Neurodevelopmental disorders (NDD) are a wide and heterogenous group of conditions due to impaired brain development, orchestrated by the crosstalk between genome and environment. Dynamic chromatin regulation during cortical development is fundamental, and chromatin remodelers are critical determinants of this process. Recently, numerous chromatin remodeling genes have been implicated in NDDs. By altering genes’ epigenetic state, mutated chromatin remodelers disrupt the spatiotemporal regulation of gene expression during development, potentially leading to severe consequences. The Remodeling and Spacing Factor 1 (RSF1) gene encodes a ubiquitous nuclear protein involved in chromatin remodeling, crucial for processes such as DNA transcription, replication, and repair. In this study, we identified by gene matching (n = 7) and literature search (n = 4) eleven unrelated individuals harboring de novo or inherited from a symptomatic parent heterozygous variants in RSF1. All individuals had an NDD, whether intellectual disability, autism spectrum disorder or developmental delay. From the seven individuals with detailed clinical information, unspecific and inconsistent associated features were described, including cranio-facial morphological features, musculoskeletal, digestive, vision, tone, epilepsy and brain MRI anomalies. Our data support the hypothesis that RSF1 is important for brain development and a novel candidate gene for syndromic NDDs.

Background:Clinical trial designs evaluating on-demand therapies for hereditary angioedema attacks have evolved in response to changes in treatment guidelines. Sebetralstat, an oral plasma kallikrein inhibitor, was evaluated in 2 randomized, placebo-controlled clinical trials, which instructed early treatment of attacks with no minimum severity requirement. Objective:Characterize the efficacy and safety of sebetralstat by pooling data from phase 2 and 3 trials. Methods:This pooled analysis included participants (phase 2, aged ≥18 years; phase 3, aged ≥12 years) who received ≥1 dose of study drug (phase 2, sebetralstat 600 mg or placebo; phase 3, sebetralstat 300 mg or 600 mg, or placebo). Efficacy outcomes included times to beginning of symptom relief within 12 h, reduction in severity within 12 h, and complete attack resolution within 24 h. P values were not adjusted for multiplicity. Results:377 attacks were treated: 87 with sebetralstat 300 mg; 151 with sebetralstat 600 mg; 139 with placebo. Median (interquartile range) time to treatment was 32.5 min (8.0-94.0). Baseline severity was rated as "Mild" (46.2%), "Moderate" (40.6%), or "Severe"/"Very Severe" (12.7%). Compared with placebo, time to beginning of symptom relief was faster with sebetralstat (300 mg; 600 mg [P = 0.0001; P < 0.0001]), as was reduction in severity (P = 0.0038; P < 0.0001) and complete attack resolution (P = 0.0021; P < 0.0001). Median time to beginning of symptom relief was 1.6 h (0.8-7.0) and 1.8 h (1.0-4.3) with sebetralstat 300 mg and 600 mg, respectively, and 8.3 h (1.5 to >12) with placebo. Sebetralstat had a safety profile comparable to placebo. Conclusion:Across phase 2 and 3 clinical trials, sebetralstat enabled early treatment, provided effective symptom relief versus placebo, and was well tolerated, regardless of attack location or baseline severity. Clinical trial registration:ClinicalTrials.gov Identifier NCT04208412, registered on 2019-07-02; ClinicalTrials.gov Identifier NCT05259917 (KONFIDENT), registered on 2022-02-22.

Genetic variants in RNU4-2, which is transcribed into the U4 small nuclear RNA component of the major spliceosome, were recently shown to cause ReNU syndrome, a prevalent dominant neurodevelopmental disorder (NDD). These variants almost exclusively arise de novo and cluster within 18 nucleotides of RNU4-2. Here we describe a new recessive NDD associated with homozygous and compound heterozygous variants in RNU4-2. We identify 38 individuals with biallelic variants outside the 18-nucleotide ReNU syndrome region that cluster within other functionally important elements of U4: Stem II, the k-turn and the Sm protein binding site. We characterize the clinical phenotype in 31 individuals, demonstrating that the recessive disorder is clinically distinct from ReNU syndrome and is associated with distinctive white matter abnormalities, including enlarged perivascular spaces. Finally, we find reduced RNU4-2 transcript levels in individuals with the recessive disorder, suggesting a loss-of-function disease mechanism that is distinct from the mechanism underlying ReNU syndrome. Together, these findings expand the genotypic and phenotypic spectrum of RNU4-2-associated NDDs.

