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ingohelbig.bsky.social

@ingohelbig.bsky.social
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ingohelbig.bsky.social @ingohelbig.bsky.social · 13/05/2026
After the Genome Comes Time | Beyond the Ion Channel ...I just published a reflection on today’s Kids First Spring Public Webinar. Once many children have genomes, the next question is how we connect genetics to phenotypes, clinical trajectories, and time. epilepsygenetics.blog/2026/05/13/a...
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ingohelbig.bsky.social @ingohelbig.bsky.social · 10/05/2026
The Spliceosome Strikes Again | Beyond the Ion Channel ...I just published a blog post on RNU2-2, a tiny spliceosomal RNA gene now linked to a frequent recessive developmental and epileptic encephalopathy. epilepsygenetics.blog/2026/05/10/t...
Figure. Bi-allelic RNU2-2 variants define a developmental and epileptic encephalopathy. Adapted from Jackson et al., 2026 under the Creative Commons Attribution 4.0 International License. Panel A shows that individuals with candidate bi-allelic RNU2-2 variants are more phenotypically similar to each other than expected from random groups of individuals with neurodevelopmental disorders in the 100,000 Genomes Project. Panel B shows the HPO enrichment analysis that defines the clinical signal. Panel C shows the proposed secondary structure of U2-2 in complex with U6, the 5′ splice site, and the splicing branchpoint, based on the four-helix U2/U6 structure. The original article is open access and licensed under CC BY 4.0, which permits use, sharing, adaptation, distribution, and reproduction with appropriate credit to the authors and source, a link to the license, and indication of changes.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 07/05/2026
The Hidden Genome of Treatment | Beyond the Ion Channel ...we just published on why treatment genetics may differ from disease genetics. A new Nature study on GLP-1 agonists offers an interesting lesson for epilepsy pharmacogenomics. 🧬🔬 epilepsygenetics.blog/2026/05/06/t...
Figure. In the study by Su et al. in Nature of nearly 28,000 individuals treated with GLP-1 receptor agonists, a genome-wide association study identified a common variant in GLP1R (rs10305420) associated with greater weight loss. The Manhattan plot (top) shows a clear genome-wide signal centered on GLP1R, the direct molecular target of semaglutide and tirzepatide. The forest plot (bottom) demonstrates that the effect is directionally consistent across ancestral groups, with the strongest signal in European participants and a significant fixed-effect meta-analysis across cohorts. Importantly, this variant is not primarily associated with obesity risk itself. Instead, it predicts response to treatment, illustrating a central concept in pharmacogenomics: the genetics of drug response may be distinct from the genetics of disease. This distinction is the starting point for understanding why pharmacogenomics in epilepsy remains so difficult.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 27/04/2026
STRIPE | Beyond the Ion Channel ...we just published on why RNA may be the missing layer in rare disease genetics. In our new Science Advances paper, STRIPE shows how targeted long-read RNA sequencing can uncover hidden disease mechanisms. epilepsygenetics.blog/2026/04/27/s...
Figure. Transcript-level diagnosis in NGLY1-related disease using STRIPE. In one of the most instructive examples from our publication by Wang et al., STRIPE resolved the transcript consequences of two variants in an individual with NGLY1 deficiency. A maternally inherited frameshift variant and a paternally inherited deep intronic variant converged on a shared transcript-level mechanism: skipping of exon 11. The sashimi plots and isoform analyses show how the paternal allele shifts transcript architecture toward an exon-skipped isoform, a pattern that was largely absent in controls. Long-read sequencing made it possible to phase these changes by parental haplotype and to directly quantify the altered isoform proportions. Genomic long-read sequencing then identified the causative intronic variant, and minigene assays confirmed its effect on splicing. This example highlights why transcript diagnostics matter: the causative variant was not in the coding sequence, but its effect became immediately visible once we looked at RNA (adapted from Wang et al, 2026).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 12/04/2026
…and suddenly, decades of cerebral palsy research became meaningful to STXBP1 and SYNGAP1. Our new study (Pierce, Orlando, et al.) shows that CP classification systems actually work in synaptic disorders 🔗 epilepsygenetics.blog/2026/04/12/w... #Neurogenetics #Epilepsy #RareDisease #STXBP1 #SYNGAP1
Figure. This figure shows how individuals with STXBP1-related and SYNGAP1-related disorders distribute across commonly used cerebral palsy classification systems and how these classifications relate to each other. Panels (a–c) display the proportion of individuals in each severity level (Levels I–V) for gross motor function (GMFCS), manual ability (MACS/Mini-MACS), and communication (CFCS), compared to a reference cerebral palsy (CP) cohort. These levels range from more independent function (Level I) to more significant support needs (Level V), providing a structured way to describe ability across domains.
Panels (d,e) take this one step further by connecting each individual’s classification across the three systems. Each line represents one person, linking their motor, manual, and communication levels. Rather than collapsing function into a single score, this visualization shows how individuals occupy different positions across domains. What becomes visible is that these conditions are not one-dimensional: a given level of motor function does not necessarily predict communication or manual ability. This multidimensional pattern is exactly what these classification systems allow us to capture (Figure 1 from Pierce, Orlando et al., 2026).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 09/04/2026
The Fluency Illusion | Beyond the Ion Channel ...we just published how singing can unlock fluency in people who stutter—and why this shows that speech depends on precise timing across brain networks, not just language. 🔗 epilepsygenetics.blog/2026/04/08/t...
