Neurodevelopmental disorders are genetically heterogeneous and often remain unresolved despite extensive clinical evaluation and genomic testing. Here, we report a proband with a progressive neurodevelopmental disorder evaluated through the Undiagnosed Diseases Network who harbored heterozygous de novo missense variants in two genes, DCLK1 (p.(S228L)) and SFPQ (p.(P623R)). To determine the clinical significance of these candidate variants, we employed an integrative pipeline combining structural modeling, cross-species functional genomics, and patient-derived neuronal analyses. While the SFPQ variant yielded no detectable phenotype in Drosophila melanogaster, modeling the DCLK1 p.S228L variant in Caenorhabditis elegans induced severe locomotor deficits and aberrant neuronal morphology, including neurite blebbing. Parallel analyses of directly reprogrammed patient-derived neurons recapitulated these neurite defects, characterized by neurite beading, swelling and fragmentation, and elevated apoptosis. Transcriptomic profiling revealed dysregulation of neurodevelopmental and axon-guidance pathways alongside molecular signatures of neurodegeneration. Crucially, exogenous expression of wild-type DCLK1 or pharmacological targeting of a downstream dysregulated pathway partially rescued the neurite defects. Collectively, our findings implicate DCLK1 in a previously unrecognized progressive neurodevelopmental disorder and demonstrate the power of integrative cross-species functional genomics in resolving ultra-rare disease variants.

Importance:Leukodystrophies are a heterogeneous group of genetic disorders affecting the white matter of the brain, often presenting with overlapping clinical features but differing in neuroanatomical involvement. There is a critical need for quantitative tools to characterize disease burden and support diagnosis, severity stratification, and clinical trial readiness. Objective:To characterize shared and distinct neuroanatomical patterns across six genetically confirmed leukodystrophies using anatomical MRI-derived phenotypes benchmarked against brain growth charts, and to assess the utility of this methodological approach for identifying imaging biomarkers of disease severity. Design:Cross-sectional neuroimaging study using retrospective clinical MRI data. Setting:Multicenter study incorporating data from the Global Leukodystrophy Initiative Clinical Trials Network (GLIA-CTN) and control data from the Children's Hospital of Philadelphia. Participants:The study included 434 MRI scan sessions from 274 patients with genetically confirmed leukodystrophies (Pelizaeus-Merzbacher disease, Metachromatic leukodystrophy, Alexander disease, Aicardi-Goutières syndrome, TUBB4A-related leukodystrophies, and POLR3-related leukodystrophy). Control MRI data (7628 scans from 7205 subjects) were drawn from the Scans with Limited Imaging Pathology cohort at the Children's Hospital of Philadelphia. Exposures:All MRI scans underwent automated segmentation using deep learning segmentation tools to derive global and regional brain volumes. Normative models of brain development ("brain growth charts") were generated for the control cohort using generalized additive models for location, scale, and shape. Centile scores were then calculated for leukodystrophy subjects to quantify deviations from typical development. Main Outcomes and Measures:Centile scores for global and regional brain volumes were compared across leukodystrophy subtypes to identify disease-specific neuroanatomical patterns and to evaluate their potential utility for severity stratification. Results:Distinct patterns of neuroanatomical deviation were observed across leukodystrophy subtypes. Certain leukodystrophies showed preferential involvement of specific cortical or subcortical regions, while others displayed more diffuse volume loss. Centile scores demonstrated potential for differentiating disease subtypes and stratifying individuals by severity. Preliminary longitudinal data suggest centile scores may also track progression over time. Conclusions and Relevance:This study demonstrates the feasibility and utility of MRI profiling of individuals with leukodystrophy using anatomical MRI-derived phenotypes benchmarked against brain growth charts. The approach enables data-driven, quantitative characterization of structural brain abnormalities, offering a scalable method for phenotyping, diagnosis, and future use in clinical trials.

