detailed analyses revealed new pathophysiological mechanisms: 25% (15/59) of variants demonstrated LOF, characterized by a “shift” of the voltage-dependent activation to more positive voltages, and nine variants resulted in a toxic gain-of-function, associated with a disrupted gate allowing inward transport at negative voltages. Functional results were not always in line with in silico pathogenicity scores, highlighting the complexity of pathogenicity assessment for accurate genetic counselling. The complex neurocognitive and psychiatric manifestations of this condition, and hitherto under-recognized impacts on growth, gastrointestinal function, and motor control are discussed. Including published cases, we summarize features in 122 individuals from 67 families with CLCN4-related neurodevelopmental condition and suggest future research directions with the aim of improving the integrated care for individuals with this diagnosis.

Purpose Phosphatidylinositol Glycan Anchor Biosynthesis, class G (PIGG) is an ethanolamine phosphate transferase catalyzing the modification of glycosylphosphatidylinositol (GPI). GPI serves as an anchor on the cell membrane for surface proteins called GPI-anchored proteins (GPI-APs). Pathogenic variants in genes involved in the biosynthesis of GPI cause inherited GPI deficiency (IGD), which still needs to be further characterized. Methods We describe 22 individuals from 19 unrelated families with biallelic variants in PIGG. We analyzed GPI-AP surface levels on granulocytes and fibroblasts for three and two individuals, respectively. We demonstrated enzymatic activity defects for PIGG variants in vitro in a PIGG/PIGO double knockout system. Results Phenotypic analysis of reported individuals reveals shared PIGG deficiency–associated features. All tested GPI-APs were unchanged on granulocytes whereas CD73 level in fibroblasts was decreased. In addition to classic IGD symptoms such as hypotonia, intellectual disability/developmental delay (ID/DD), and seizures, individuals with PIGG variants of null or severely decreased activity showed cerebellar atrophy, various neurological manifestations, and mitochondrial dysfunction, a feature increasingly recognized in IGDs. Individuals with mildly decreased activity showed autism spectrum disorder. Conclusion This in vitro system is a useful method to validate the pathogenicity of variants in PIGG and to study PIGG physiological functions. Unlabelled Image

This is the second of a three-part series that explores different aspects of uncertainty, certainty and hope in the context of providing clinical care for children with rare and life-limiting neurological disorders. When caring for families impacted by an overwhelming complex disorder in a child, complicated by threatening uncertainties and potentially more threatening certainties, clinicians utilise skills drawn from differing fields to make the load of information, and the emotional impact more manageable. The first article in this series addressed how clinicians might manage the 'accumulation of uncertainties' and to provide compassionate care not only to their patients, and their families, but also to themselves. This second paper delves into the less helpful aspects of 'certainty', including the associated losses and griefs endured by parents responding to threatening fears associated with their child's condition. In the extreme, disconnection and psychological isolation borne by parents can lead to a sense of hopelessness and desperation. Facing unwelcome certainties - clinicians and parents together - forms the basis of future trust and hope. Clinicians who share the field of trust with families and show commitment to helping parents, even when cure remains elusive, build a sense of hope. This is the sort of hopefulness that clinicians need to have and to offer as they share the journey with families. In this series, we seek to harness a shared approach to face unwelcome certainties and to kindle a sense of hope that is both credible and meaningful to the parents, family and clinician.