Figure. The Fluency Illusion across systems and scales. This composite figure illustrates how seemingly simple fluent speech emerges from multiple layers of biological organization. Top left, zebra finches, a key model system for vocal learning, show natural interruptions and blocks in their song, highlighting that even well-conserved vocal behaviors can be inherently variable. Top right, I introduce the concept of the “user illusion” from The User Illusion, which inspired the idea of the fluency illusion as presented in this blog post, framing fluent speech as a process that appears simple but reflects hidden complexity. Bottom left, I explain the stuttering and fluency circuit using a brain model, emphasizing the distributed network of cortical and subcortical regions required for timing, initiation, and coordination of speech. Bottom right, functional imaging from my own brain demonstrates bilateral language representation with relatively greater right-sided involvement, one example of the many variations in language organization observed in people who stutter. Together, these panels illustrate that fluency is not a single function but an emergent property of interacting systems that remain largely invisible until disrupted.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 29/03/2026
Moving AI in epilepsy beyond the buzzwords | Beyond the Ion Channel …we just published a short reflection after the AI in Epilepsy Conference 2026. In rare epilepsies, we aren't there yet. We are still building data/models, but other fields show what is next. epilepsygenetics.blog/2026/03/29/m...
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ingohelbig.bsky.social @ingohelbig.bsky.social · 11/03/2026
Familial Epilepsy Is Not as Simple as We Think | Beyond the Ion Channel ...we just published a blog post about what genetic testing in 484 real-world families tells us about familial epilepsy in 2026. epilepsygenetics.blog/2026/03/11/f...
Figure. Genetic testing in familial epilepsies in 484 consecutive families evaluated through ENGIN, our epilepsy genetics program. (1) Bar chart showing the number of diagnoses per gene among solved familial epilepsy cases. KCNQ2, NPRL3, and PRRT2 were the most frequently identified etiologies, with 46 additional genes identified in single families each. (2) Comparative bar chart showing the proportion of each gene among all genetic epilepsies versus the familial epilepsy subset, highlighting enrichment of dominantly inherited, incompletely penetrant genes including SCN1A, DEPDC5, and NPRL3. (3) Pedigree examples illustrating unexpected inheritance patterns, including de novo variants, bi-lineal inheritance, and parental mosaicism, with corresponding genetic etiologies listed. The overall diagnostic yield was 20%, and approximately one-fifth of solved families showed an inheritance pattern inconsistent with the presenting pedigree (Figure adapted from Ellis et al., 2026).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 08/03/2026
New blog post: The Landscape of Communication in Genetic Neurodevelopmental Disorders Hsu et al. compare communication abilities across many genetic neurodevelopmental disorders. www.epilepsygenetics.net/the-landscap... #RareDisease #Neurogenetics #Autism #Epilepsy #Genetics
Figure. Communication profiles across genetic neurodevelopmental disorders. Left: Heatmap reproduced from the recent preprint by Hsu et al. (2026), based on data from the Simons Searchlight and SPARK cohorts, showing multiple measures of communicative ability across genetic neurodevelopmental disorders. Measures include Vineland-3 expressive and receptive subdomains, speech milestone items, and single-item questionnaire responses. Across conditions, different measures of communication tend to agree, suggesting that both standardized scales and simple parent-reported questions capture related aspects of communicative function, although the strength of impairment differs by genetic etiology. Right: Scatterplot derived from the Vineland-3 values shown in the table on the left, plotting mean expressive versus receptive v-scores for each genetic condition. While communication abilities differ substantially across disorders, expressive and receptive skills generally move in parallel, with clear gene-specific profiles. STXBP1-related disorders show particularly low scores in both domains, consistent with the severe early developmental impairment observed clinically, whereas other conditions cluster at higher levels of communicative ability. Together, these data illustrate how large cohort datasets make it possible to map communication phenotypes across many genetic disorders simultaneously, revealing both shared patterns and disorder-specific signatures.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 03/03/2026
Preprint alert 🧬 Characterizing SCN1A-Related Disorders Using Real-World Data Across 681 Patient-Years. Real-world data adds texture and scale to natural history studies — and helps sharpen endpoints for upcoming SCN1A trials. 🔗 www.medrxiv.org/content/10.6... #Epilepsy #SCN1A #RareDisease
Seizure frequency by individual and semiology. Seizure frequency is
represented overall (A) and by semiology (B-D) over the first 18 years of life. Each segment of the y-axis represents one individual, with panel A being grouped by clinical diagnosis: Dravet syndrome (top), genetic epilepsy with febrile seizures plus (GEFS+; middle), and non-Dravet developmental and epileptic encephalopathy (nd-DEE; bottom).
The x-axis represents age on a logarithmic scale from 0-18 years. Seizure frequency is indicated by color as outlined in the legend. White space indicates months where seizure frequency is unknown for a given individual.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 28/02/2026
Phenotypes are like Water | Beyond the Ion Channel ...for #RareDiseaseDay 2026, I revisited a 2023 post arguing that phenotypes exist in phases: ice, water, and vapour 🔗https://epilepsygenetics.blog/2026/02/28/phenotypes-are-like-water-rare-disease-day-2026/
Figure 1. There are different ways to gain understanding of rare disease phenotypes, ranging from approaches with large patient numbers and core phenotypes to smaller studies with highly granular phenotypes. In our blog post, we use the analogy of the different phases of water (ice, water, vapor) to represent the three main approaches to phenotype studies. Importantly, these approaches are not mutually exclusive but complement each other. For example, Natural History Studies and clinical trial readiness studies would be limited if longitudinal phenotype studies were not available to provide a broad overview of the disease trajectory. However, in turn, these longitudinal studies depend on large-scale phenotyping studies to provide an overview of broader disease patterns and subgroups.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 24/02/2026
An Atlas into Pediatric Neuroimmunity | Beyond the Ion Channel We profiled CSF immune landscapes in 85 children. Rare disease discovery requires biobanking beyond genomics. epilepsygenetics.blog/2026/02/23/a...