ABSTRACT Biallelic pathogenic variants in PNPT1 cause combined oxidative phosphorylation deficiency 13 (COXPD13) (MIM #614932), linking mitochondrial dysfunction to type I interferon (IFN) activation through cytosolic leakage of mitochondrial double‐stranded RNA (mt‐dsRNA). This mechanism connects mitochondrial disease to interferonopathies such as Aicardi–Goutières syndrome (AGS). We describe a 7‐month‐old female infant with compound heterozygous PNPT1 variants presenting with severe hypotonia, feeding difficulties necessitating gastrostomy, dystonia, and elevated serum lactate. Brain magnetic resonance imaging (MRI) demonstrated marked cerebellar, brainstem, and basal ganglia atrophy, with a lactate peak on MR spectroscopy (consistent with an inverted doublet). Serum immune profiling revealed a mild but elevated type I IFN signature. Given the mechanistic overlap with AGS, off‐label tofacitinib, a Janus kinase (JAK) inhibitor that blocks IFN‐driven JAK/STAT signaling, was initiated following pediatric interferonopathy dosing protocols. Tofacitinib was associated with normalization of serum type I IFN biomarkers, reduction in lactate and transaminases, improvement in dystonic movements, ventilatory stability, and improved growth/nutrition without treatment‐limiting adverse events. To our knowledge, this represents the first reported use of JAK inhibition in COXPD13. The observed clinical and biochemical stabilization supports defining COXPD13 as a “mitochondrial interferonopathy” and suggests that IFN‐signature screening may identify mitochondrial disease patients who could benefit from targeted immunomodulation.

Introduction Stem cell transplant (SCT) is an effective therapy for patients with IEM, which if left untreated can cause devastating complications ultimately leading to death. Objectives Evaluate long-term survival outcomes of pediatric IEM patients undergoing SCT at Texas Children's Hospital to assess the impact of transplant era, donor source, and conditioning intensity on overall survival and graft failure. Methods Here we present a retrospective analysis of a single center experience between 2000-2024 of 33 patients undergoing initial SCT for IEM with Hurler (n=11, 33%), cerebral Adrenoleukodystrophy (n=8, 24%), Metachromatic Leukodystrophy (n=4, 12%), Krabbe (n=2, 6%), I-Cell (n=2, 6%), Mannosidosis (n=2, 6%), Neiman-Pick (n=1, 3%), or “Other” disease (n=3, 9%). The majority of patients were male (n=23, 70%), White (n=28, 85%), Hispanic (n=17; 52%), and were insured through public insurance (n=20, 61%). The median age at transplant was 2.8 years old (range: 0.2 - 21.5). The average diagnosis to transplant interval was 433 days (range: 53-2,596). Most transplants were performed after 2010 (n=20, 61%), while 39% (n=13) were performed prior to 2010. Of the patients who were transplanted prior to 2010, 8% were cord blood transplants (CBT, n=1), 77% were unrelated donor (URD, n=10), and 15% were related donor (RD, n=2). In contrast, among those transplanted after 2010, 55% were CBT (n=11), 25% were URD (n=5), and 20% were RD (n=4). Most patients received myeloablative conditioning (27/33) and six patients received a reduced intensity regimen. While CBT performed after 2010 did not use serotherapy (Alemtuzumab/ATG), it was used in 57% of transplants (n=19). Results The 1- and 2-year overall survival (OS) was 85% with a median follow-up of 6.8 years (range: 1-24.4, n=33) and 81% with a median follow-up of 8.2 years (range: 2.1-24.4, n=31); respectively. One year OS was 95% after 2010 compared to 69% before 2010, and with CBT (92%), URD (73%), and RD (100%), respectively. Acute GVHD was seen in 31% of patients (n=10) with most having a maximum grade of 1-2 (80%, n=8), with chronic GVHD seen in 3 patients. Six patients (18.2%) developed graft failure (GF), receiving either RD (n=1) or URD (n=5), of which 3 received a reduced intensity conditioning regimen. GF was treated with either additional SCT (n=4) or no additional therapy (n=2). Conclusion Survival outcomes for pediatric patients with IEM have markedly improved since 2010. Earlier transplant referral, refined conditioning regimens, and expanded use of CBT may be contributing to improvements, as CBT offers rapid donor availability and shortens time to transplant, limiting disease progression and irreversible organ damage. While graft failure can be a challenge, these results suggest that CBT is a strong alternative donor source and highlight the need for continued optimization of timing and conditioning to achieve durable, long-term cure.

