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Background The ALG1-congenital disorder of glycosylation condition is a rare autosomal recessive disorder with approximately 80 patients reported worldwide up to now. This disorder is caused by a deficiency of 1,4 mannosyltransferase due to the pathogenic variants within the ALG1 gene which leads to impaired protein glycosylation. This disorder usually causes multiorgan damage. This is the first report of ALG1-CDG cases from Iran who are bearing a novel variant in a homozygote state. Case presentation The clinical and molecular features of three cases have been described. All three cases in this study had experienced seizures at a young age and had developmental delays. They were suffering from speech and learning disabilities, and in one case, cerebral atrophy was also present. Although they all had walking problems, the youngest case gained the ability to walk by occupational therapy. Additionally, they all survived to childhood and adulthood which indicates a mild phenotype. Despite several years of delayed diagnosis, a novel variant p.Leu375Gln was identified in the cases in homozygous form through whole exome sequencing, which ultimately established a diagnosis. The pathogenic effect of the novel variant was assessed computationally. It has been evaluated using prediction tools including SIFT, Poly-Phen2, and Mutation taster. The protein homology modeling was performed, and the variant effect on hydrogen bonds and protein stability was assessed. Conclusion The findings of this study expand our knowledge of clinical and genetic features of ALG1-CDG and present the significant role of next-generation sequencing technologies in the diagnosis of rare disorders.

Background The relationship between thrombophilia genes and recurrent pregnancy loss has been discussed. The aim of this study was to investigate the association between of MTHFR C677T, A1298C, F2G20210A, and F5 G1691A genetic variants among Iranian women with recurrent miscarriage. Methods A total of 245 women with two or more recurrent pregnancy loss, with mean age years were enrolled in the study. To compare genotypes, we have selected 250 healthy women without history of miscarriage as control group. Genomic DNA of participants was evaluated using polymerase chain reaction followed by Sanger sequencing to determine the genotype frequency. Results The mean age were 32.16 ± (21–42) and 31.81 ± (19–40) for case and control groups respectively. MTHFR C677T and A1298C mutant alleles were found to be significantly more prevalent in patients than control. However, F2G20210A and F5 G1691A genetic variants showed no significance. Conclusion The allele frequencies for the assessed genotypes in this study are consistent with the data obtained for other countries. We observed significant susceptible effects of MTHFR C677T, and A1298C among participants. According to the relatively high prevalence of these variants, we recommend genetic testing for women with RPL before therapeutic decisions.

Background Autosomal recessive polycystic kidney disease (ARPKD) is a genetically inherited pediatric disorder. It is caused by a mutation in the PKHD1 gene located on chromosome 6. The predominant phenotype is characterized by early-onset bilateral enlarged kidneys, as well as fibrocystic changes in the kidney and liver. Fetuses or infants usually present with Potter syndrome, and they are more likely to develop severe renal insufficiency. Generally, patients die perinatally or in infancy. Liver involvement has been reported in adults with ARPKD who have survived the neonatal period and childhood. However, renal involvement is rarely expected in adulthood. The case is being presented for its clinical rarity, in addition to emphasize the critical role of NGS approaches in diagnosis. Case presentation We hereby describe a 33-year-old female with adult-onset proteinuria and nephromegaly. She had a rare homozygous missense mutation of the PKHD1 gene with autosomal recessive inheritance. The proband has consanguineous heterozygote parents. The mutation was identified by whole-exome sequencing, and the results were confirmed by segregation analysis. Conclusion Here, we reported a thorough literature review of late-onset autosomal recessive polycystic kidney disease. Furthermore, we explored the importance of genetic work-up in families with genetic disorders and consanguineous marriages, particularly in underdeveloped countries.

Objective Intracellular signaling networks rely on proper membrane organization to control an array of cellular processes such as metabolism, proliferation, apoptosis, and macroautophagy in eukaryotic cells and organisms. Phosphatidylinositol 4‐phosphate (PI4P) emerged as an essential regulatory lipid within organelle membranes that defines their lipid composition and signaling properties. PI4P is generated by four distinct phosphatidylinositol 4‐kinases (PI4K) in mammalian cells: PI4KA, PI4KB, PI4K2A, PI4K2B. Animal models and human genetic studies suggest vital roles of PI4K enzymes in development and function of various organs, including the nervous system. Bi‐allelic variants in PI4KA were recently associated with neurodevelopmental disorders (NDD), brain malformations, leukodystrophy, primary immunodeficiency, and inflammatory bowel disease. Here, we describe patients from two unrelated consanguineous families with PI4K2A deficiency and functionally explored the pathogenic mechanism. Methods Two patients with PI4K2A deficiency were identified by exome sequencing, presenting with developmental and epileptic‐dyskinetic encephalopathy. Neuroimaging showed corpus callosum dysgenesis, diffuse white matter volume loss, and hypoplastic vermis. In addition to NDD, we observed recurrent infections and death at toddler age. We further explored identified variants with cellular assays. Results This clinical presentation overlaps with what was previously reported in two affected siblings with homozygous nonsense PI4K2A variant. Cellular studies analyzing these human variants confirmed their deleterious effect on PI4K2A activity and, together with the central role of PI4K2A in Rab7‐associated vesicular trafficking, establish a link between late endosome‐lysosome defects and NDD. Interpretation Our study establishes the genotype–phenotype spectrum of PI4K‐associated NDD and highlights several commonalities with other innate errors of intracellular trafficking.