Figure 1. Pediatric CSF immune profiling highlights a distinct intrathecal signature in MS. This figure shows that while B cells are increased across acquired demyelinating syndromes (ADS), pediatric multiple sclerosis (MS) is uniquely characterized by marked expansion of antibody-secreting cells (ASCs) and relative reduction of CD14+ myeloid cells in the cerebrospinal fluid (CSF). The upper panels display cell frequencies and the lower panels absolute counts (cells/mL) across diagnostic groups: non-inflammatory neurological disease (NIND), peripheral inflammatory neurological disease (PIND), autoimmune encephalitides (AIE), inherited disorders of white matter (IDWM), other ADS, myelin oligodendrocyte glycoprotein antibody–associated disease (MOGAD), and MS. Together, the enrichment of ASCs and relative depletion of CD14+ myeloid cells in MS support the concept that MS establishes compartmentalized humoral immune activity within the CNS early in disease, distinguishing it from MOGAD and other ADS. Adapted from Espinoza et al., 2025 (CC BY-NC-ND 4.0).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 19/02/2026
Decoding CACNA1A | Beyond the Ion Channel We analyzed 42 CACNA1A missense variants and linked functional data to phenotype. Half showed loss of current. Function simplifies. Phenotype remains complex. 🔗https://epilepsygenetics.blog/2026/02/18/decoding-cacna1a-how-function-shapes-phenotypes/
Figure. Functional landscape of CACNA1A variants across structure, biophysics, and phenotype. A. Schematic of the hCaV2.1 channel topology illustrating domains DI–DIV as transmembrane segments, with S4 voltage-sensing regions highlighted in light blue. De novo missense variants are shown in red and population variants from gnomAD in gray. B. Hierarchical clustering heatmap of CACNA1A variants based on z scores of electrophysiological parameters. Each row represents a single variant and each column corresponds to an individual functional parameter. z score magnitudes are color-coded as indicated in the inset. The dendrogram groups variants with similar functional profiles. C. Forest plots showing odds ratios from logistic regression analyses for peak current density, V1/2 activation, and V1/2 inactivation across 16 phenotypes. Solid circles denote statistically significant associations and horizontal bars represent 95% confidence intervals. Analyses include data from both the GeneDx cohort and the clinically reviewed cohort. Modified from Kurganov et al., 2025. Figures used with permission as co-author of the publication.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 16/02/2026
I wrote about how neuroscience advances not only through new data, but through new language. “Glymphatic system” (introduced in 2012), E–I imbalance in epilepsy, mirror neurons, channelopathies — all useful frameworks. But frameworks are not mechanisms. epilepsygenetics.blog/2026/02/15/g...
Figure 1. A modern map for an old pathway. Schematic of interstitial solute and fluid clearance in the brain as conceptualized in the glymphatic model. Cerebrospinal fluid (CSF) enters along para-arterial spaces, exchanges with interstitial fluid through astrocyte endfeet enriched in aquaporin-4 (AQP4), and exits along paravenous routes carrying metabolic waste toward the bloodstream and cervical lymphatics. While the anatomical components — perivascular spaces, astrocytes, CSF flow, and interstitial solute movement — have long been recognized, the “glymphatic system” framework, introduced in 2012, integrates these elements into a unified clearance pathway. This model has been influential in linking sleep, fluid dynamics, and neurodegeneration, even as the precise mechanisms and relative contributions of bulk flow versus diffusion remain under active investigation.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 13/02/2026
Minimal Fusion at WHX 2026 | Beyond the Ion Channel At WHX 2026 in Dubai, participants were greeted by a large scale animation of synaptic vesicle fusion that we developed to visualize mechanisms in genetic neurodevelopmental disorders. epilepsygenetics.blog/2026/02/13/m...
Figure 1. Minimal fusion at scale. Our animation of synaptic vesicle fusion displayed at the Emirati Health Services booth at World Health Expo WHX 2026 in Dubai. The installation visualized SNARE complex assembly guided by MUNC-18 (STXBP1), attempting to illustrate disease mechanisms in synaptic disorders. It was projected prominently in the South Hall and formed part of the broader exhibition space.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 07/02/2026
The Long Arc of TBC1D24 | Beyond the Ion Channel …we just published our blog post on our longitudinal reconstruction of TBC1D24-related disorders, tracking nearly 200 patient-years. 🔗 Read more: epilepsygenetics.blog/2026/02/07/t...
Figure. Longitudinal trajectories in TBC1D24-related disorders. Left: Age-dependent frequency of neurological features. Seizure types including focal seizures, myoclonic seizures, and status epilepticus are most common in early infancy and early childhood. Movement disorders such as tremor and ataxia become more prominent later, illustrating how the clinical picture evolves over time. Right: Individual seizure frequencies across the lifespan. Each row represents one person, with color indicating seizure burden from seizure-free to many seizures per day. Most individuals experience the highest seizure burden in infancy, with fluctuating but often persistent drug-resistant epilepsy over time. Figure adapted from Mondragon et al., 2025.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 05/02/2026
Preprint alert 🚀 Our new paper outlines a prospective NHS protocol built to support clinical trial readiness in SYNGAP1 and STXBP1. The protocol already powers STARR and ProMMiS. 🔗 www.medrxiv.org/content/10.6... #SYNGAP1 #STXBP1 #DEE #ClinicalTrials
Protocol and Recruitment.