Primary mitochondrial diseases (PMDs) affect approximately 1 in 4300 individuals and cause early-onset neuromuscular and multisystem dysfunction with reduced lifespan. They result from pathogenic variants in mitochondrial or nuclear DNA that impair oxidative phosphorylation. Cytochrome c oxidase (COX; complex IV) deficiency is a well-established cause of PMD, leading to a broad spectrum of phenotypes. COXFA4 (cytochrome c oxidase subunit FA4), formerly NDUFA4, is a nuclear-encoded COX subunit, but its role in disease remains poorly defined. We report the largest genetically confirmed cohort of COXFA4-related PMD to date, comprising 13 individuals from 12 families with biallelic pathogenic COXFA4 variants. All present with Leigh-like encephalopathy and complete loss of COXFA4 protein; however, patient-derived fibroblasts retain residual COX activity, with upregulation of COXFA4L2 (cytochrome c oxidase subunit FA4-like 2), a poorly characterised paralog. Here, we show that COXFA4 is a late-stage COX assembly subunit and identify a paralog-mediated compensatory mechanism with translational potential.

Purpose:Aicardi-Goutières syndrome (AGS) is a type I interferonopathy presently associated with nine genes. PTPN1 is a negative regulator of the interferon pathway previously associated with chronic inflammation and recently type 1 IFN autoinflammation. Methods:Genomic data from undiagnosed individuals with suspected AGS were interrogated for PTPN1 variants, and predicted loss-of-function (pLOF) and damaging missense variants in PTPN1 were sought in two additional academic databases as well as the All of Us database. Results:We identified 13 cases with ultra-rare heterozygous pLOF or highly damaging missense variants in PTPN1. Nine cases were identified in a cohort of 53 individuals (~ 17%) with clinical, imaging and persistent biochemical features of AGS. Median age of onset is 1.75 years (IQR 0.67), significantly later (p< 0.0001) than other AGS genotypes. Four additional cases were identified in academic datasets with variable clinical features suggestive of autoinflammation. Additionally, 49 individuals with ultra-rare, damaging PTPN1 variants were identified in the All of Us database, none had features suggestive of AGS, but autoimmunity was highly prevalent (~21.6%). Conclusion:Our data implicate PTPN1 as a cause of later-onset presentations of AGS within a broader spectrum of autoinflammatory phenotypes. Segregation and biobank data demonstrate reduced penetrance, with carriers being enriched for autoimmune disorders.