The phenotypic range of limb-girdle muscular dystrophies (LGMDs) varies significantly because of genetic heterogeneity ranging from very mild to severe forms. Molecular analysis of the gene is challenging due to the wide range of mutations and associated complications in interpretations of novel variants with uncertain significance. Thus, in the current study, we performed the NGS analysis and its results are confirmed with Sanger sequencing to find the plausible disease-causing variants in patients with muscular dystrophy and their relatives via segregation analysis. Nine patients with LGMD type 2B (LGMD2B) characteristics were screened for putative mutations by the whole-exome sequencing (WES) test. Either the patients themselves or their parents and first relatives were investigated in the segregation analysis through Sanger sequencing. The majority of variants were classified as pathogenic through American College of Medical Genetics and Genomics (ACMG) guidelines, segregation results, and predictions. Results revealed eight variants in gene, including three splicing (c.1149+4A>G, c.2864+1G>A, and c.5785-7G>A), two nonsense (p.Gln112Ter and p.Trp2084Ter), two missense (p.Thr1546Pro and p.Tyr1032Cys), and one frameshift (p.Asp1067Ilefs), among nine Iranian families. One of the eight identified variants was novel, including p.Asp1067Ilefs, which was predicted to be likely pathogenic based on the ACMG guidelines. Notably, prediction tools suggested the damaging effects of studied variants on dysferlin structure. Conclusively, the current report introduced eight variants including a novel frameshift in gene with noticeable pathogenic effects. This study significantly can broaden the diagnostic spectrum of LGMD2B in combination with previous reports about mutations and may pave the way for a rapidly high-ranked identification of the accurate type of dysferlinopathy.

Congenital myotonia is a non-dystrophic musculoskeletal disease that causes abnormal muscle relaxation. The prevalence of congenital disorders is notably high in Iran, emphasizing the importance of genetic assessment in suspicious cases. In this study, we aim to report cases with the chloride channel gene, CLCN1, mutations leading to significant morbidity. This case report study investigated four patients from four families with clinically defined congenital myotonia. Inclusion criteria were increased creatinine kinase (CK) and muscle stiffness. We collected data regarding family history, age of onset, and current therapeutic plan. All patients underwent skeletal muscle electromyography, cardiological evaluation, spirometry study, and hematochemistry assessment, including but not limited to muscle enzyme levels. Afterward, DNA was extracted from peripheral blood. Subsequently, whole exome sequencing (WES) and Sanger sequencing were done to detect and confirm variants, respectively. Age of onset ranged from 1 to 12 years in these patients, which are years apart from their first visit to the clinic. The warm-up phenomenon was present in all of them. A variant of uncertain clinical significance was found. We recommend that future research projects should study the efficiency of collaboration between clinicians, molecular geneticists, and other healthcare providers in order to find out about unclear variants as quickly as possible.

Background Zellweger spectrum disorders (ZSDs) are a group of peroxisome biogenesis disorders (PBDs) with different variants in the PEX genes. The main biochemical marker for screening peroxisomal disorders is very long-chain fatty acids (VLCFAs). The study reveals a rare case of PBD in the Zellweger spectrum in which she had normal plasma VLCFA levels. Case presentation Here, we report a 10-year-old girl with neurodevelopmental delay, facial dysmorphism, and hearing impairment. A brain magnetic resonance imaging scan was done to determine the reason for the seizures and neurodevelopmental delay. MRI images showed a mild widening in sulci especially in frontal lobes and sylvian fissures with pachygyria in the perisylvian regions. Biochemical analysis was done to detect ZSD. However, plasma VLCFA levels were normal. The diagnosis was made using whole-exome sequencing (WES). A homozygous variant of uncertain significance (VUS) in PEX6 NM_000287.4: c.1992G > C (p. Glu664Asp) was identified which has been confirmed through Sanger sequencing in probands and her parents. Conclusions According to the case report, plasma VLCFA levels can be normal in patients with PBDs in the Zellweger spectrum. Furthermore, we could re-classify the c.1992G > C variant in the PEX6 gene from VUS to likely pathogenic based on clinical manifestations including facial dysmorphism, and hearing impairment.