Here we present a comprehensive and feasible protocol for evaluating the natural history of STXBP1 (STARR) and SYNGAP1 (ProMMiS) using existing outcome measures within the framework of a clinical visit. Recruitment is ongoing, with n=323 individuals evaluated to date. Study protocol includes standardized clinical assessments, parent-reported outcomes, quantitative EEG and movement sensors, and detailed seizure histories. Consortium structures have been established for both studies allowing data generation from multiple sites in an FDA-compliant format for collaboration with industry partners, advocacy organizations, and researchers.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 01/02/2026
USP25 and the gravity well of evidence | Beyond the Ion Channel …we just published a new post about how gene–disease claims change over time. Using USP25 as an example, we explore how accumulating data can deepen confidence or lead to reclassification. 🔗 epilepsygenetics.blog/2026/01/31/u...
Figure 1. Each point represents a gene–disease assertion curated by the ClinGen Epilepsy Gene Curation Expert Panel, positioned by the date of its most recent evaluation and arranged vertically by strength of evidence. Darker blues indicate stronger support, with Definitive gene–disease relationships at the top and Refuted relationships at the bottom. The vertical spread reflects jitter added for visibility, emphasizing that evidence strength behaves more like a gradient than a set of rigid tiers. Gene labels are shown to highlight how individual genes move within this landscape of confidence. This is the broader context for USP25. Strength of gene-disease associations is not an isolated debate for any particular gene, but part of the ongoing process by which gene–disease claims are tested against accumulating data that either support or question validity. All gene–disease validity classifications shown here are publicly available through the ClinGen gene validity curation interface.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 29/01/2026
Cure vs. Treat | Beyond the Ion Channel ...we just published a new post exploring how “cure” and “treat” mean different things to scientists and families — and why the translation gap between those words matters so much in rare disease. epilepsygenetics.blog/2026/01/29/c...
Figure 1. Conceptual illustration of cure versus treat as a Babel-like translation problem in rare disease. Echoing the visual language of RF Kuang’s Babel cover, twin Oxford-like towers face each other across a fractured silver-working tablet, the Translation Gap. Floating pages and cryptic glyphs evoke untranslatable meaning, where promise, hope, and trust accumulate. In rare disease, these gaps shape expectations, advocacy narratives, and the clinician–family contract.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 27/01/2026
Ten Years of Accumulation: Snow-Day Thoughts Between Jonas and Fern | Beyond the Ion Channel ...we just published a new post reflecting on how a decade of progress reshaped epilepsy genetics between two historic winter storms. epilepsygenetics.blog/2026/01/27/t...
Figure 1. Artistic adaptation of a forecast map originally produced by the U.S. National Weather Service (NOAA). Colors indicate the maximum probability of exceeding warning criteria, meaning the likelihood that a given location will experience winter weather severe enough to trigger official warnings (such as heavy snowfall, ice accumulation, or dangerous travel conditions) at some point during the event. Warmer colors reflect a higher probability that warning thresholds will be met or exceeded. The map illustrates the expected large-scale impact pattern of Winter Storm Fern across the United States in January 2026, re-rendered here for conceptual and narrative purposes rather than operational forecasting.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 24/01/2026
𝗨𝗡𝗖𝟭𝟯𝗔 𝗮𝗻𝗱 𝘁𝗵𝗲 𝗴𝗮𝘁𝗲 𝗼𝗳 𝘀𝘆𝗻𝗮𝗽𝘁𝗶𝗰 𝗿𝗲𝗹𝗲𝗮𝘀𝗲 | 𝗕𝗲𝘆𝗼𝗻𝗱 𝘁𝗵𝗲 𝗜𝗼𝗻 𝗖𝗵𝗮𝗻𝗻𝗲𝗹 ...we just published a new post on UNC13A, a synaptic priming gene that sits beside STXBP1 at the gate of neurotransmitter release.https://epilepsygenetics.blog/2026/01/24/unc13a-and-the-gate-of-synaptic-release/
Figure 1. UNC13A (MUNC13-1) as a synaptic priming factor and the landscape of UNC13A missense variation in neurodevelopmental disorders. Top panels (a–d): Working model of the Munc18–Munc13 route to SNARE complex assembly during synaptic vesicle priming and fusion. (a) Membrane association and pre-alignment: interactions between synaptic vesicle synaptobrevin/VAMP2 (Syb2) and the MUN domain, together with C1–C2B binding to DAG/PIP2, position vesicles near the plasma membrane and facilitate engagement of the Munc18-1/Syntaxin-1 (Syx1) complex. (b) Priming: coordinated Munc18-1/Syx1/Munc13 interactions promote Syb2 binding and stabilize a primed intermediate. (c) Proofreading and nucleation: entry of SNAP-25 (SN25) supports N-terminal SNARE nucleation and formation of a half-zippered SNARE complex, releasing Syntaxin-1 from Munc18-1 clamping. (d) Completion: full SNARE zippering drives membrane merger and vesicle fusion. Adapted from Figure 8 in Nature Communications (2019), licensed under CC BY 4.0 (changes made: figure cropped and incorporated into composite). Bottom panel: Pathogenic missense variants identified in UNC13A overlaid on a domain schematic, highlighting a recurrent “UNC13A hinge” hotspot, together with a gene-wide tolerance landscape derived from population variation (MetaDome/gnomAD-based tolerance scores; red = intolerant, blue = tolerant). Reproduced/adapted from Asadollahi et al. (2025) licensed under CC BY 4.0 (changes made: figure cropped and incorporated into composite; author is a coauthor).\
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ingohelbig.bsky.social @ingohelbig.bsky.social · 22/01/2026
...and here is the link epilepsygenetics.blog/2026/01/21/t...