This is the third article of a three-part series and addresses how clinicians provide hopefulness meaningfully to families coping with life-limiting and quality of life impairing neurological conditions. The first two articles addressed the enormous challenges faced by carers and also explored the struggles of clinicians trying to provide relief and comfort. Can these families, and those helping clinically, legitimately hope? It is expectation that consolidates desire into a substantial hope that may motivate finding a way forward. Hope must be realistic and directed to something in particular and in someone in particular. Hope and despair are not monolithic but often travel together for both children, families and clinicians. Hope is not denial but a belief that there are positive possibilities. Finding what can be helpfully hoped for and what must be realistically despaired of, is the discerning struggle. Clinicians aim to change what we can and accept what we cannot. Acceptance and grief are arrived at slowly for carers and families. Similarly, clinicians struggle with the hopes of bringing meaningful solace and are supported by trusted colleagues who have shared the same experience. Clinicians strive to respond appropriately and effectively in a dynamic process based on trust, providing presence and compassion when cure is not possible. Clinicians help find the small doable things that foster hope and lessen isolation and abandonment, mindful of the limits of their medical expertise. Surprisingly these modest hopes and faltering acceptances often provide a different form of strength and comfort to sustain a family.

ObjectiveTo assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE).MethodsWe performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray and either research ES (n = 15) or diagnostic MGP (n = 15).ResultsEight diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants, which now had additional evidence for pathogenicity. Eleven diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n = 10) involved genes not included in the panel, particularly in individuals with postneonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features, or multiorgan involvement. A total of 42% of diagnoses were autosomal recessive or X-chromosome linked.ConclusionWGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n = 3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel noncoding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.

Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.

IntroductionDevelopmental and epileptic encephalopathies (DEEs) are rare epilepsy conditions that collectively impact 1 in 2000 children. They are highly genetically heterogeneous, resulting in significant barriers to accurate and adequate information for caregivers. This can lead to increased distress and dissatisfaction with the healthcare system. To address this gap, we developed ‘GenE Compass’ to provide caregivers with the highest-quality possible, understandable and relevant information in response to specific questions about their child’s DEE. Using a mixed-method design, we will now pilot GenE Compass to evaluate the acceptability to caregivers and clinicians, feasibility and impact to caregivers.Methods and analysisWe will recruit 88 caregivers (estimated final sample of 50 at follow-up) who have a child under 18 years of age with a suspected or confirmed DEE diagnosis. Following consent and a baseline questionnaire (questionnaire 1 (Q1)), participants will be able to submit questions to GenE Compass over a 3-month period. After 3 months, participants will complete a follow-up questionnaire (Q2) and an optional telephone interview to answer the research questions. Primary outcomes are acceptability of GenE Compass and feasibility of delivering the intervention (eg, cost of the intervention, number of questions submitted and time taken to respond to questions). Secondary outcomes include the impact of GenE Compass on caregivers’ quality of life, information searching behaviours, perceptions of their child’s illness and activation.Ethics and discussionThe study protocol (V.2, dated 16 September 2021) has been approved by the Sydney Children’s Hospitals Network Human Research Ethics Committee (ETH11277). The results will be disseminated in peer-reviewed journals and at scientific conferences. A lay summary will be disseminated to all participants.Trial registration numberACTRN12621001544864.

Developmental and epileptic encephalopathies (DEEs) are chronic and life-threatening conditions, frequently with a genetic basis and infantile-onset. Caregivers often experience enduring distress adapting to their child's diagnosis and report a deficit of accessible psychological supports. We aimed to pilot a novel, empirically-driven suite of audio-visual positive psychology resources tailored for caregivers of children with a DEE, called 'Finding a Way'.We recruited caregivers through two paediatric hospital databases, and we also shared an invitation to the online questionnaire via genetic epilepsy advocacy organisations. The online questionnaire included a combination of validated, purpose-designed, and open-ended questions to assess the acceptability, relevance, and emotional impact of the resources among caregivers.167 caregivers from 18 countries reviewed the resources, with 56 caregivers completing over 85% of the evaluation. Caregivers rated the resources as highly acceptable and relevant to their experiences. In both the quantitative and qualitative data, caregivers reported that the resources normalised their emotional experiences and provided helpful suggestions about managing their personal relationships, seeking support and accepting help from others. Frequently reported emotional responses after viewing the resources included feeling "comforted", "hopeful", "connected" and "reassured". Suggestions for improvement included, expanding the suite of resources and embedding the resources with links to specialised psychological services.'Finding a Way' is a novel codesigned suite of audio-visual positive psychology resources tailored for caregivers of children with DEEs. Our results suggest that 'Finding a Way' is acceptable to caregivers and may contribute towards enhanced emotional adaptation and coping.

