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Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clusteredin exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K(26%) and 11 had G947R (8%) mutations [corrected].Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

Interstitial deletions of 6q are associated with variable phenotypes, including growth retardation, dysmorphic features, upper limb malformations, and Prader–Willi (PW)-like features. Only a minority of cases in the literature have been characterized with high resolution techniques, making genotype–phenotype correlations difficult. We report 12 individuals with overlapping, 200-kb to 16.4-Mb interstitial deletions within 6q15q22.33 characterized by microarray-based comparative genomic hybridization to better correlate deletion regions with specific phenotypes. Four individuals have a PW-like phenotype, though only two have deletion of SIM1 , the candidate gene for this feature. Therefore, other genes on 6q may contribute to this phenotype including multiple genes on 6q16 and our newly proposed candidate, the transcription cofactor gene VGLL2 on 6q22.2. Two individuals present with movement disorders as a major feature, and ataxia is present in a third. The 4.1-Mb 6q22.1q22.2 critical region for movement disorders includes the cerebellar-expressed candidate gene GOPC . Observed brain malformations include thick corpus callosum in two subjects, cerebellar vermal hypoplasia in two subjects, and cerebellar atrophy in one subject. Seven subjects' deletions overlap a ~250-kb cluster of four genes on 6q22.1 including MARCKS , HDAC2 , and HS3ST5 , which are involved in neural development. Two subjects have only this gene cluster deleted, and one deletion was apparently de novo, suggesting at least one of these genes plays an important role in development. Although the phenotypes associated with 6q deletions can vary, using overlapping deletions to delineate critical regions improves genotype–phenotype correlation for interstitial 6q deletions.

Anna-Elina Lehesjoki and colleagues report exome sequencing of 84 cases of progressive myoclonus epilepsy (PME) and targeted resequencing of an additional 28 cases. They identify de novo mutations in KCNC1 in 13 cases and mutations in genes not previously associated with PME, including PRNP , SACS and TBC1D24 , in additional cases. Progressive myoclonus epilepsies (PMEs) are a group of rare, inherited disorders manifesting with action myoclonus, tonic-clonic seizures and ataxia. We sequenced the exomes of 84 unrelated individuals with PME of unknown cause and molecularly solved 26 cases (31%). Remarkably, a recurrent de novo mutation, c.959G>A (p.Arg320His), in KCNC1 was identified as a new major cause for PME. Eleven unrelated exome-sequenced (13%) and two affected individuals in a secondary cohort (7%) had this mutation. KCNC1 encodes K V 3.1, a subunit of the K V 3 voltage-gated potassium ion channels, which are major determinants of high-frequency neuronal firing. Functional analysis of the Arg320His mutant channel showed a dominant-negative loss-of-function effect. Ten cases had pathogenic mutations in known PME-associated genes ( NEU1 , NHLRC1 , AFG3L2 , EPM2A , CLN6 and SERPINI1 ). Identification of mutations in PRNP , SACS and TBC1D24 expand their phenotypic spectra to PME. These findings provide insights into the molecular genetic basis of PME and show the role of de novo mutations in this disease entity.

Leanne Dibbens, Ingrid Scheffer and colleagues report the identification of mutations in DEPDC5 that cause familial focal epilepsy with variable foci. The majority of epilepsies are focal in origin, with seizures emanating from one brain region. Although focal epilepsies often arise from structural brain lesions, many affected individuals have normal brain imaging. The etiology is unknown in the majority of individuals, although genetic factors are increasingly recognized. Autosomal dominant familial focal epilepsy with variable foci (FFEVF) is notable because family members have seizures originating from different cortical regions 1 . Using exome sequencing, we detected DEPDC5 mutations in two affected families. We subsequently identified mutations in five of six additional published large families with FFEVF. Study of families with focal epilepsy that were too small for conventional clinical diagnosis with FFEVF identified DEPDC5 mutations in approximately 12% of families (10/82). This high frequency establishes DEPDC5 mutations as a common cause of familial focal epilepsies. Shared homology with G protein signaling molecules and localization in human neurons suggest a role of DEPDC5 in neuronal signal transduction.

Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy. Individuals of any age were recruited between Nov 26, 2007, and Aug 2, 2013, through the multicentre Epilepsy Phenome/Genome Project and Epi4K collaborations, and samples were sequenced at the Institute for Genomic Medicine (New York, USA) between Feb 6, 2013, and Aug 18, 2015. To identify epilepsy risk signals, we tested all protein-coding genes for an excess of ultra-rare genetic variation among the cases, compared with control samples with no known epilepsy or epilepsy comorbidity sequenced through unrelated studies. We separately compared the sequence data from 640 individuals with familial genetic generalised epilepsy and 525 individuals with familial non-acquired focal epilepsy to the same group of 3877 controls, and found significantly higher rates of ultra-rare deleterious variation in genes established as causative for dominant epilepsy disorders (familial genetic generalised epilepsy: odd ratio [OR] 2·3, 95% CI 1·7–3·2, p=9·1 × 10−8; familial non-acquired focal epilepsy 3·6, 2·7–4·9, p=1·1 × 10−17). Comparison of an additional cohort of 662 individuals with sporadic non-acquired focal epilepsy to controls did not identify study-wide significant signals. For the individuals with familial non-acquired focal epilepsy, we found that five known epilepsy genes ranked as the top five genes enriched for ultra-rare deleterious variation. After accounting for the control carrier rate, we estimate that these five genes contribute to the risk of epilepsy in approximately 8% of individuals with familial non-acquired focal epilepsy. Our analyses showed that no individual gene was significantly associated with familial genetic generalised epilepsy; however, known epilepsy genes had lower p values relative to the rest of the protein-coding genes (p=5·8 × 10−8) that were lower than expected from a random sampling of genes. We identified excess ultra-rare variation in known epilepsy genes, which establishes a clear connection between the genetics of common and rare, severe epilepsies, and shows that the variants responsible for epilepsy risk are exceptionally rare in the general population. Our results suggest that the emerging paradigm of targeting of treatments to the genetic cause in rare devastating epilepsies might also extend to a proportion of common epilepsies. These findings might allow clinicians to broadly explain the cause of these syndromes to patients, and lay the foundation for possible precision treatments in the future. National Institute of Neurological Disorders and Stroke (NINDS), and Epilepsy Research UK.

Labate et al . argue that benign mesial temporal lobe epilepsy (bMTLE)—defined as at least 24 months of seizure freedom with or without antiepileptic medication—has been under-recognized because of a bias in the literature towards refractory forms of epilepsy. Here, the authors discuss emerging concepts on bMTLE, some of which were formulated during an international workshop held in Italy. Benign mesial temporal lobe epilepsy (bMTLE), which is defined as at least 24 months of seizure freedom with or without antiepileptic medication, has probably been under-recognized because of a literature bias toward refractory epilepsy cases. Seizure onset in bMTLE tends to be in adolescence or adulthood, and patients frequently have a family history of febrile seizures and epilepsy. Long-term seizure freedom is observed with or without antiepileptic medication. On brain MRI, nearly 40% of patients with long-standing bMTLE show evidence of hippocampal sclerosis, a feature usually associated with refractory temporal lobe epilepsy. Prospective studies are needed to determine the features that allow prediction of a benign course, and to clarify the significance of hippocampal MRI changes.

Rasmussen encephalitis (RE) is a rare, inflammatory, and possibly immuno-mediated disease that typically affects one hemisphere. The two cardinal symptoms are progressive neurological deficits and intractable seizures, often in the form of epilepsia partialis continua and recurring epileptic status. Distinctive MRI features include progressive unilateral focal cortical atrophy and gray or white matter high-signal changes with basal ganglion involvement. Histopathology is characterized by brain inflammation dominated by T cells, microglial activation, and microglial nodules, followed by neuronal loss and astrogliosis. The diagnosis of RE, which may be particularly challenging in the initial stages, is based on clinical and laboratory findings. The diagnosis requires the exclusion of other causes of epilepsia partialis continua, and other cerebral focal inflammatory diseases. The treatment of RE is often demanding: antiepileptic drugs are of limited effect, whereas the surgical exclusion of the affected hemisphere offers a very high chance of seizure freedom but at the price of irreversible neurological deficits. By contrast, long-term immunotherapy may delay hemispheric tissue loss and neurological deficits, but has a lesser effect on total seizure burden. Given that the severity of symptoms varies among different patients and phases, the therapeutic strategy, including medical and surgical options, must be tailored to the need of each patient.