Background: The alkaline ceramidase 3 (ACER3) gene encodes an enzyme that regulates bioactive lipids, including ceramides, sphingosine, and sphingosine-1-phosphate, whose balance is essential for cell viability. Biallelic ACER3 variants have been associated with early-onset progressive leukodystrophy/leukoencephalopathy, previously reported only in seven patients from five families. Methods: Exome and genome sequencing of individuals with undiagnosed neurodevelopmental disorders, combined with international data sharing, identified multiple families with biallelic ACER3 variants. Enzymatic assays, lipidomics, mutagenesis, and protein modelling were used to assess variant pathogenicity. Findings: We describe 61 patients from 56 families (54 patients from 51 newly reported families), defining the clinical and molecular spectrum of ACER3-related disease. Infantile onset occurred in 89%, with moderate (54%) or rapid (37%) progression. Premature death occurred in 28% (mean age 6.0±4.3 years); mean age of living patients was 6.2±5.0 years. Core features included developmental regression or stagnation (100%/89%), global developmental delay (72%), limb spasticity (92%), axial hypotonia (74%), dystonia (73%), feeding difficulties (72%), contractures (45%), scoliosis (39%), and epilepsy (32%). A consistent facial gestalt was observed in 9/17 assessed patients. Neuroimaging showed posterior-predominant periventricular and deep white matter abnormalities, typically with minimal cerebral atrophy (86%). Functional studies demonstrated markedly reduced or absent ceramidase activity for all tested variants, total alkaline ceramidase activity of 0–34.4% in patient fibroblasts, and accumulation of ceramides and dihydroceramides, identifying critical functional hotspots. Interpretation: Together, these findings enhance the clinical, molecular, and biochemical understanding of ACER3-related disease, underscore the critical role of ACER3 in maintaining sphingolipid homeostasis, and provide a foundation for future therapeutic avenues.

Aromatic ʟ-amino acid decarboxylase (AADC) deficiency is a rare pediatric neurotransmitter disorder that typically necessitates lifelong care, and that carries a risk of childhood mortality. Eladocagene exuparvovec gene therapy is designed to restore AADC production. Study GT-002 (NCT04903288) is a phase 2, multicenter, open-label trial assessing the pharmacodynamics, safety, and efficacy of eladocagene exuparvovec administered to the putamen bilaterally in pediatric patients with AADC deficiency using a magnetic resonance (MR)-compatible cannula. Patients received eladocagene exuparvovec at 1.8 × 1011 vector genomes via the SmartFlow MR-compatible cannula in a single operative session. Endpoints include the change from baseline in cerebrospinal fluid homovanillic acid levels, motor milestone achievement, and safety. Here we report results from 48 weeks of follow-up. Mean (SD) cerebrospinal fluid homovanillic acid levels increased from baseline (22.5 [32.3] nmol/L; n = 13) to week 48 (55.3 [45.6] nmol/L; change from baseline: 28.3 [13.7] nmol/L; p = 0.0003; n = 9), indicating de novo dopamine production. At baseline (n = 13), all patients showed severe motor developmental delay; at week 48 (n = 12), nine achieved full head control, four could sit unassisted, two could stand with support, and two could walk independently to a toy. Overall, 260 treatment-emergent adverse events were reported in 13 patients; 259 were deemed unrelated and one likely unrelated to the MR-compatible cannula. No treatment-emergent adverse events led to study withdrawal and no deaths occurred. This study provides further evidence of the favorable pharmacodynamic, efficacy, and safety profile of eladocagene exuparvovec in children with AADC deficiency; intraputaminal administration using an MR-compatible cannula was well tolerated. Study GT-002 (NCT04903288) provides further evidence of the favourable pharmacodynamic, efficacy and safety profile of eladocagene exuparvovec gene therapy in children with AADC deficiency over 48 weeks and demonstrates that intraputaminal administration using an MR-compatible cannula was well tolerated, allowing for real-time MRI confirmation of cannula placement and infusate coverage, and for accurate dosing to the putamen.

Despite significant knowledge advances in recent decades, the role of most protein-coding genes in human disease remains incompletely understood. Exome sequencing continues to improve our understanding by elucidating novel genotype-phenotype associations. Across multiple healthcare centers, either exome or genome sequencing was performed in 18 patients with shared features of global developmental delay, hypotonia, and dysmorphisms. De novo, truncating variants in ZNF865 were identified in all 18 patients, with all but one clustered toward the C-terminus. Four variants were seen more than once in unrelated patients. No disease-causing variants were identified in other genes that would explain the patients' phenotypes. Little is known of the function of ZNF865, which belongs to the poly-zinc finger family of proteins that contain a large array of tandem C2H2 zinc finger DNA binding domains. Our findings suggest that protein-truncating variants in this gene lead to intellectual disability with a recognizable phenotypic pattern.

