Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition.

Pathogenic variants in ATP-dependent chromatin remodeling proteins are a recurrent cause of neurodevelopmental disorders (NDDs). The NURF complex consists of BPTF and either the SNF2H (SMARCA5) or SNF2L (SMARCA1) ISWI-chromatin remodeling enzyme. Pathogenic variants in BPTF and SMARCA5 were previously implicated in NDDs. Here, we describe 40 individuals from 30 families with de novo or maternally inherited pathogenic variants in SMARCA1. This novel NDD was associated with mild to severe ID/DD, delayed or regressive speech development, and some recurrent facial dysmorphisms. Individuals carrying SMARCA1 loss-of-function variants exhibited a mild genome-wide DNA methylation profile and a high penetrance of macrocephaly. Genetic dissection of the NURF complex using Smarca1, Smarca5, and Bptfsingle and double mouse knockouts revealed the importance of NURF composition and dosage for proper forebrain development. Finally, we propose that genetic alterations affecting different NURF components result in a NDD with a broad clinical spectrum.

Applying whole exome sequencing in a consanguineous population with autism spectrum disorder.

This study aimed to systematically assess the impact of clinical and demographic variables on the diagnostic yield of Whole Exome Sequencing (WES) when applied to children with Autism Spectrum Disorder (ASD) from a consanguineous population. Ninety-seven children were included in the analysis, 63% were male and 37% were females. 77.3% had a suspected syndromic aetiology of which 68% had co-existent central nervous system (CNS) clinical features, while 69% had other systems involved. The diagnostic yield of WES in our cohort with ASD was 34%. Children with seizures were more likely to have positive WES results (46% vs. 31%, p = 0.042). Probands with suspected syndromic ASD aetiology showed no significant differential impact on the diagnostic yield of WES.

Genetic Causes, Clinical Features, and Survival of Underlying Inborn Errors of Immunity in Omani Patients: a Single-Center Study.

PURPOSE: Early identification of inborn errors of immunity (IEIs) is crucial due to the significant risk of morbidity and mortality. This study aimed to describe the genetic causes, clinical features, and survival rate of IEIs in Omani patients. METHODS: A prospective study of all Omani patients evaluated for immunodeficiency was conducted over a 17-year period. Clinical features and diagnostic immunological findings were recorded. Targeted gene testing was performed in cases of obvious immunodeficiency. For cases with less conclusive phenotypes, a gene panel was performed, followed by whole-exome sequencing if necessary. RESULTS: A total of 185 patients were diagnosed with IEIs during the study period; of these, 60.5% were male. Mean ages at symptom onset and diagnosis were 30.0 and 50.5 months, respectively. Consanguinity and a family history of IEIs were present in 86.9% and 50.8%, respectively. Most patients presented with lower respiratory infections (65.9%), followed by growth and development manifestations (43.2%). Phagocytic defects were the most common cause of IEIs (31.9%), followed by combined immunodeficiency (21.1%). Overall, 109 of 132 patients (82.6%) who underwent genetic testing received a genetic diagnosis, while testing was inconclusive for the remaining 23 patients (17.4%). Among patients with established diagnoses, 37 genes and 44 variants were identified. Autosomal recessive inheritance was present in 81.7% of patients with gene defects. Several variants were novel. Intravenous immunoglobulin therapy was administered to 39.4% of patients and 21.6% received hematopoietic stem cell transplantation. The overall survival rate was 75.1%. CONCLUSION: This study highlights the genetic causes of IEIs in Omani patients. This information may help in the early identification and management of the disease, thereby improving survival and quality of life.

The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families.

Global Developmental Delay/Intellectual disability (ID) is the term used to describe various disorders caused by abnormal brain development and characterized by impairments in cognition, communication, behavior, or motor skills. In the past few years, whole-exome sequencing (WES) has been proven to be a powerful, robust, and scalable approach for candidate gene discoveries in consanguineous populations. In this study, we recruited 215 patients affected with ID from 118 Middle Eastern families. Whole-exome sequencing was completed for 188 individuals. The average age at which WES was completed was 8.5 years. Pathogenic or likely pathogenic variants were detected in 32/118 families (27%). Variants of uncertain significance were seen in 33/118 families (28%). The candidate genes with a possible association with ID were detected in 32/118 (27%) with a total number of 64 affected individuals. These genes are novel, were previously reported in a single family, or cause strikingly different phenotypes with a different mode of inheritance. These genes included: AATK, AP1G2, CAMSAP1, CCDC9B, CNTROB, DNAH14, DNAJB4, DRG1, DTNBP1, EDRF1, EEF1D, EXOC8, EXOSC4, FARSB, FBXO22, FILIP1, INPP4A, P2RX7, PRDM13, PTRHD1, SCN10A, SCYL2, SMG8, SUPV3L1, TACC2, THUMPD1, XPR1, ZFYVE28. During the 5 years of the study and through gene matching databases, several of these genes have now been confirmed as causative of ID. In conclusion, understanding the causes of ID will help understand biological mechanisms, provide precise counseling for affected families, and aid in primary prevention.