Adult-onset neuronal ceroid lipofuscinoses (ANCL, Kufs disease) are rare hereditary neuropsychiatric disorders characterized by intralysosomal accumulation of ceroid in tissues. The ceroid accumulation primarily affects the brain, leading to neuronal loss and progressive neurodegeneration. Although several causative genes have been identified (DNAJC5, CLN6, CTSF, GRN, CLN1, CLN5, ATP13A2), the genetic underpinnings of ANCL in some families remain unknown. Here we report one family with autosomal dominant (AD) Kufs disease caused by a 30 bp in-frame duplication in DNAJC5, encoding the cysteine-string protein alpha (CSPα). This variant leads to a duplication of the central core motif of the cysteine-string domain of CSPα and affects palmitoylation-dependent CSPα sorting in cultured neuronal cells similarly to two previously described CSPα variants, p.(Leu115Arg) and p.(Leu116del). Interestingly, the duplication was not detected initially by standard Sanger sequencing due to a preferential PCR amplification of the shorter wild-type allele and allelic dropout of the mutated DNAJC5 allele. It was also missed by subsequent whole-exome sequencing (WES). Its identification was facilitated by reanalysis of original WES data and modification of the PCR and Sanger sequencing protocols. Independently occurring variants in the genomic sequence of DNAJC5 encoding the cysteine-string domain of CSPα suggest that this region may be more prone to DNA replication errors and that insertions or duplications within this domain should be considered in unsolved ANCL cases.

Purpose: To identify the probable etiologies and characteristics of new-onset seizures after orthotopic liver transplantation (OLT) and to assess their clinical implications and prognosis. Methods: We retrospectively analyzed the clinical, electrophysiologic and laboratory data of 17 patients with new-onset seizures after OLT among 367 adult and pediatric patients who underwent OLT between 1999 and 2001. Results: A suspected etiology of seizures was identified in most patients, including 6 (35.2%) with neurotoxicity due to immunosuppressive therapy, 4 (23.5%) with cerebrovascular disease, 3 (17.6%) with severe metabolic derangement by sepsis or rejection, and 1 each (5.8%) with hyperglycemia and brain edema due to fulminant hepatic failure. Causative factors could not be identified in 2 patients (11.8%). Seizures recurred in 15 patients (88.2%), with 9 occurring on the same day as the original seizure. Attacks caused by neurotoxicity tended to have an earlier onset, within 1 week in 4 of 6 patients, than those caused by cerebrovascular disease and sepsis/rejection, but this was not statistically significant. A total of 21 EEGs were performed in 13 patients. Eleven patients had abnormal EEG findings, of whom 4 (30.7%) showed epileptiform discharges, but the outcome of patients with epileptiform activity did not differ statistically from that of patients without such discharges (p > 0.6). The incidence of poor outcome (death or persistent vegetative state) in the group with seizures was almost 10 times higher than in the group without seizures (52.9 vs. 5.7%, p < 0.001). The prognosis of patients with seizures due to cerebrovascular disease and severe metabolic derangement by sepsis/rejection was poorer than that of patients with seizures caused by the neurotoxicity of immunosuppressive drugs (p < 0.02), suggesting that the underlying cause of seizures is important in determining prognosis. Of 8 patients who survived, 1 was lost to follow-up. The long-term outcome of seizures in surviving patients was excellent, with all survivors available for follow-up being seizure-free for a mean follow-up of 42.5 months (range, 16–58 months). Conclusion: New-onset seizures after OLT may herald fatal outcome, especially in patients with cerebrovascular disease or sepsis. The prognosis of seizures in survivors is excellent, and long-term antiepileptic drugs are not required in most cases.