epilepsygenetics.blog
The MACF1 puzzle: when a cytoskeletal giant causes multiple brain disorders
Connections. Spectraplakins sit at the interface of architecture and motion inside a cell. They do not merely hold structures together but coordinate how the cytoskeleton rearranges itself when neu…
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ingohelbig.bsky.social @ingohelbig.bsky.social · 22/01/2026
The MACF1 puzzle: when a cytoskeletal giant causes multiple brain disorders | Beyond the Ion Channel ...we just published our new post on why interpreting MACF1 variants is so difficult, highlighting how this massive spectraplakin gene can produce distinct neurodevelopmental phenotypes.
Figure 1. Spectraplakins, including MACF1, are large cytoskeletal scaffold proteins that crosslink actin filaments and microtubules to coordinate cellular architecture, polarity, and intracellular organization. This group of proteins has a modular architecture consisting of an N-terminal actin-binding domain, central spectrin-repeat rod regions, and C-terminal microtubule-binding motifs (left). These complex proteins have various functions in neurons, including regulation of neurite outgrowth, axon guidance, synapse organization, and intracellular trafficking (right). Figures from Cusseddu et al. (2021) under a Creative Commons CC BY license.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 18/01/2026
Signals in the noise – qEEG patterns in genetic epilepsies | Beyond the Ion Channel ...we just published our new post on extracting hidden qEEG signals from routine clinical EEGs, showing patterns in STXBP1-, SCN1A-, and SYNGAP1-related epilepsies. epilepsygenetics.blog/2026/01/17/s...
Figure 1. Quantitative EEG features in genetic epilepsies. Using machine learning, we were able to extract specific qEEG features that were more most important in separating controls from individuals with STXBP1-, SYNGAP1-, and SCN1A-related epilepsies (feature importance, left). The global alpha-delta ratio is a previously studied qEEG feature. When assessing this across age groups and various genetic epilepsies, we saw that this measure is most prominent in STXBP1-related disorders across all age groups, while it was only significantly lower than controls in other conditions (e.g. SCN1A) at specific ages.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 04/09/2025
The quiet revolution – revising ACMG criteria for epilepsy genes | Beyond the Ion Channel ...we just published our blog post on the revision of ACMG criteria for epilepsy-related sodium channels epilepsygenetics.blog/2025/09/04/t...
Figure 1. Visualizing the new ACMG/AMP points-based classification system. The diagram shows how different combinations of evidence criteria contribute to variant interpretation under the updated framework. Each bar represents a typical evidence scenario, broken down by individual ACMG/AMP rules such as PVS1 (very strong), PS2–PS4 (strong), PM1–PM6 (moderate), and PP1–PP5 (supporting). Conflicting evidence is indicated by hatched bars, highlighting situations where pathogenic and benign signals pull in opposite directions. Colored background zones indicate the thresholds that define final classifications: Pathogenic (≥10 points), Likely Pathogenic (6–9 points), VUS (0–5 points), Likely Benign (−1 to −6 points), and Benign (≤−7 points, or BA1 as a stand-alone benign criterion). This new quantitative framework turns what once felt like a “word salad” of rules into a transparent and teachable scoring system, marking a quiet revolution in how we approach clinical variant interpretation.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 04/09/2025
The quiet revolution – revising ACMG criteria for epilepsy genes VUS. The story begins with a patient in clinic. A young child with severe epilepsy, carrying a variant in SCN1A, the classic gene for Dravet Syndrome. But the variant is labeled a variant of uncertain significance (VUS). Dravet…
epilepsygenetics.blog
The quiet revolution – revising ACMG criteria for epilepsy genes
VUS. The story begins with a patient in clinic. A young child with severe epilepsy, carrying a variant in SCN1A, the classic gene for Dravet Syndrome. But the variant is labeled a variant of uncertain significance (VUS). Dravet Syndrome is a clinical diagnosis, and the treatments we have today do not hinge on whether the variant is clearly pathogenic or not.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 30/08/2025
The gentle singularity that cannot draw a synapse | Beyond the Ion Channel ..we just published our blog post on the struggle of generative AI to draw a synapse. epilepsygenetics.blog/2025/08/30/t...
Figure 1. The Ice Neurons of Delaware County. When I moved to the United States in 2014, I first encountered a phenomenon on frozen ponds that I had never seen in Europe: neuron-like dendritic patterns etched into lake ice after snowfall. These “ice neurons” arise when wet, heavy snow falls on thin ice, followed by rapid thaw and refreeze. Meltwater seeps through cracks and imperfections, radiating outward in branching channels reminiscent of axons and dendrites. In Delaware County, with its many shallow ponds and frequent freeze–thaw cycles, these conditions align perfectly—creating striking natural structures at the intersection of weather and biology.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 30/08/2025
The gentle singularity that cannot draw a synapse Singularity. A few months ago, Sam Altman, the CEO of OpenAI, published a short essay about the future of artificial intelligence. His central message was a gentle role for AI—a vision in which technology supports us quietly in the background…
epilepsygenetics.blog
The gentle singularity that cannot draw a synapse
Singularity. A few months ago, Sam Altman, the CEO of OpenAI, published a short essay about the future of artificial intelligence. His central message was a gentle role for AI—a vision in which technology supports us quietly in the background rather than staging some dramatic takeover of human life. What caught my attention, however, was not the word “gentle” but the word “singularity.” For science fiction readers, this term carries weight.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 28/08/2025
Influenza and acute necrotizing encephalopathy – the genetic dimension | Beyond the Ion Channel ...we just published our blog post on Acute necrotizing encephalopathy (ANE). epilepsygenetics.blog/2025/08/28/i...