Uptake of prenatal genetic diagnosis and termination of pregnancy by Omani Muslim families at risk of genetic disorders: experience over a 9-year period.

Studies on the acceptance of prenatal diagnosis and termination of pregnancy for single gene disorders within Islamic societies in the Middle East are limited. A few have examined the attitudes toward pregnancy termination for fetal indications, but a dearth of published data exists on actual behavior and uptake. This study reports on all prenatal diagnosis requests for single gene disorders, from the Sultanate of Oman, over 9 years. A retrospective study was conducted during which the medical records of all women who performed prenatal diagnoses for single gene disorders were reviewed. A total of 148 invasive procedures were performed for 114 families. The total number of yearly requests for prenatal diagnosis increased exponentially from three in 2012 to 21 in 2020. Sixty-four different diagnoses were tested for with the majority being autosomal recessive in nature. Seventy-one percent (28/39) of cases where an affected pregnancy was identified were terminated. Fifty-two of the 114 women (45.6%) repeated prenatal diagnosis in a future pregnancy. Seventy-two couples (63%) were consanguineous parents related as second cousins or closer. The majority of tests performed were for couples from Muscat (27%), Albatinah (27%), and Alsharqiya (20.3%) governorates in Oman. The findings of this study provide evidence that prenatal diagnosis is an acceptable reproductive option to prevent the occurrence of genetic disorders that meet termination eligibility criteria as outlined by the Islamic Jurisprudence (Fiqh) Council Fatwa, among Omani Muslim couples.

Biallelic loss-of-function variants of GFRA1 cause lethal bilateral renal agenesis.

Bilateral renal agenesis belongs to a group of perinatal lethal renal diseases. To date, pathogenic variants in three genes (ITGA8, GREB1L, and FGF20) have been shown to cause renal agenesis in humans. Recently GFRA1 has been linked to a phenotype consistent with a nonsyndromic form of bilateral renal agenesis. GFRA1 encodes a member of the glial cell line-derived neurotrophic factor receptor family of proteins. The receptor on the Wolffian duct regulates ureteric bud outgrowth in developing a functional renal system. We report on four additional affected neonates from a consanguineous family who presented with a similar lethal phenotype whereby whole exome sequencing identified a homozygous deleterious sequence variant in GFRA1 (NM_005264.8:c.628G > T:p.[Gly210Ter]). The current study represents a second confirmation report on the causal association of GFRA1 pathogenic variants with lethal nonsyndromic bilateral renal agenesis in humans.

The experience of Preimplantation Genetic Testing (PGT) among Muslim couples in Oman in the Middle East.

Preimplantation genetic testing (PGT) is an alternative reproductive technology integrated with in vitro fertilization (IVF). It is a well-established technique offering a reproductive option for families at a high risk of transmitting a genetic disorder, allowing them to avoid making a decision about termination of an affected pregnancy (TOP). In Arab communities and particularly in Oman, where TOP is not favored under the majority of implemented Muslim law, termination of pregnancy for fetal indications is not always possible. As these communities are in favor of consanguineous marriage, they are at increased risk of serious and lethal autosomal recessive conditions, and as a result, PGT is a feasible option as a TOP decision can be avoided. However, undergoing PGT is relatively new in the Arab Muslim countries and Omani patients have only recently had access to the service. This qualitative study utilized a phenomenological approach to explore the experience of Omani families who had selected to undergo PGT as a means of reducing the risk of having a child affected with a genetic disorder. Fourteen participants from eight families who underwent PGT were interviewed. Data collected were analyzed using thematic analysis. The research identified four main themes: Anxiously waiting 'Taraqub'; Unforeseen; Secrecy; and Me and My Partner. The findings of the research have provided insight into the PGT experiences of Omani families. Unique cultural and religious perspectives should be considered when counseling Omani Muslim couples.

Spinocerebellar ataxia with axonal neuropathy type 1 revisited.

Spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1; OMIM #607250), an exceedingly rare disorder having been documented in only a single family from Saudi Arabia, is the result of an unusual mutation in the tyrosyl DNA phosphodiesterase 1 gene (TDP1). We performed high-throughput sequencing (whole exome and ataxia gene panel) in two apparently unrelated Omani families segregating sensorimotor neuropathy and ataxia in an autosomal recessive fashion. Following validation by Sanger sequencing, all affected subjects (n = 4) were confirmed to carry the known SCAN1 pathogenic homozygous variant in the TDP1 gene, NM_001008744.1:c.1478A > G (p.His493Arg). In keeping with the initial description, our patients demonstrated progressive ataxia, cerebellar atrophy and disabling axonal sensori-motor neuropathy (n = 4), hypercholesterolemia (n = 2) and elevated serum alpha fetoprotein (n = 3). In addition, our patients also had mild cognitive deficits in multiple domains (n = 3), a feature not previously reported. Our findings independently revalidate the phenotype of TDP1 mutation and expand the clinical spectrum to include mild cognitive deficits. Haplotype sharing, as determined by DNA microarray (CytoScan HD), attests to a possible common founder mutation in the Arab population.

Inborn errors of metabolism in a cohort of pregnancies with non-immune hydrops fetalis: a single center experience.

OBJECTIVE: The purpose of this study was to determine the frequency of non-immune hydrops fetalis (NIHF) among all pregnancies referred for prenatal care at Sultan Qaboos University Hospital (SQUH) during the study period and to evaluate the underlying etiologies of NIH. STUDY DESIGN: All pregnancies referred to SQUH between February 2014 and December 2015 were identified, and all pregnancies meeting the diagnosis of NIHF were included in this study. All cases of NIHF referred to our center during this period underwent standard systematic diagnostic work-up that included biochemical and molecular studies in addition to the standard investigations for hydrops fetalis. Clinical characteristics and results of the diagnostic work-up were retrospectively reviewed. RESULTS: A total of 3234 pregnancies were referred for prenatal care at SQUH during the study period, and 12 pregnancies were affected by NIHF. An underlying diagnosis was established in nine cases, and the majority of cases (7/9) were caused by inborn errors of metabolism (IEM). These included a novel homozygous variant in the AARS2 gene (5/7) and two cases of galactosialidosis (2/7). CONCLUSION: IEM was a major cause of NIHF in this cohort. The AARS2 variant accounts for a significant number of cases with NIHF in this cohort of Omani patients.

Segmental Spinal Muscular Atrophy Localised to the Lower Limbs: First case from Oman.

Spinal muscular atrophy (SMA) is a genetic lower motor neuron disease. It usually involves all of the skeletal muscles innervated by the anterior horn cells of the spinal cord. In rare cases, there is also localised involvement of the spinal cord. We report a 10-year-old boy who presented to the Sultan Qaboos University Hospital, Muscat, Oman, in 2015 with muscle weakness restricted to the lower limbs. The presence of a homozygous deletion within the survival of motor neuron 1 gene confirmed the diagnosis of SMA. To the best of the authors' knowledge, this is the first report of an Omani patient with segmental SMA involving only the lower limbs. Treatment for this rare and relatively benign form of SMA is symptomatic and includes physiotherapy.

Occurrence of Optic Neuritis and Cervical Cord Schwannoma with Charcot-Marie-Tooth Type 4B1 Disease.

Charcot-Marie-Tooth neuropathy type 4B1 (CMT4B1) disease is a rare subtype of CMT4 with reported association of facial weakness, vocal cord paresis, chest deformities, and claw hands. We report the unusual occurrence of optic neuritis and cervical cord schwannoma in a male individual with confirmed CMT4B1 disease. Sequencing of the MTMR2 gene revealed a novel nonsense homozygous mutation c.1768C>T (p.Gln590*). The mutation was identified in affected relatives of the proband and a second, apparently unrelated, family. The rare association of optic neuritis or schwannoma with genetically confirmed CMT1A has been individually observed, but never with recessive CMT. To the best of our knowledge, the occurrence of optic neuritis and cervical cord schwannoma in the same patient has never been reported with any form of CMT including CMT4B1. In similar cases, we recommend immediate medical attention to rule out the possibility of schwannomas in patients with all demyelinating CMT subtypes in case of the development of focal neurological signs or acute worsening of clinical status.

EPG5-related Vici syndrome: a paradigm of neurodevelopmental disorders with defective autophagy.