Parents and carers of children with developmental and epileptic encephalopathies (DEEs) experience high rates of mental health disorders including depression and posttraumatic stress disorder. Physical activity is an evidence-based strategy which may help to improve the wellbeing of this population.We delivered a 4-week physical activity group program via a private Facebook group for carers of children with DEEs and their nominated support person. The facilitators provided education and motivation on different weekly topics (e.g. goal setting, overcoming barriers to exercise) and encouraged social support between participants. All participants were provided with a physical activity tracker (Fitbit). The primary outcome was feasibility and secondary outcomes included psychological distress, quality of life, physical activity levels, and PTSD symptoms.N=20 (parents and support partners) were recruited. All participants remained in the program for the full duration and 85% completed the post assessment questionnaires. High acceptability was observed in the qualitative interviews and exploratory analysis of pre-post outcomes found significant improvements in psychological distress and quality of life (ps0.01), while changes in physical activity levels and PTSD symptoms were non-significant.A mental health informed physical activity program delivered via Facebook is feasible for carers of children with DEEs and may help improve wellbeing.

Genetic risk information is relevant to individual patients and also their blood relatives. Health practitioners (HPs) routinely advise patients of the importance of sharing genetic information with family members, especially for clinically actionable conditions where prevention is possible. However, some patients refuse to share genetic results with at-risk relatives, and HPs must choose whether to use or disclose genetic information without consent. This requires an understanding of their legal and ethical obligations, which research shows many HPs do not have. A recent UK case held that HPs have a duty to a patient's relatives where there is a proximate relationship, to conduct a balancing exercise of the benefit of disclosure of the genetic risk information to the relative against the interest of the patient in maintaining confidentiality. In Australia, there is currently no legal duty to disclose genetic information to a patient's at-risk relatives, but there are laws and guidelines governing unconsented use/disclosure of genetic information. These laws are inconsistent across different Australian states and health contexts, requiring greater harmonisation. Here we provide an up-to-date and clinically accessible resource summarising the laws applying to HPs across Australia, and outline five Australian case studies which have arisen in clinical genetics services, regarding the disclosure of genetic results to relatives without consent. The issues addressed here are relevant to any Australian HP with access to genetic information, as well as HPs and policy-makers in other jurisdictions considering these issues.

Summary: Early infantile epileptic encephalopathies (EOEE) are a debilitating spectrum of disorders associated with cognitive impairments. We present a clinical report of a KCNT2 mutation in an EOEE patient. The de novo heterozygous variant Phe240Leu SLICK was identified by exome sequencing and confirmed by Sanger sequencing. Phe240Leu rSlick and hSLICK channels were electrophysiologically, heterologously characterized to reveal three significant alterations to channel function. First, [Cl−]i sensitivity was reversed in Phe240Leu channels. Second, predominantly K+-selective WT channels were made to favor Na+ over K+ by Phe240Leu. Third, and consequent to altered ion selectivity, Phe240Leu channels had larger inward conductance. Further, rSlick channels induced membrane hyperexcitability when expressed in primary neurons, resembling the cellular seizure phenotype. Taken together, our results confirm that Phe240Leu is a “change-of-function” KCNT2 mutation, demonstrating unusual altered selectivity in KNa channels. These findings establish pathogenicity of the Phe240Leu KCNT2 mutation in the reported EOEE patient. : Gururaj et al. report a KCNT2 mutation in a patient with epileptic encephalopathy and employ electrophysiological analyses to establish channel properties that could underlie epileptogenesis: namely, inhibition by high [Cl−]i and loss of exclusive selectivity to K+. Furthermore, primary neurons expressing Ph240Leu display a hyperexcitable phenotype. Keywords: seizures, epileptic encephalopathy, ion channels, potassium channels, Slick, KCNT2, selectivity, Xenopus oocytes, Slack, KCNT1