PURPOSE:Genetic causes of surfactant dysfunction are associated with childhood interstitial lung disease. Lysosome-associated membrane glycoprotein 3 (LAMP3) is highly expressed within lamellar bodies of alveolar epithelial type II cells, and variants in LAMP3 have recently been suggested as a novel cause of childhood interstitial lung disease. This study describes the phenotypes of participants with biallelic variants in LAMP3 and presents functional studies evaluating the role of specific LAMP3 variants. METHODS:Phenotypic data were collected through chart review and clinical evaluation. In vitro effects of LAMP3 variants were evaluated through immunohistochemistry, western blot, and flow cytometry. RESULTS:Thirteen participants were identified with biallelic variants in LAMP3. They presented with variable phenotypes ranging from neonatal respiratory distress to asymptomatic in adulthood. All symptomatic participants demonstrated ground glass opacities early in life and lung fibrosis later in life. For 1 participant, BAL analysis showed abnormal surfactant protein composition and lung biopsy revealed irregular lamellar bodies. In vitro studies in lung epithelial cells with induced expression of specific LAMP3 variants demonstrated reduced protein expression and abnormal glycosylation. CONCLUSION:Biallelic LAMP3 variants are associated with an interstitial lung disease phenotype with variable expressivity. Evaluation for LAMP3 variants should be considered in individuals with unexplained interstitial lung disease.

Myhre syndrome is a rare genetic disorder caused by pathogenic variants in SMAD4. The neurocognitive profile may include intellectual disability and developmental delay across a wide spectrum of domains. Four individuals with Myhre syndrome and psychosis and/or schizophrenia have been reported. We discuss three additional individuals (one briefly mentioned in a review of patients with Myhre syndrome) with SMAD4 pathogenic variants at codon Arg496Cys (two cases) and codon Ile500Val (one case). All had social challenges and variable developmental delays. They presented with acute-onset psychosis and were diagnosed with either psychosis, not otherwise specified, or psychosis associated with bipolar disorder. The seven individuals (5 female, 2 male) ranged in age from 13 to 24 years (mean 18.7 years) and had variable responses to pharmacologic and behavioral interventions. The underlying mechanism of psychosis in Myhre syndrome may be due to disruptions in the TGF-β signaling pathway, which involves the interactions of TGF-β family members and SMAD proteins, including SMAD4. Although additional cases are needed to verify our observations, psychosis may be a component of the neurodevelopmental phenotype of Myhre syndrome, highlighting the importance of rapid psychiatric evaluation and intervention.

We recently showed that mutations in the snRNA genes RNU4-2 and RNU2-2 are prevalent causes of dominant neurodevelopmental disorders (NDDs). Here, by genetic association, we demonstrate the existence of a recessive form of RNU2-2 syndrome. We inferred a log Bayes factor for a recessive model of association of 18.2. Conditional on that model, 17 rare variants had a posterior probability of pathogenicity >0.8. This conservative threshold identified 18 probands and 5 affected siblings, each carrying two alleles in trans at these variants. A relaxed threshold of >0.6 identified a further 13 candidate probands. We identified nine further cases in replication collections. Affected individuals have intellectual disability, global developmental delay and seizures. Recessive RNU2-2 syndrome accounts for ~10% of families with a recessive NDD presently diagnosable by sequencing and affects ~60% as many families as the dominant RNU4-2-related NDD ReNU syndrome. The variants are predicted to destabilize stem loops and binding domains of U2-2 snRNA. Whole-blood RNA sequencing data showed a >90% reduction in the expression of pathogenic U2-2 alleles in biallelic cases and monoallelic carriers, albeit with wild-type compensation in carriers, pointing to a loss-of-expression mechanism.

Metabolites present in the mother traverse the placenta to supply energy, essential nutrients, and communication signals to the fetus. To gain a deeper understanding of fetal metabolism and the impacts of maternal metabolic health and medications on the fetus, we have created CordDB. Using mass spectrometry, we systematically document the metabolites and medications that enter and leave the fetus during birth, as well as the associated health records of the mother and newborn. These data reveal the metabolites consumed by the fetus, microbial metabolites (e.g., 3-indolepropionic acid), metabolites obtained from diet, and medications, as well as create a healthy newborn signature. Our study demonstrates that the mother’s microbial interactions and nutrition, premature birth, and the mother’s use of drugs such as bupivacaine and betamethasone are linked to variations in the metabolic profiles and health of newborns.