RNA sequencing (RNA-seq) has emerged as a powerful tool for resolving variants of uncertain significance (VUSs), particularly those affecting gene expression and splicing. However, most reference datasets and diagnostic protocols employ relatively modest sequencing depths (∼50-150 million reads), which may fail to detect low-abundance transcripts and rare splicing events critical for accurate diagnosis. We evaluated the diagnostic and translational utility of ultra-high-depth (up to ∼1 billion unique reads) RNA-seq in four clinically accessible tissues using the Ultima sequencing platform. After validating the performance of Ultima RNA-seq, we investigated how increasing sequencing depth affects gene and isoform detection, splicing variant discovery, and clinical interpretation of VUSs. Deep RNA-seq substantially improved sensitivity for detecting lowly expressed genes and isoforms, achieving near saturation for detection at 1 billion reads. In two probands with VUSs, pathogenic splicing abnormalities were undetectable at 50 million reads but emerged at 200 million reads, becoming even more pronounced at 1 billion reads. Using deep RNA-seq data, we constructed a resource, MRSD-deep, to estimate the minimum required sequencing depth to achieve desired coverage thresholds. MRSD-deep provided gene- and junction-level guidelines, helping labs select appropriate coverage targets for specific applications. Leveraging deep RNA-seq data on fibroblasts, we also built an expanded splicing-variation reference that successfully identified low-abundance splicing events missed by standard-depth data. Our findings underscore the diagnostic and research benefits of deep RNA-seq for Mendelian disease investigations.

The 3-methylglutaconic aciduria (3-MGA-uria) syndromes comprise a heterogeneous group of inborn errors of metabolism defined biochemically by detectable elevation of 3-methylglutaconic acid (3-MGA) in the urine. In type 1 (or primary) 3-MGA-uria, distal defects in the leucine catabolism pathway directly cause this elevation. Secondary 3-MGA-uria syndromes, however, are unrelated to leucine metabolism-specific defects but share a common biochemical phenotype of elevated 3-MGA. It is currently thought that this accumulation is due to an underlying buildup of acetyl-CoA in the mitochondria from impaired function of the TCA cycle with ensuing formation of trans-3-methylglutaconyl CoA and its subsequent byproducts, including 3-MGA. In these disorders, urine 3-MGA levels are known to be fluctuant and at times undetectable by standard urine organic acid analysis (UOA), thereby reducing the utility of this biochemical screening method. Here, we retrospectively evaluated a cohort of nine patients with confirmed 3-MGA-uria syndromes. It was observed that UOA analysis obtained from three separate patients did not identify detectable 3-MGA levels. This inherent limitation highlights the need for a more sensitive clinical modality. Untargeted metabolomics profiling is a rapidly emerging technology that is being used to detect and characterize biochemical abnormalities in many inborn errors of metabolism. Untargeted metabolomics profiling performed on plasma samples in this cohort identified significant elevations of 3-MGA in all nine individuals. This high degree of clinical sensitivity demonstrates the promising potential for untargeted metabolomics analysis as both an effective biochemical screening tool for 3-MGA-uria syndromes and a functional method to assist with validation of genomic variants of uncertain significance in these disorders.

ATP5F1A encodes the α-subunit of complex V of the respiratory chain, which is responsible for mitochondrial ATP synthesis. We describe 6 probands with heterozygous de novo missense ATP5F1A variants that presented with developmental delay, intellectual disability, and movement disorders. Functional evaluation in C. elegans revealed that all variants tested were damaging to gene function via a dominant negative genetic mechanism. Biochemical and proteomics studies showed a marked reduction in complex V abundance and activity in proband-derived blood cells and fibroblasts. Mitochondrial physiology studies in fibroblasts revealed increased oxygen consumption, yet decreased mitochondrial membrane potential and ATP levels indicative of uncoupled oxidative phosphorylation as a pathophysiologic mechanism. Our findings contrast functionally and clinically with the previously reported ATP5F1A variant, p.Arg207His, suggesting a distinct pathological mechanism. This study therefore expands the phenotypic and genotypic spectrum of ATP5F1A-associated conditions and highlights how functional studies can provide understanding of the genetic, molecular, and cellular mechanisms of ATP5F1A variants of uncertain significance. With 12 heterozygous individuals now reported, ATP5F1A is the most frequent nuclear genome cause of complex V deficiency.