The Clinical Immunogenomics Research Consortium Australasia (CIRCA) crowdsources expertise in medicine, genomics, data science, and fundamental biology to diagnose and treat patients with rare inborn errors of immunity. This distributed network model operates free of geographic borders and allows rapid progression through the full research/translation/clinical management pipeline, from initial gene variant discovery, through functional validation, and on to precision mechanism-based treatment of patients throughout Australia and New Zealand. The model is scalable and applicable to other rare diseases where clinical experience and scientific know-how are limited, and enables efficient delivery of genomics for all.

Epileptic encephalopathy (EE) is a descriptive term for a group of severe epilepsy disorders characterised predominantly by early onset drug-resistant seizures, accompanied by developmental stagnation or regression secondary to epileptiform activity. The aetiological diagnosis of EE is challenging, as causes are numerous with significant phenotypic overlap: these include acquired causes as well as numerous de novo or inherited monogenic seizure disorders, genetic inborn errors of metabolism, intellectual disability syndromes and chromosomal aberrations. A diagnostic pathway should include consultation with a Paediatric Neurologist and Clinical Geneticist, screening for immediately treatable causes, neuroimaging and electroencephalogram (EEG) and genetic testing including chromosomal microarray and consideration of a next generation sequencing technique that can interrogate multiple genetic causes, such as a multigene panel, or exome/genome sequencing. Understanding the underlying genetic cause of EE can allow accurate genetic counselling for the family and providing personalised management and support. Key Concepts EE is a descriptive term for a group of disorders where epileptiform activity itself contributes to severe cognitive and behavioural impairments above and beyond what might be expected from the underlying pathology. Although EE can be acquired, most cases of previously considered cryptogenic EE are now recognised to be due to single gene disorders. The majority of monogenic EE are due to de novo pathogenic variants: however, up to 10% of EE may be due to X-linked or autosomal recessive conditions, with higher rates in populations where consanguineous marriage is more common. Although there are some genotype/phenotype correlations, a single genetic cause can result in a variety of EE and non-EE phenotypes, and each subtype of EE can have a variety of genetic causes. Genetic heterogeneity in EE limits the value of targeted genetic testing. An optimal, cost-effective diagnostic approach involves first-tier tests that target common and treatable conditions, followed by second-tier tests including sequencing of a panel of genes known to cause EE or exome/whole genome sequencing to allow genome-wide interrogation. Factors influencing choice of type of genetic test (multigene panel versus exome/genome sequencing) include epilepsy semiology, developmental regression, additional neurological or extra-cerebral manifestations, family history and clinician and patient choice and cost. Phenotypic factors that suggest exome/genome sequencing may be valuable and include developmental regression and progressive features, multiorgan involvement including dysmorphism, additional neurological features and cerebral malformations. Evaluation of the likely pathogenicity of a novel genetic variant should include consideration of similarity with the types of genetic variants previously identified as causal of EE for that gene, including which functional domain(s) are implicated as well as overlap with the associated clinical features previously described for that condition. For variants remaining of uncertain clinical significance, ongoing pathogenicity assessment will be required in the light of advances in the understanding of the genetics of EE. Keywords: early infantile epileptic encephalopathy; neurodevelopmental disorder; intellectual disability; epilepsy; exome sequencing; next generation sequencing; genetic counselling

