Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy

The solute carrier (SLC) superfamily encompasses >400 transmembrane transporters involved in the exchange of amino acids, nutrients, ions, metals, neurotransmitters and metabolites across biological membranes. SLCs are highly expressed in the mammalian brain; defects in nearly 100 unique SLC-encoding genes (OMIM: https://www.omim.org) are associated with rare Mendelian disorders including developmental and epileptic encephalopathy (DEE) and severe neurodevelopmental disorders (NDDs). Exome sequencing and family-based rare variant analyses on a cohort with NDD identified two siblings with DEE and a shared deleterious homozygous splicing variant in SLC38A3. The gene encodes SNAT3, a sodium-coupled neutral amino acid transporter and a principal transporter of the amino acids asparagine, histidine, and glutamine, the latter being the precursor for the neurotransmitters GABA and glutamate. Additional subjects with a similar DEE phenotype and biallelic predicted-damaging SLC38A3 variants were ascertained through GeneMatcher and collaborations with research and clinical molecular diagnostic laboratories. Untargeted metabolomic analysis was performed to identify novel metabolic biomarkers. Ten individuals from seven unrelated families from six different countries with deleterious biallelic variants in SLC38A3 were identified. Global developmental delay, intellectual disability, hypotonia, and absent speech were common features while microcephaly, epilepsy, and visual impairment were present in the majority. Epilepsy was drug-resistant in half. Metabolomic analysis revealed perturbations of glutamate, histidine, and nitrogen metabolism in plasma, urine, and cerebrospinal fluid of selected subjects, potentially representing biomarkers of disease. Our data support the contention that SLC38A3 is a novel disease gene for DEE and illuminate the likely pathophysiology of the disease as perturbations in glutamine homeostasis

Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families

Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved

Loss-of-function variants in <em>JPH1 </em>cause congenital myopathy with prominent facial and ocular involvement

\ua9 Author(s) (or their employer(s)) 2024.Background Weakness of facial, ocular and axial muscles is a common clinical presentation in congenital myopathies caused by pathogenic variants in genes encoding triad proteins. Abnormalities in triad structure and function resulting in disturbed excitation-contraction coupling and Ca2+ homeostasis can contribute to disease pathology. Methods We analysed exome and genome sequencing data from four unrelated individuals with congenital myopathy characterised by facial, ocular and bulbar involvement. We collected deep phenotypic data from the affected individuals. We analysed the RNA-sequencing (RNA-seq) data of F3-II.1 and performed gene expression outlier analysis in 129 samples. Results The four probands had a remarkably similar clinical presentation with prominent facial, ocular and bulbar features. Disease onset was in the neonatal period with hypotonia, poor feeding, cleft palate and talipes. Muscle weakness was generalised but prominent in the lower limbs with facial weakness also present. All patients had myopathic facies, bilateral ptosis, ophthalmoplegia and fatigability. Muscle biopsy on light microscopy showed type 1 myofiber predominance and ultrastructural analysis revealed slightly reduced triads, and structurally abnormal sarcoplasmic reticulum. DNA sequencing identified four unique homozygous loss-of-function variants in JPH1, encoding junctophilin-1 in the four families; one stop-gain (c.354C&gt;A;p.Tyr118*) and three frameshift (c.373delG;p.Asp125Thrfs*30, c.1738delC;p.Leu580Trpfs*16 and c.1510delG;p. Glu504Serfs*3) variants. Muscle RNA-seq showed strong downregulation of JPH1 in the F3 proband. Conclusions Junctophilin-1 is critical for the formation of skeletal muscle triad junctions by connecting the sarcoplasmic reticulum and T-tubules. Our findings suggest that loss of JPH1 results in a congenital myopathy with prominent facial, bulbar and ocular involvement

Urban-rural difference in satisfaction with primary healthcare services in Ghana

Abstract Background Understanding regional variation in patient satisfaction about healthcare systems (PHCs) on the quality of services provided is instrumental to improving quality and developing a patient-centered healthcare system by making it more responsive especially to the cultural aspects of health demands of a population. Reaching to the innovative National Health Insurance Scheme (NHIS) in Ghana, surpassing several reforms in healthcare financing has been a milestone. However, the focus of NHIS is on the demand side of healthcare delivery. Studies focusing on the supply side of healthcare delivery, particularly the quality of service as perceived by the consumers are required. A growing number of studies have focused on regional differences of patient satisfaction in developed countries, however little research has been conducted concerning patient satisfaction in resource-poor settings like in Ghana. This study was therefore dedicated to examining the variation in satisfaction across rural and urban women in Ghana. Methods Data for the present study were obtained from the latest demographic and health survey in Ghana (GDHS 2014). Participants were 3576 women aged between 15 and 49 years living in non-institutional settings in Ghana. Summary statistics in percentages was used to present respondents’ demographic, socioeconomic characteristics. Chi-square test was used to find association between urban-rural differentials with socio-economic variables. Multiple logistic regression was performed to measure the association of being satisfied with primary healthcare services with study variables. Model fitness was tested by pseudo R 2. Statistical significance was set at p < 0.05. Results The findings in this study revealed that about 57.1% were satisfied with primary health care services. The urban and rural areas reported 57.6 and 56.6% respectively which showed no statistically significant difference (z = 0.64; p = 0.523; 95%CI: -0.022, 0.043). Bivariate analysis showed that region, highest level of education, wealth index and type of facility were significantly associated with location of residence (urban-rural areas). After adjusting for confounding variables using logistic regression, geographical location became a key factor of satisfaction with primary healthcare services by location of residence. In urban areas, respondents from Greater Accra had 64% increase in the level of satisfaction when compared to those in Western region (OR = 1.64; 95CI: 1.09–2.47), Upper East had 75% increase in satisfaction compared to Western region (OR = 1.75; 95%CI: 1.08–2.84), Northern had an estimated 44% reduction in satisfaction when compared to Western region (OR = 0.56; 95%CI: 0.34–0.92). However, rural areas in Central, Volta, Eastern, Ashanti, Brong Aghafo, Northern and Upper West region had 51, 81, 69, 46, 62, 75 and 61% reduction respectively in the level of satisfaction when compared to Western region. Conclusions Patient satisfaction is an important indicator of health outcomes. Quality of care and measuring level of patient satisfaction has been found to be the most useful tool to predict utilization and compliance. In fact, satisfied patients are more likely than unsatisfied ones to continue using health care services. Our results suggest that policymakers need to better understand the determinants of satisfaction with the health system and how different socio-demographic groups perceive satisfaction with healthcare services so as to address health inequalities between urban and rural areas within the same country