Figure 1. Function of RANBP2 and neuroimaging in ANE. Figure. Structural model of RanBP2/Nup358 and neuroimaging in acute necrotizing encephalopathy. RanBP2/Nup358 is a major component of the cytoplasmic filaments of the nuclear pore complex, which has an eightfold symmetry with each symmetrical unit referred to as a ‘spoke’. Five copies of RanBP2/Nup358 are found at each spoke, for a total of 40 copies per pore. The N-terminal domain attaches to the pore and is the spot where ANE1 mutations cluster. On the right, magnetic resonance imaging from a 3-year-old child presenting with a viral prodrome and rapid neurological decline. T2-weighted axial images demonstrate the characteristic bilateral thalamic lesions typical of acute necrotizing encephalopathy (figure adapted from Palazzo et al., 2022 under CC BY 4.0, http://creativecommons.org/licenses/by/4.0/).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 28/08/2025
Influenza and acute necrotizing encephalopathy – the genetic dimension ANE. A rare complication with hidden genetic clues. Imagine a healthy child who goes to bed with a fever and wakes up unable to recognize their parents, slipping rapidly into coma. This is the terrifying course of acute…
epilepsygenetics.blog
Influenza and acute necrotizing encephalopathy – the genetic dimension
ANE. A rare complication with hidden genetic clues. Imagine a healthy child who goes to bed with a fever and wakes up unable to recognize their parents, slipping rapidly into coma. This is the terrifying course of acute necrotizing encephalopathy (ANE), one of the most severe neurological complications of influenza. In a recent study, children with influenza who developed ANE showed an unexpected pattern: nearly half of those tested carried genetic variants that might predispose them to this devastating complication.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 26/08/2025
Different genes, convergent processes – rare disease lessons from neurogenesis | Beyond the Ion Channel ...we just published our blog post on the recent publication by Zhou et al. in Nature Neuroscience epilepsygenetics.blog/2025/08/26/d...
Figure 1. Gene ontology enrichment and overlapping genes in a cross-species analysis for immature granule cell (imGCs). On the left, the top biological pathways are shown for imGC-enriched genes across humans, macaques, pigs, and mice. These pathways, grouped and color-coded by Gene Ontology (GO) terms, highlighting the processes most important for immature neurons, such as neuronal development, synaptic plasticity, and ion transport. This view emphasizes that, while the precise genes differ from species to species, the biological themes remain consistent. On the right, a Venn diagram illustrates how few imGC-enriched genes are shared between species. Only a small set of genes is common to all four, with an additional subset found only in humans and macaques. The lists of shared genes in the boxes serve as concrete examples of this limited overlap, reinforcing the central message of the study: processes can be conserved even when the genes executing them diverge. [Figure modified from data provided by the authors].
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ingohelbig.bsky.social @ingohelbig.bsky.social · 26/08/2025
Different genes, convergent processes – rare disease lessons from neurogenesis A paradox in the hippocampus. Immature dentate granule cells are often described as the “plasticity reserve” of the hippocampus. They provide a pool of neurons that integrate into existing circuits, supporting learning,…
epilepsygenetics.blog
Different genes, convergent processes – rare disease lessons from neurogenesis
A paradox in the hippocampus. Immature dentate granule cells are often described as the “plasticity reserve” of the hippocampus. They provide a pool of neurons that integrate into existing circuits, supporting learning, memory, and repair. In neurological disease, these cells have been suggested to buffer against injury or degeneration. In a recent publication, researchers showed that the hippocampus continues to generate new neurons throughout life, but that the molecular instructions for doing so vary dramatically across species.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 24/08/2025
The placental mirror – methylation and neurodevelopment in congenital heart disease – Beyond the Ion Channel ...we just published our blog post on our recent publication on neuronal signatures in umbilical cord blood methylation patterns. epilepsygenetics.blog/2025/08/24/t...
Figure 1. Placental weight and fetal growth stratification with corresponding methylation pathways. The nine-block classification system (left) combines placental weight (x-axis, low to high) and fetal-to-placental weight ratio (y-axis, high to low) to categorize neonatal growth patterns. In our cohort, analyses focused on three groups: light placenta with heavy infant (Group A), light placenta with balanced infant growth (Group D), and balanced placenta and infant (Group E, highlighted in red). DNA methylation differences across these groups revealed pathway-specific alterations (right), with gene-set enrichment analyses pointing to biological processes relevant for neurodevelopmental vulnerability in congenital heart disease.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 24/08/2025
The placental mirror – methylation and neurodevelopment in congenital heart disease Neurodevelopment. Congenital heart disease (CHD) refers to a broad group of structural abnormalities of the heart that are present at birth and affect approximately 1% of all live births. Over the past two decades,…
epilepsygenetics.blog
The placental mirror – methylation and neurodevelopment in congenital heart disease
Neurodevelopment. Congenital heart disease (CHD) refers to a broad group of structural abnormalities of the heart that are present at birth and affect approximately 1% of all live births. Over the past two decades, advances in neonatal surgery and perioperative care have dramatically increased survival rates. Yet this success has revealed an important challenge, and focus has gradually shifted from the heart alone to the brain.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 16/08/2025
Three things the beach told me about science in 2025 | Beyond the Ion Channel ...we just published our annual blog post about insights into rare disease research at the beach epilepsygenetics.blog/2025/08/16/t...