ABSTRACT Importance Leukodystrophies are a diverse group of rare disorders that disrupt central myelination. These disorders present with a broad spectrum of neurological severity and are associated with a range of potential secondary complications, such as scoliosis and failure of independent feeding. Objective We explore real‐world data of leukodystrophy complications to inform future evidence‐based care guidelines across these rare diseases. Design In a cross‐sectional observational study, we use a leukodystrophy‐specific research consortium and the availability of electronic health records (EHR) to capture a cross‐section of real‐world data. Setting Study participants were identified using EHR data from five hospital systems with established expertise in leukodystrophies. Participants Principal investigators or genetic counselors confirmed leukodystrophy diagnoses in all participants. Exposures Time‐to‐event measures were collected, including orthopedic complications (scoliosis, hip subluxation/dislocation), loss of ambulation, artificial ventilation, gastrostomy tube placement, and urinary tract infections (UTIs). Maximum motor milestones, including gain of ambulation by 2 years of age, were captured to stratify cohorts by neurological severity. Main Outcome and Measure A primary outcome was not prespecified, as this was an observational study. Results In total, 1203 participants were identified across 42 leukodystrophies (age range of 9 days to 89 years at last encounter). The most common event was feeding tube placement, and the median time to any first complication varied between disorders (Fleming–Harrington weighted log‐rank test). The specific diagnosis correlated with maximum gross motor milestone attainment (chi‐square test of independence). When all disorders were stratified by maximum motor milestone attainment (not specific diagnosis), the median time to adverse events was significantly associated with function (Fleming–Harrington weighted log‐rank test). Conclusions This cross‐sectional, retrospective observational study demonstrated that key medical events could be identified across institutions using EHR capture. Rates of health events and attainment of maximum motor milestones varied by specific leukodystrophy type. However, when the overall cohort was stratified by severity of motor impairment rather than individual diagnoses, the frequency of health events was associated with motor function. Our findings suggest utility for development of comprehensive care models for leukodystrophies as stratified by motor function and demonstrate the utility of integrated EHR review for real‐world data analyses.