Rare disease research and diagnosis rely on the integration of genomic and phenotypic data generated across diverse clinical sites; however, the absence of widely adopted standards for representing genomic data and associated metadata has limited data interoperability, reuse, and cross-study analysis. The Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was established to investigate challenging rare disease cases and evaluate emerging multi-omic technologies for clinical translation. To support coordinated data integration across distributed research sites, we developed a common Consortium Data Model in partnership with domain experts to standardize the capture of participant-, family-, phenotype- and assay-level metadata, with a particular emphasis on using a modular architecture to support linking of multiple data versions from multiple omic technologies to a single individual and attribution of a genetic finding to the specific technology used for its initial discovery. Adoption of the GREGoR Data Model has enabled continued generation and public release of a harmonized, analysis-ready Consortium Dataset. The most recent release includes phenotypic, family and multi-omic data from 12,292 participants in 5,029 families. Other rare disease data sharing efforts are beginning to adopt this data model which will facilitate cross consortium analyses and empower rare disease research. This work demonstrates that a collaborative, flexible, and scalable data model can enable large-scale rare disease research, facilitate cross-center data harmonization, and enable data interoperability.

PURPOSE:We aim to better define the genotype and phenotype spectrum of RNU4ATAC-opathy, demonstrate the utility of RNA sequencing (RNA-seq) for variant classification, and highlight the challenges in detecting variants in this noncoding gene. METHODS:Sixty individuals with molecularly confirmed RNU4ATAC-opathy were recruited from multiple clinical and research centers internationally. RNA-seq was available for 7 affected individuals. RESULTS:We report the clinical and molecular findings of 60 individuals, including 42 not previously described, and 33 distinct RNU4ATAC variants, 13 of which are novel. Core features in this cohort-present in most individuals assessed and varying in severity-include microcephaly, short stature, skeletal anomalies, developmental delay, cerebral anomalies, skin conditions, and immune deficiency. Additional findings, such as diabetes, holoprosencephaly, and the absence of various core features in some individuals, highlight the broad phenotypic spectrum. All individuals who underwent RNA-seq showed a consistent pattern of minor intron retention. In 6 individuals, RNA-seq enabled the reclassification of variants of uncertain significance as likely pathogenic. Although RNU4ATAC variants are generally covered by clinical exomes, they are often overlooked in analysis because of their noncoding nature. CONCLUSION:This study highlights the variability of phenotypes and genotypes associated with RNU4ATAC-opathy. Laboratories should ensure RNU4ATAC and other noncoding genes are appropriately assessed by their analysis pipelines.

PURPOSE:In recent years, researchers have brought attention to the underrepresentation of people with disabilities in biomedical research, including genomics research. However, little is known about how disability-related experiences influence participation in rare disease research. This omission is striking because rare diseases are associated with disabling phenotypes that affect multiple body systems. As part of a study interrogating the relationship between rare disease status and disability identity, we conducted mixed-methods research to address this knowledge gap. METHODS:Parents of children enrolled in the Undiagnosed Diseases Network (UDN) (n = 25) completed semi-structured interviews to assess disability-related experiences in research participation. Directed content analysis was used to identify common themes. RESULTS:Participants' disability-related research experiences were characterized by 1) disability-related facilitators to research participation, including benefits of research participation and disability-conscious approaches; 2) disability-related logistical barriers to research participation; and 3) research procedures and the perception of research as being minimally burdensome relative to clinical encounters. CONCLUSION:Parents of children in the UDN make considerable investments of time and resources to accommodate their children's disabilities and facilitate their participation. Future research should explore these issues in other genomics research studies and identify practical approaches to mitigating barriers to and employing facilitators of disability-related research participation.

Transient beta events (TBE) during electroencephalography (EEG) reflect thalamocortical activity, bridging genotype to phenotype and impacting sensory responsivity. Compared to typically developing controls, we found elevated TBE rate in some children with idiopathic Autism Spectrum Disorder (ASD) and a majority of children with Phelan-McDermid Syndrome, Rett Syndrome, and SYNGAP1-related disorder. TBE rate thus offers promise as a stratification biomarker with divergent and convergent properties across ASD and neurogenetic conditions, respectively.