Vici syndrome is a progressive neurodevelopmental multisystem disorder due to recessive mutations in the key autophagy gene EPG5. We report genetic, clinical, neuroradiological, and neuropathological features of 50 children from 30 families, as well as the neuronal phenotype of EPG5 knock-down in Drosophila melanogaster. We identified 39 different EPG5 mutations, most of them truncating and predicted to result in reduced EPG5 protein. Most mutations were private, but three recurrent mutations (p.Met2242Cysfs*5, p.Arg417*, and p.Gln336Arg) indicated possible founder effects. Presentation was mainly neonatal, with marked hypotonia and feeding difficulties. In addition to the five principal features (callosal agenesis, cataracts, hypopigmentation, cardiomyopathy, and immune dysfunction), we identified three equally consistent features (profound developmental delay, progressive microcephaly, and failure to thrive). The manifestation of all eight of these features has a specificity of 97%, and a sensitivity of 89% for the presence of an EPG5 mutation and will allow informed decisions about genetic testing. Clinical progression was relentless and many children died in infancy. Survival analysis demonstrated a median survival time of 24 months (95% confidence interval 0-49 months), with only a 10th of patients surviving to 5 years of age. Survival outcomes were significantly better in patients with compound heterozygous mutations (P = 0.046), as well as in patients with the recurrent p.Gln336Arg mutation. Acquired microcephaly and regression of skills in long-term survivors suggests a neurodegenerative component superimposed on the principal neurodevelopmental defect. Two-thirds of patients had a severe seizure disorder, placing EPG5 within the rapidly expanding group of genes associated with early-onset epileptic encephalopathies. Consistent neuroradiological features comprised structural abnormalities, in particular callosal agenesis and pontine hypoplasia, delayed myelination and, less frequently, thalamic signal intensity changes evolving over time. Typical muscle biopsy features included fibre size variability, central/internal nuclei, abnormal glycogen storage, presence of autophagic vacuoles and secondary mitochondrial abnormalities. Nerve biopsy performed in one case revealed subtotal absence of myelinated axons. Post-mortem examinations in three patients confirmed neurodevelopmental and neurodegenerative features and multisystem involvement. Finally, downregulation of epg5 (CG14299) in Drosophila resulted in autophagic abnormalities and progressive neurodegeneration. We conclude that EPG5-related Vici syndrome defines a novel group of neurodevelopmental disorders that should be considered in patients with suggestive features in whom mitochondrial, glycogen, or lysosomal storage disorders have been excluded. Neurological progression over time indicates an intriguing link between neurodevelopment and neurodegeneration, also supported by neurodegenerative features in epg5-deficient Drosophila, and recent implication of other autophagy regulators in late-onset neurodegenerative disease.

Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of Patients with Autism Spectrum Disorders from a Highly Consanguineous Population.

Autism Spectrum Disorders are a complicated group of disorders characterized with heterogeneous genetic etiologies. The genetic investigations for this group of disorders have expanded considerably over the past decade. In our study we designed a tired approach and studied the diagnostic yield of chromosomal microarray analysis on patients referred to the Genetic and Developmental Medicine clinic in Sultan Qaboos University in Oman for autism spectrum disorders in a highly consanguineous population. Copy number variants were seen in 27% of our studied cohort of patients and it was strongly associated with dysmorphic features and congenital anomalies.

Existing challenges associated with offering prenatal genetic diagnosis in an Arab society in the Sultanate of Oman.

The incidence of congenital anomalies and/or genetic disorders in the Omani population has reached figures greater than double the global statistics. Preference for consanguineous unions together with the fact that termination of pregnancy in Muslim communities are largely avoided, have been highlighted as contributing factors. This overview identifies a third significant aspect contributing to the elevated rate of genetic disorders in the Omani population. Namely, a lack of services that are able to offer termination of pregnancy for severe congenital anomalies, to requesting parents. In this report we select an unusual case of a family at risk for two distinct genetic disorders--6q micro-deletion and unbalanced products of conception attributed to a balanced parental translocation involving chromosome 3 and 13, to portray and examine the current situation faced by Omani couples interested in prenatal diagnosis for termination of pregnancy. Additional challenges and pitfalls to developing a prenatal diagnostic service as part of the genetic service in Oman are discussed.

Predictive genetic testing in children: constitutional mismatch repair deficiency cancer predisposing syndrome.