Figure 1. Dunes at Rehoboth Beach, Delaware. A stretch near the beach, looking at the beach from the boardwalk facing away from the crowds. Much like rare disease research, some of the most valuable insights happen off the expected path when looking in a different direction. This can often happens in spaces that are less visible.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 16/08/2025
Three things the beach told me about science in 2025 Rehoboth. It has been a while since I posted my annual post-beach-vacation thoughts about how my experiences at the shore made me think about science. I initially started these posts after a vacation in Marielyst, Denmark when I realized that my…
epilepsygenetics.blog
Three things the beach told me about science in 2025
Rehoboth. It has been a while since I posted my annual post-beach-vacation thoughts about how my experiences at the shore made me think about science. I initially started these posts after a vacation in Marielyst, Denmark when I realized that my sandcastle building skills were not appreciated as much as I thought. This reminded me that similar things happen with our scientific achievements.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 13/08/2025
Chasing the Demosthenes gene – the complex genetics of stuttering | Beyond the Ion Channel ...we just published our blog post on a recent large-scale genetic study on stuttering. epilepsygenetics.blog/2025/08/13/c...
Figure 1. Miami plot of genome-wide association studies (GWAS) for stuttering in females (top) and males (bottom) of European ancestry. The female GWAS analyzed 570,071 individuals (40,137 cases), identifying nine genome-wide significant loci. The male GWAS included 374,279 individuals (38,257 cases), identifying ten such loci. The x-axis shows genomic coordinates (hg19), the y-axis the −log10(P) values from logistic regression. Dashed lines mark the significance threshold (P < 5 × 10⁻⁸). Genes shown are predicted functional candidates for each locus from the Open Targets Genetics V2G pipeline. This side-by-side view highlights both shared and sex-specific genetic architecture in stuttering (modified from Polikowsky et al, 2025 under a modified from Polikowsky et al., 2025 under a Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/)
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ingohelbig.bsky.social @ingohelbig.bsky.social · 13/08/2025
Chasing the Demosthenes gene – the complex genetics of stuttering Fluency. When we think of stuttering, we might first think of speech therapy, of pauses and repetitions, and of the courage it takes to speak when words get stuck. But what if we could step back and see its genetic architecture laid…
epilepsygenetics.blog
Chasing the Demosthenes gene – the complex genetics of stuttering
Fluency. When we think of stuttering, we might first think of speech therapy, of pauses and repetitions, and of the courage it takes to speak when words get stuck. But what if we could step back and see its genetic architecture laid out across the globe? A recent study looked at the genetics of stuttering at an unprecedented scale: over 1.1 million individuals, including almost 100,000 people who self-reported a history of stuttering.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 11/08/2025
Beyond Sleep: BMAL1 links circadian time to neurodevelopment and epilepsy | Beyond the Ion Channel ...here is our blog post on BMAL1 (ARNTL), a core component of the circadian clock, and neurodevelopmental disorders. epilepsygenetics.blog/2025/08/10/b...
Figure 1. The core circadian oscillator in human cells is driven by a transcription–translation feedback loop. BMAL1 (ARNTL) dimerizes with CLOCK to form a transcriptional activator complex that binds to E-box elements in the promoters of PER and CRY genes. The translated PER and CRY proteins accumulate in the cytoplasm, heterodimerize, and translocate back into the nucleus, where they inhibit the activity of BMAL1 and CLOCK, repressing their own transcription. This cycle takes approximately 24 hours to complete and represents the molecular pacemaker that governs circadian rhythms such as sleep-wake cycles, hormonal secretion, and metabolic regulation. In our study by Cuddapah and collaborators, we identified ten individuals with de novo or rare heterozygous variants in ARNTL. All individuals presented with neurodevelopmental features, including intellectual disability, hypotonia, and epilepsy. (Figure created with Biorender).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 10/08/2025
Beyond Sleep: BMAL1 links circadian time to neurodevelopment and epilepsy The clock gene. Every cell in the human body keeps time. This intrinsic rhythm is roughly 24 hours long and driven by the molecular circadian clock: a transcriptional feedback loop that helps regulate sleep, metabolism, and…
epilepsygenetics.blog
Beyond Sleep: BMAL1 links circadian time to neurodevelopment and epilepsy
The clock gene. Every cell in the human body keeps time. This intrinsic rhythm is roughly 24 hours long and driven by the molecular circadian clock: a transcriptional feedback loop that helps regulate sleep, metabolism, and hormone release. But what happens when these timekeepers stop working? In a recent study, we explored the role of BMAL1 (ARNTL), a core circadian regulator, in neurodevelopmental disorders.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 08/08/2025
Tenure into the Unknown | Beyond the Ion Channel ...in July 2025, I was granted tenure at the University of Pennsylvania. ...here is my blog post about the historic Cistercian abbey in my hometown, academic reforms in the 19th century, and what to do with tenure in 2025.
Figure 1. The Kamp Abbey in Kamp-Lintfort, Germany, viewed from the entrance. Founded in 1123, this Cistercian monastery has played a pivotal role in shaping the intellectual and spiritual landscape of the region, including contributions to monastic scholarship and agricultural innovations.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 08/08/2025
Tenure into the Unknown Monastic. I am now roughly one month into the first real job of my life. I celebrated this transition by spending a week with my family in Kamp-Lintfort, Germany, a small town at the Western edge of the Ruhr area known for its coal mining heritage and Cistercian abbey.…
epilepsygenetics.blog
Tenure into the Unknown
Monastic. I am now roughly one month into the first real job of my life. I celebrated this transition by spending a week with my family in Kamp-Lintfort, Germany, a small town at the Western edge of the Ruhr area known for its coal mining heritage and Cistercian abbey. After two decades of training roles and academic positions that were either time-limited or contingent, I was tenured at the University of Pennsylvania in July 2025.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 29/07/2025
The power of paralogs in epilepsy genetics | Beyond the Ion Channel ...we just published our post on our recent publication on the importance of identical variants at conserved sites in epilepsy genes. epilepsygenetics.blog/2025/07/29/t...