Background:Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. Methods:We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. Results:METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. Conclusions:METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

The vast majority of individuals with autosomal recessive (AR) conditions demonstrate biparental inheritance of the disease-causing alleles; however, de novo variants also contribute to AR disease. This report represents the largest cohort to-date of rare AR conditions in which one of the disease-causing alleles was inherited and one occurred de novo. Clinical and research staff at Stanford University, clinical sites of the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) Consortium, and a large clinical genetic testing laboratory were contacted to identify cases of an AR diagnosis resulting from an inherited and de novo disease-causing variant in trans. Fifteen cases of AR conditions caused by one inherited and one de novo variant in a gene consistent with the clinical phenotype were identified; all had undergone trio exome or genome sequencing with genetic confirmation of reported relationships. Variants were confirmed to be in trans in eight of the 15 cases. The de novo variant was confirmed (n = 7) or presumed (n = 7) to have arisen on the paternal allele in 14/15 (93%) of cases. Phenotypic and/or molecular evidence of an AR condition should prompt parental segregation analysis to inform diagnosis, recurrence risks, and variant classification. Additional studies are needed to determine the incidence of this phenomenon given the implications for the interpretation of genetic testing and counseling for AR conditions.

PURPOSE:The application of next-generation sequencing in prenatal and neonatal genomic medicine provides definite diagnosis and affects clinical decision making and reproductive planning. Despite recent advances, interpretation of variants identified by genome/exome sequencing in cases lacking obvious phenotypic abnormalities (stillbirth, miscarriage, and neonatal death) remains challenging. METHODS:To improve diagnostic accuracy, we created the Intolerome Database, a curated resource of 934 genes essential for viability in humans. This database has accumulated details on genes' mechanisms of action, phenotypes, inheritance, the mortality timing, and supporting publications. RESULTS:The Intolerome includes 59 (6.3%) genes linked to the first/second trimester miscarriages, 525 (56.2%) genes associated with stillbirth/neonatal death, and 350 (37.5%) genes with variants that can cause lethality at any prenatal/postnatal stage. De novo inheritance was documented for 159 autosomal-dominant genes. Heterozygous potentially lethal variants in 39 autosomal-recessive genes were present in all ancestries in gnomADv4.1.0 at a frequency of ≥1/100 individuals, underlining the major pregnancy loss contributors. CONCLUSION:The Intolerome serves as a comprehensive resource for identifying and interpreting genomic variants linked to fetal and neonatal mortality. It will support clinicians, laboratory professionals, and researchers in advancing the diagnosis and understanding of lethal genetic conditions, offering new insights into their clinical presentations and inheritance patterns.

We report three individuals with bi-allelic variants in RNU6ATAC, which encodes the U6atac minor spliceosomal small nuclear RNA (snRNA), causing a multisystem minor spliceopathy. Through RNA sequencing analysis, we identified a distinctive excess of minor intron retention (MIR) in two unrelated individuals, which guided the identification of bi-allelic RNU6ATAC variants. The discovery cohort presented with variable multisystem manifestations. One individual presented with refractory epilepsy, microcephaly, developmental delay, ataxia, bilateral toe syndactyly, hypereosinophilia, and short stature, whereas the other exhibited failure to thrive, short stature, primary hypothyroidism, combined variable immunodeficiency, eosinophilic colitis, ichthyosis vulgaris, scoliosis, and chronic inflammatory demyelinating polyneuropathy without neurodevelopmental involvement. Despite organ-specific variation, both individuals displayed impaired growth and eosinophil-driven inflammation. Recently, we identified a third affected individual from an independent cohort whose phenotype bridges these features, combining microcephaly, growth failure with severe immunodeficiency, and skeletal abnormalities. The distinctive excess of MIR outliers in the discovery cohort supports minor spliceosome dysfunction, mirroring the molecular signature of RNU4ATAC-opathy. These findings nominate RNU6ATAC as a disease-associated gene, defining an expanded clinical spectrum of minor spliceopathies. Our study supports the power of integrating genomic and transcriptomic approaches for diagnosing splicing disorders and highlights the critical role of spliceosomal snRNAs in human disease.

There have been significant breakthroughs in understanding the pathophysiology of hereditary angioedema in the past several years. Owing to this, patients now have several therapeutic options for management of both acute attacks and prophylactic therapy. Navigating these options can be confusing to patients and clinicians alike. This is even more evident in the pediatric and adolescent populations secondary to differing lifestyles in these age groups, needing to understand the goals of various family members, and differing ages of approvals for medications. This Yardstick provides evidence-based, expert opinion on how to diagnose and manage pediatric and adolescent hereditary angioedema.