Biallelic germline mutations in mismatch repair genes predispose to constitutional mismatch repair deficiency syndrome (CMMR-D). The condition is characterized by a broad spectrum of early-onset tumors, including hematological, brain and bowel and is frequently associated with features of Neurofibromatosis type 1. Few definitive screening recommendations have been suggested and no published reports have described predictive testing. We report on the first case of predictive testing for CMMR-D following the identification of two non-consanguineous parents, with the same heterozygous mutation in MLH1: c.1528C > T. The genetic counseling offered to the family, for their two at-risk daughters, is discussed with a focus on the ethical considerations of testing children for known cancer-causing variants. The challenges that are encountered when reporting on heterozygosity in a child younger than 18 years (disclosure of carrier status and risk for Lynch syndrome), when discovered during testing for homozygosity, are addressed. In addition, the identification of CMMR-D in a three year old, and the recommended clinical surveillance that was proposed for this individual is discussed. Despite predictive testing and presymptomatic screening, the sudden death of the child with CMMR-D syndrome occurred 6 months after her last surveillance MRI. This report further highlights the difficulty of developing guidelines, as a result of the rarity of cases and diversity of presentation.

An update on ocular involvement in mucopolysaccharidoses.

PURPOSE OF REVIEW: The purpose of this review is to provide an update on ocular manifestations of mucopolysaccharidoses (MPS), to highlight diagnostic pitfalls in the evaluation of affected patients, and to briefly review etiopathogenesis, systemic manifestations, and therapeutic interventions in MPS. RECENT FINDINGS: Advances in hematopoietic stem cell transplantation and enzyme replacement therapy for MPS have led to decreased morbidity and increased life-span of patients. Besides other causes, visual impairment because of corneal opacification, retinal degeneration, and optic atrophy remains a common cause of disability in MPS. The application of a standard ophthalmic evaluation protocol may serve as an important diagnostic and disease monitoring tool in patients. SUMMARY: Diagnostic delays are not uncommon in patients with MPS. Given the early ocular involvement in MPS, ophthalmologists play a crucial role in early detection and follow-up of patients with MPS. Ophthalmic evaluation can be impeded by corneal opacification and patient cooperation. Altered corneal biomechanics confound intraocular pressure measurements. Recently developed therapies have made early detection increasingly important. Accurate diagnosis of specific MPS subtypes is of paramount importance for initiating appropriate therapy. Combined with advances in supportive care of ocular and systemic manifestations, the prognosis for patients with MPS has vastly improved.

Communicating cancer risk within an African context: experiences, disclosure patterns and uptake rates following genetic testing for Lynch syndrome.

OBJECTIVE: Data pertaining to Lynch syndrome within a developing country are sparse. This study explored the emotional reaction to a mutation-positive test result among a group of individuals from South Africa. As genetic information is not only limited to the individual but extends to the biological family, communication patterns and uptake of testing among at-risk family members was also investigated. METHODS: Eighty individuals participated in this qualitative interview study. RESULTS: Eight emotional reactions were observed, of which two were of particular concern: (1) secrecy due to disbelief and (2) interpretation of a mutation-positive result as a cancer diagnosis. Disclosure rates of personal genetic test results were high to family members, but low to general healthcare providers. Disclosing the test result was not always followed by a discussion of implications of the genetic information or availability of predictive testing for at-risk family members. The uptake rate of predictive testing among the participants' siblings and children was 97% and 73.6%, respectively. CONCLUSION: Awareness of concerning emotional reactions following the delivery of a genetic test result and insight into disclosure patterns, especially the information that is not communicated, will prove beneficial in improving the effectiveness of counselling and management in Lynch syndrome families. PRACTICE IMPLICATIONS: Implementation of these findings into the PT programme will have a positive effect on the genetic counseling process.

A mobile colonoscopic unit for lynch syndrome: trends in surveillance uptake and patient experiences of screening in a developing country.

The Genetic and Endoscopic Surveillance Clinic is an annual outreach service offering accessible colonoscopic surveillance to known families with Lynch syndrome living in remote areas of the Western and Northern Cape Province of South Africa. Unfortunately attendance at this outreach clinic has been declining over several years and fewer than a quarter of participants, attending for surveillance, have been adherent with all their recommended screening appointments. Concerns exist for non-adherent individuals as screening can prevent colorectal cancer by removing the precancerous lesion or enabling the treatment of a malignancy at an early stage. This study explored the experience of surveillance from both the non-adherers' and adherers' perspectives and identified unique factors affecting attendance at the outreach clinic. Rates of compliance are calculated for 191 mutation-positive cases of Lynch syndrome, using strict attendance criteria, and compared to figures obtained from self-reported attendance. Non-compliance was under-reported and compliance was exaggerated when basing data on self-reported adherence to recommendations. Specific characteristics of the outreach clinic affecting compliance are identified and recommendations are made to facilitate improvements to the service. These improvements can result in increased compliance with screening regimens and ultimately reduce cancer-related mortality.