Alterations of Ca 2+ homeostasis have been implicated in a wide range of neurodegenerative diseases. Ca 2+ efflux from the endoplasmic reticulum into the cytoplasm is controlled by binding of inositol 1,4,5-trisphosphate to its receptor. Activated inositol 1,4,5-trisphosphate receptors are then rapidly degraded by the endoplasmic reticulum-associated degradation pathway. Mutations in genes encoding the neuronal isoform of the inositol 1,4,5-trisphosphate receptor ( ITPR1 ) and genes involved in inositol 1,4,5-trisphosphate receptor degradation ( ERLIN1, ERLIN2 ) are known to cause hereditary spastic paraplegia (HSP) and cerebellar ataxia. We provide evidence that mutations in the ubiquitin E3 ligase gene RNF170 , which targets inositol 1,4,5-trisphosphate receptors for degradation, are the likely cause of autosomal recessive HSP in four unrelated families and functionally evaluate the consequences of mutations in patient fibroblasts, mutant SH-SY5Y cells and by gene knockdown in zebrafish. Our findings highlight inositol 1,4,5-trisphosphate signaling as a candidate key pathway for hereditary spastic paraplegias and cerebellar ataxias and thus prioritize this pathway for therapeutic interventions. Disturbances in IP3 receptor-mediated release of Ca 2 + from the endoplasmatic reticulum are associated with neurodegenerative disease. Here, the authors identify in four families with hereditary spastic paraplegia biallelic mutations in RNF170 that associate with increased basal levels of IP3 receptors.

Purpose Dioxygenases are oxidoreductase enzymes with roles in metabolic pathways necessary for aerobic life. 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL), encoded by HPDL , is an orphan paralogue of 4-hydroxyphenylpyruvate dioxygenase (HPD), an iron-dependent dioxygenase involved in tyrosine catabolism. The function and association of HPDL with human diseases remain unknown. Methods We applied exome sequencing in a cohort of over 10,000 individuals with neurodevelopmental diseases. Effects of HPDL loss were investigated in vitro and in vivo, and through mass spectrometry analysis. Evolutionary analysis was performed to investigate the potential functional separation of HPDL from HPD. Results We identified biallelic variants in HPDL in eight families displaying recessive inheritance. Knockout mice closely phenocopied humans and showed evidence of apoptosis in multiple cellular lineages within the cerebral cortex. HPDL is a single-exonic gene that likely arose from a retrotransposition event at the base of the tetrapod lineage, and unlike HPD, HPDL is mitochondria-localized. Metabolic profiling of HPDL mutant cells and mice showed no evidence of altered tyrosine metabolites, but rather notable accumulations in other metabolic pathways. Conclusion The mitochondrial localization, along with its disrupted metabolic profile, suggests HPDL loss in humans links to a unique neurometabolic mitochondrial infantile neurodegenerative condition.

Skeletal dysplasia with multiple dislocations are severe disorders characterized by dislocations of large joints and short stature. The majority of them have been linked to pathogenic variants in genes encoding glycosyltransferases, sulfotransferases or epimerases required for glycosaminoglycan synthesis. Using exome sequencing, we identify homozygous mutations in SLC10A7 in six individuals with skeletal dysplasia with multiple dislocations and amelogenesis imperfecta. SLC10A7 encodes a 10-transmembrane-domain transporter located at the plasma membrane. Functional studies in vitro demonstrate that SLC10A7 mutations reduce SLC10A7 protein expression. We generate a Slc10a7 −/− mouse model, which displays shortened long bones, growth plate disorganization and tooth enamel anomalies, recapitulating the human phenotype. Furthermore, we identify decreased heparan sulfate levels in Slc10a7 −/− mouse cartilage and patient fibroblasts. Finally, we find an abnormal N -glycoprotein electrophoretic profile in patient blood samples. Together, our findings support the involvement of SLC10A7 in glycosaminoglycan synthesis and specifically in skeletal development. The majority of skeletal dysplasia are caused by pathogenic variants in genes required for glycosaminoglycan (GAG) metabolism. Here, Dubail et al. identify genetic variants in the solute carrier family protein SLC10A7 in families with skeletal dysplasia and amelogenesis imperfecta that disrupt GAG synthesis.