Figure 1. Study by Brünger et al., 2025: Presence of pathogenic missense variants at conserved paralogous amino acid residues within genes of the same gene family can inform variant pathogenicity classification, thereby increasing the number of pathogenic variants that can be classified using the PS1 and PM5 ACMG criteria. In brief, pathogenicity echoes across paralogs, and our findings provide a roadmap that allowed for the extension of the ACMG/AMP criteria released in January 2025. [Figure modified from Brünger et al., 2025 under a CC BY license.]
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ingohelbig.bsky.social @ingohelbig.bsky.social · 29/07/2025
The power of paralogs in epilepsy genetics Paralogs. Every week in our variant review meetings, we encounter a familiar issue: understanding a missense variant of uncertain significance. Unless it matches a known disease-associated variant or is found to be de novo, our confidence often stalls.…
epilepsygenetics.blog
The power of paralogs in epilepsy genetics
Paralogs. Every week in our variant review meetings, we encounter a familiar issue: understanding a missense variant of uncertain significance. Unless it matches a known disease-associated variant or is found to be de novo, our confidence often stalls. But what happens if we stopped looking at genes in isolation? In a recent publication, we had the opportunity to explore this idea by looking at paralogs and variants at identical sites across gene families, and we found evidence that was strong enough to be included in the official ACMG/AMP variant curation criteria.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 26/07/2025
The rare disease with fastest growing knowledge – the 2025 STXBP1 Summit+ | Beyond the Ion Channel ...we just published our blog post on the 2025 STXBP1 Family Summit+ in Westminster, Colorado epilepsygenetics.blog/2025/07/26/t...
Figure 1. Impressions from the 2025 STXBP1 Summit+, including Sarah’s award as the 2025 Clinical Champion, our “Bee Brave” painted stone at our conference table, the interactive word cloud at the start of the meeting, the epic Colorado sunrise, and a view of the Westin in Westminster, Colorado that hosted the STXBP1 family meeting for the second time in 2025. More impressions of the 2025 STXBP1 Summit+ can be found at https://www.stxbp1disorders.org/2025-summit.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 22/07/2025
AP2M1 and the mystery of missing haploinsufficient genes | Beyond the Ion Channel ...we just published our blog post on AP2M1 as the candidate gene in the 3q27 microdeletion ...and the broader issue of missing haploinsufficient genes epilepsygenetics.blog/2025/07/21/a...
Figure 1. Schematic representation of overlapping 3q26.3-3q27.2 deletions, and genes involved. The smallest region of overlap (light blue) is 0.43 Mb, encompassing 20 protein-coding genes including AP2M1. The AP2M1 gene encodes a presynaptic adapter protein involved in initiating the first step of synaptic vesicle recycling. The recurrent AP2M1 p.Arg170Trp variant had previously been identified to impair synaptic vesicle recycling and cause genetic epilepsies with clinical features of myoclonic astatic epilepsies (MAE). However, prior to the publication by Gear et al., 2025, haploinsufficiency in AP2M1 had not been known as a disease mechanism (adapted from Gear et al., 2025 under a under the terms of the Creative Commons Attribution and Supplemental data by Helbig et al., 2019).
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ingohelbig.bsky.social @ingohelbig.bsky.social · 14/07/2025
RT @NeuroWoodworks: An astrocyte sculpture made out of cherry wood. Neurons are not the only important cells of the brain!!!
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ingohelbig.bsky.social @ingohelbig.bsky.social · 11/07/2025
Beyond the Ion Channel | RBFOX3 and the Hunt for Epilepsy Genes in 100,000 Genomes ...we just published our post of the discovery of RBFOX3 as a candidate gene from the 100,000 Genomes Project
Figure 1. Burden analysis of rare variants in 34,000 individuals of the 100,000 Genomes Project before applying additional prioritization filters. Well-established epilepsy genes including SCN1A, KCNQ2, and DEPDC5 show strong associations, including associations through different analysis methods (duplicate dots for SCN1A). This QQ plot was generated from the Open Access Supplemental Data by Cipriani and collaborators. The insert compares data from the 100K Genomes Project to raw Epi25 data from the Epi25 browser.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 08/07/2025
Five principles for teaching epilepsy genetics | Beyond the Ion Channel ...our blog post celebrating the 5th anniversary of our ENGIN epilepsy genetics fellowship epilepsygenetics.blog/2025/07/08/f...
Epilepsy Genetics Graduation 2025. Our ENGIN fellowship team 2025 including (left to right from myself) our incoming fellow Riley Kessler, graduating fellow Laura McGarry, and current fellowship director Jill McKee. The CHOP Neurology graduation typically takes place in the Philadelphia College of Physicians aka the “hall of old white men with beards”. This is us under the portrait of Alfred Stillé (1813–1900) who advanced American medicine through education reforms and who help shape modern medical professionalism by being a critical part in founding the American Medical Association.
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ingohelbig.bsky.social @ingohelbig.bsky.social · 08/07/2025
RT @NTFabiano: This is the Atlas of Cognitive Disorders
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