Background Mutations in the gene encoding stimulator of interferon genes (STING) underlie a type I interferon (IFN) associated disease, STING-associated vasculopathy with onset in infancy (SAVI). Patients suffer cutaneous vasculopathy and interstitial lung disease, but are not known to suffer life-threatening infection. Case We describe a child who presented with Pneumocystis jirovecii pneumonia in early life, from which he recovered. He went on to suffer failure to thrive, developmental delay, livedo reticularis, and vesicular rash, but without cutaneous vasculitis, and with normal C-reactive protein and erythrocyte sedimentation rates. At 3 years of age, he developed life-threatening pulmonary hypertension. Methods Whole genome sequencing (WGS) was performed using the Illumina HiSeqX10 platform and the Seave platform was used for bioinformatic analysis. mRNA expression of IFN-stimulated genes and inflammatory cytokines from peripheral blood mononuclear cells was determined by quantitative polymerase chain reaction. Luciferase assay was used to model IFNβ and NF-κB activity in vitro. Results WGS revealed a de novo mutation p.Arg284Ser in STING at an amino acid previously associated with SAVI. Although this mutation did not fall in the dimerization domain (DD), mRNA analysis revealed constitutive IFN-gene activation consistent with an interferonopathy, which correlated to STING activation in vitro. The patient was treated with corticosteroids and the JAK inhibitor Ruxolitinib, resulting in a rapid improvement of pulmonary hypertension, general well-being, and resolution of the IFN gene signature. However, he did go on to evolve a nasal septal erosion suggesting incomplete control of disease. Conclusion This case provides molecular evidence to support the p.Arg284Ser variant in STING exerting pathogenicity through a gain-of-function mechanism. The lack of cutaneous vasculitis or elevated systemic inflammatory markers, and the occurrence of an opportunistic infection are notable, and raise the possibility that variants outside the STING DD may potentially manifest with an atypical SAVI phenotype. Nevertheless, there was an objective clinical improvement in response to JAK inhibition.

A Mild PUM1 Mutation Is Associated With Adult-Onset Ataxia, Whereas Haploinsufficiency Causes Developmental Delay and Seizures Gennarino VA, Palmer EE, McDonell LM, et al. Cell. 2018;172(5):924-936.e11. doi:10.1016/j.cell.2018.02.006. Certain mutations can cause proteins to accumulate in neurons, leading to neurodegeneration. We recently showed, however, that upregulation of a wild-type protein, Ataxin1, caused by haploinsufficiency of its repressor, the RNA-binding protein Pumilio1 (PUM1), also causes neurodegeneration in mice. We therefore searched for human patients with PUM1 mutations. We identified 11 individuals with either PUM1 deletions or de novo missense variants who suffer a developmental syndrome (PUM1-associated developmental disability, ataxia, and seizure). We also identified a milder missense mutation in a family with adult-onset ataxia with incomplete penetrance (PUM1-related cerebellar ataxia). Studies in patient-derived cells revealed that the missense mutations reduced PUM1 protein levels by ∼25% in the adult-onset cases and by ∼50% in the infantile-onset cases; levels of known PUM1 targets increased accordingly. Changes in protein levels thus track with phenotypic severity, and identifying posttranscriptional modulators of protein expression should identify new candidate disease genes.

Background. Spontaneously diabetic NOD mice rapidly reject microencapsulated islet xenografts via an intense pericapsular inflammatory response. Methods. Tilapia (fish) islets were encapsulated in 1.5% alginate gel microspheres. Recipients in series 1 were spontaneously diabetic NOD mice and streptozotocin-diabetic nude, euthymic Balb/c, prediabetic NOD, and NOR (a recombinant congenic strain not prone to autoimmune diabetes) mice. Recipients in Series 2 were STZ-diabetic NOD, NOD-scid, NOD CD4 T-cell KO, NOD CD8 T-cell KO, and NOD B-cell KO mice. Results. In Series 1, encapsulated fish islet grafts uniformly survived long-term in nude mice but were rejected in Balb/c and, at a markedly accelerated rate, in spontaneously diabetic NOD, streptozotocin-diabetic NOD and NOR recipients. Histologically, intense inflammation (macrophages and eosinophils) surrounding the microcapsules was seen only in NOD and NOR recipients. In Series 2, encapsulated fish islets uniformly survived long-term in NOD-scid and NOD CD4 KO mice; graft survival was markedly prolonged in B-cell KO (P