Abstract Background Native long-read DNA sequencing simultaneously captures genetic variants and epigenetic modifications from single molecules, but preserving molecular length and base modifications currently depends on cold-chain infrastructure that limits access to well-resourced settings. Results We demonstrate that ensilication, the encapsulation of DNA within silica matrices, preserves DNA at ambient temperature for 30 days with sequencing performance equivalent to conventional − 80 °C freezing. Across three Genome-in-a-Bottle reference genomes, ensilicated and frozen samples show no significant differences in read length (N50 ~ 8,000–11,000 bp), variant-calling accuracy, or genome-wide CpG methylation. Single-read methylation calls benchmarked against an independent bisulfite-sequencing reference confirm that ensilication introduces no detectable bias, with per-read accuracy differing by less than 0.4% between preservation conditions. Ensilicated DNA tolerates repeated handling better than frozen samples and maintains fragment integrity under accelerated weathering. In two patients with rare genetic disorders, ambient-preserved DNA resolves a de novo variant in the segmentally duplicated GTF2I locus and detects methylation patterns consistent with KDM2A-related disorder. Conclusions Ensilication enables diagnostic-quality native long-read sequencing without cold-chain infrastructure, supporting ambient storage and transport while preserving both sequence and methylation information.

Objective. Biallelic loss-of-function variants in DNASE1L3 cause inherited systemic lupus erythematosus and hypocomplementemic urticarial vasculitis. These disorders arise from defective clearance of extracellular chromatin, leading to autoantibody formation, immune complex deposition, and complement consumption. The full clinical and therapeutic spectrum of DNASE1L3 deficiency remains incompletely defined. Methods. We evaluated a 24-year-old woman with lifelong systemic inflammation characterized by polyarthritis, urticarial vasculitis, episcleritis, recurrent abdominal pain with intestinal angioedema, and persistent hypocomplementemia. Testing included autoantibody profiling, whole-exome sequencing, DNASE1L3 enzymatic assays in cell lysates and supernatants, and plasma analysis of cell-free DNA fragmentation. Results. The patient lacked antinuclear, anti-double-stranded DNA, and anti-Smith antibodies, though antiphospholipid antibodies were intermittently positive. The disease was refractory to multiple immunosuppressive agents but showed partial improvement with JAK inhibition. Genetic analysis revealed compound heterozygous DNASE1L3 variants: a pathogenic frameshift (c.290_291delCA) and a novel missense change (c.179T>G, p.Ile60Ser). Functional testing showed markedly impaired DNA degradation for both variants, with residual activity in the missense mutant. Plasma DNA analysis demonstrated reduced mononucleosomal peaks, altered fragment length distribution, and loss of cytosine-cytosine-rich end motifs, confirming reduced nuclease activity in vivo. Conclusion. This case supports the pathogenicity of the DNASE1L3 p.Ile60Ser variant broadening the genetic spectrum. Plasma DNA fragment analysis provides a sensitive biomarker of impaired nuclease function, and JAK inhibition may offer partial therapeutic benefit in DNASE1L3-related systemic inflammation.

Abstract The interpretation of missense variants remains a major challenge in clinical genetics. “Meta-domains” aggregate population and pathogenic variation across homologous Pfam domain instances in the human proteome, providing per-residue context for interpreting variants of uncertain significance (VUS). Our 2019 implementation, MetaDome, is widely used and named in clinical variant-classification guidelines. Here we present the MetaDome 2027 update, featuring a comprehensively updated dataset and GRCh38 support. The redesigned pipeline enables incremental updates of GENCODE, UniProtKB/Swiss-Prot, Pfam, gnomAD, and ClinVar while maintaining 100% sequence-identity gene-to-protein mapping. Annotated Pfam domain instances grew 14.9% from 71,419 to 82,069 and meta-domain-eligible Pfam families (≥2 human occurrences) by 73.3% from 3,334 to 5,778; Pfam domains are annotated to 92% of human proteins. Approximately 43% of mapped protein-coding nucleotides (14.3 million in GRCh38, 13.8 million in GRCh37) are in a meta-domain; in GRCh38 67.9% (37,692 of 55,548) of pathogenic or likely pathogenic ClinVar missense variants fall at such a position. We show how MetaDome helped reclassify a de novo missense VUS in RALA and identify 52,463 ClinVar missense VUS for which meta-domains supply otherwise unavailable pathogenic evidence. MetaDome is freely available at www.metadome.app . Graphical Abstract