Purpose: SLC4A10 encodes a plasma membrane -bound transporter, which mediates Na+-dependent HCO3- import, thus mediating net acid extrusion. Slc4a10 knockout mice show collapsed brain ventricles, an increased seizure threshold, mild behavioral abnormalities, impaired vision, and deafness. Methods: Utilizing exome/genome sequencing in families with undiagnosed neurodevelopmental disorders and international data sharing, 11 patients from 6 independent families with biallelic variants in SLC4A10 were identified. Clinico-radiological and dysmorphology assessments were conducted. A minigene assay, localization studies, intracellular pH recordings, and protein modeling were performed to study the possible functional consequences of the variant alleles. Results: The families harbor 8 segregating ultra -rare biallelic SLC4A10 variants (7 missense and 1 splicing). Phenotypically, patients present with global developmental delay/intellectual disability and central hypotonia, accompanied by variable speech delay, microcephaly, cerebellar ataxia, facial dysmorphism, and infrequently, epilepsy. Neuroimaging features range from some non-specific to distinct neuroradiological findings, including slit ventricles and a peculiar form of bilateral curvilinear nodular heterotopia. In silico analyses showed 6 of 7 missense variants affect evolutionarily conserved residues. Functional analyses supported the pathogenicity of 4 of 7 missense variants. Conclusion: We provide evidence that pathogenic biallelic SLC4A10 variants can lead to neurodevelopmental disorders characterized by variable abnormalities of the central nervous system, including altered brain ventricles, thus resembling several features observed in knockout mice. (c) 2023 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Background and Objectives:Heterozygous pathogenic variants in ATP1A3, which encodes the catalytic alpha subunit of neuronal Na+/K+-ATPase, cause primarily neurologic disorders with widely variable features that can include episodic movement deficits. One distinctive presentation of ATP1A3-related disease is recurrent fever-triggered encephalopathy. This can occur with generalized weakness and/or ataxia and is described in the literature as relapsing encephalopathy with cerebellar ataxia. This syndrome displays genotype-phenotype correlation with variants at p.R756 causing temperature sensitivity of ATP1A3. We report clinical and in vitro functional evidence for a similar phenotype not triggered by fever but associated with protein loss-of-function.Methods:We describe the phenotype of an individual with de novo occurrence of a novel heterozygous ATP1A3 variant, NM_152296.5:c.388_390delGTG; p.(V130del). We confirmed the pathogenicity of p.V130del by cell survival complementation assay in HEK293 cells and then characterized its functional impact on enzymatic ion transport and extracellular sodium binding by two-electrode voltage clamp electrophysiology in Xenopus oocytes. To determine whether variant enzymes reach the cell surface, we surface-biotinylated oocytes expressing N-tagged ATP1A3.Results:The proband is a 7-year-old boy who has had 2 lifetime episodes of paroxysmal weakness, encephalopathy, and ataxia not triggered by fever. He had speech regression and intermittent hand tremors after the second episode but otherwise spontaneously recovered after episodes and is at present developmentally appropriate. The p.V130del variant was identified on clinical trio exome sequencing, which did not reveal any other variants possibly associated with the phenotype. p.V130del eliminated ATP1A3 function in cell survival complementation assay. In Xenopus oocytes, p.V130del variant Na+/K+-ATPases showed complete loss of ion transport activity and marked abnormalities of extracellular Na+ binding at room temperature. Despite this clear loss-of-function effect, surface biotinylation under the same conditions revealed that p.V130del variant enzymes were still present at the oocyte's cell membrane.Discussion:This individual's phenotype expands the clinical spectrum of ATP1A3-related recurrent encephalopathy to include presentations without fever-triggered events. The total loss of ion transport function with p.V130del, despite enzyme presence at the cell membrane, indicates that haploinsufficiency can cause relatively mild phenotypes in ATP1A3-related disease.

Fine-Lubinsky syndrome is a rare clinically defined syndrome sometimes referred to as brachycephaly, deafness, cataract, microstomia, and impaired intellectual development syndrome. Here we provide a clinical and molecular update for a sibling pair diagnosed with Fine-Lubinsky syndrome. An extensive genetic work-up, including chromosomal microarray analysis and quad exome sequencing, was nondiagnostic. However, a research reanalysis of their exome sequencing data revealed that both were homozygous for an intronic c.749+39G>A [NM_001383.6] variant in DPH1. RNAseq analysis performed on RNA from fibroblasts revealed significantly reduced expression of DPH1 transcripts suggestive of abnormal splicing followed by nonsense mediated mRNA decay. Since the phenotypes of this sibling pair were consistent with those associated with the inheritance of biallelic pathogenic variants in DPH1, they were given a diagnosis of developmental delay with short stature, dysmorphic facial features, and sparse hair 1 (DEDSSH1). This leads us to recommend that all individuals with a clinical diagnosis of Fine-Lubinsky syndrome be screened for variants in DPH1. The clinical histories of this sibling pair emphasize that hearing loss associated with DEDSSH1 may remit over time and that individuals with DEDSSH1 should be monitored for the development of cardiomyopathy. This case also demonstrates the clinical utility of RNAseq as a means of functionally validating the effects of intronic variants that may affect splicing.