Expanding the clinical spectrum of cytosolic phosphoenolpyruvate carboxykinase deficiency: novel PCK1 variants in four Arabian Gulf families.

BACKGROUND: In metabolic stress, the cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) enzyme is involved in energy production through the gluconeogenesis pathway. PEPCK-C deficiency is a rare childhood-onset autosomal recessive metabolic disease caused by PCK1 genetic defects. Previous studies showed a broad clinical spectrum ranging from asymptomatic to recurrent hypoglycemia with/without lactic acidosis, encephalopathy, seizures, and liver failure. RESULTS: In this article, we discuss the occurrence of PEPCK-C deficiency in four families from the United Arab Emirates and Oman. All patients presented with unexplained hypoglycemia as a common feature. Two out of the seven patients presented with episodes of encephalopathy that resulted in seizures and neuroregression leading to global developmental delay and one patient had a neonatal presentation. Observed biochemical abnormalities include elevated lactate, transaminases, and tricarboxylic acid cycle metabolites in most patients. Elevated creatine kinase was documented in two patients. Whole exome sequencing revealed two novel (c.574T > C, and c.1268 C > T) and a previously reported splice site (c.961 + 1G > A) PCK1 variant in the affected families. CONCLUSION: Patients become vulnerable during intercurrent illness; thus, prevention and prompt reversal of a catabolic state are crucial to avoid irreversible brain damage. This report will help to expand the clinical understanding of this rare disease and recommends screening for PEPCK-C deficiency in unexplained hypoglycemia.

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.

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.

A SWOT analysis of parent-mediated intervention for children with autism spectrum disorder: Oman as a Regional Model.

The prevalence of autism in the Arabian Gulf region is on the rise leading to overstretching of the pre-existing intervention services. The World Health Organization Caregiver Skills Training Program is a novel renovation being studied around the globe to overcome the scarcity of resources, improve autistic children's outcome and empower parents with comparable results to therapist-based models. Recently, Oman achieved great success in advocating for autism and initiated the first screening program for autism in the region. This review aims to use a Strength, Weakness, Opportunities and Threats (SWOT) analysis matrix to investigate the potential for using a parent-mediated intervention program as a supplementary approach to the currently used therapist-based intervention model in the country as an example for Gulf region.

Further phenotypic delineation of Alazami syndrome.

Alazami syndrome (AS) is an autosomal recessive condition characterized by the cardinal features of severe growth restriction, moderate to severe intellectual disability, and distinctive facial features. Biallelic pathogenic variants of the LARP7, encoding a chaperone of 7SK noncoding RNA, is implicated in this disease. There are <35 reported cases in the literature. All reported cases share the same three cardinal features of the syndrome. Herein, we report on 12 patients with a confirmed diagnosis of AS from eight unrelated families. The cohort shares the same key feature of the syndrome. Moreover, we report additional phenotypic features, including genito-renal anomalies, ophthalmological abnormalities, and congenital heart disease. Whole-exome sequencing was used in all reported cases, implicating a clinical under-recognition of the syndrome. This report further expands the clinical and molecular characteristics of Alazami syndrome.

THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder.

Covalent tRNA modifications play multi-faceted roles in tRNA stability, folding, and recognition, as well as the rate and fidelity of translation, and other cellular processes such as growth, development, and stress responses. Mutations in genes that are known to regulate tRNA modifications lead to a wide array of phenotypes and diseases including numerous cognitive and neurodevelopmental disorders, highlighting the critical role of tRNA modification in human disease. One such gene, THUMPD1, is involved in regulating tRNA N4-acetylcytidine modification (ac4C), and recently was proposed as a candidate gene for autosomal-recessive intellectual disability. Here, we present 13 individuals from 8 families who harbor rare loss-of-function variants in THUMPD1. Common phenotypic findings included global developmental delay, speech delay, moderate to severe intellectual deficiency, behavioral abnormalities such as angry outbursts, facial dysmorphism, and ophthalmological abnormalities. We demonstrate that the bi-allelic variants identified cause loss of function of THUMPD1 and that this defect results in a loss of ac4C modification in small RNAs, and of individually purified tRNA-Ser-CGA. We further corroborate this effect by showing a loss of tRNA acetylation in two CRISPR-Cas9-generated THUMPD1 KO cell lines. In addition, we also show the resultant amino acid substitution that occurs in a missense THUMPD1 allele identified in an individual with compound heterozygous variants results in a marked decrease in THUMPD1 stability and RNA-binding capacity. Taken together, these results suggest that the lack of tRNA acetylation due to THUMPD1 loss of function results in a syndromic form of intellectual disability associated with developmental delay, behavioral abnormalities, hearing loss, and facial dysmorphism.

Intellectual Profile of Children with Autism Spectrum Disorder: Identification of verbal and nonverbal subscales predicting intelligence quotient.

OBJECTIVES: This study aimed to explore the intelligence quotient (IQ) profile among children with autism spectrum disorder (ASD) and identify the most important subscales that predict the IQ. The analysis of an intellectual profile with age and gender differentials and the identification of a battery of subscales of intelligence are important for clinical management of ASD among children and for facilitating placement for remedial and educational services. METHODS: Data were collected through an exploratory study of 100 children aged between three and 13 years, who were referred to the department of child health and development in Sultan Qaboos University Hospital, a tertiary hospital, in Oman between June 2016 and June 2019. RESULTS: Among the 100 participants of this study, 79% were male, resulting in a male-female ratio of 4:1. The mean of full-scale IQ was found to be 68.6 ± 18.1. Furthermore, the mean of nonverbal IQ (73.5 ± 17.5) was significantly higher than that of verbal IQ (65.5 ± 17.6). Finally, more than half (61%) of the children were observed to have had mild to moderate impairment in their IQ levels. CONCLUSIONS: Age and gender showed no significant association with IQ level. The regression analysis identified nonverbal fluid reasoning, nonverbal visual-spatial processing, nonverbal working memory and verbal knowledge as the significant predictors of total IQ. The crucial dimensions of verbal and nonverbal IQ identified in this study can be used to evaluate complicated cases.

Parental Age and the Risk of Autism Spectrum Disorder in Oman: A case-control study.

OBJECTIVES: This study aimed at evaluating advanced parental age as a risk factor for autism spectrum disorder (ASD) in an Omani cohort. METHODS: This case-control study compared 278 ASD cases with 722 gender-matched controls, retrieved from the electronic records of the Developmental Paediatric Clinic, Sultan Qaboos University Hospital, Muscat, Oman, between January 2015 and June 2016. RESULTS: Most ASD cases were male (76.6%) and mostly diagnosed between 3-4 years of age, with more than 50% of the cases originating from Muscat and Batinah governorates. Compared to controls, mothers from the case group had significantly higher educational levels (post-secondary education versus high school/no formal education: odds ratio [OR] = 1.62, 95% confidence interval [CI]: 1.197-2.192). In a multivariate logistic regression, the OR of maternal age as a risk for ASD increased dramatically with advancing age category (using age <25 as reference, OR = 3.39, 6.12, 7.86 and 13.13 for age categories 25-29, 30-34, 35-39 and ≥40 years, respectively). The ORs of advancing paternal age as a risk for ASD were also statistically significant (using age <30 as reference, OR = 2.20, 2.36 and 3.12 for age categories 30-34, 35-39 and 40-44 years, respectively); however, there was a drop in the effect with paternal age ≥45 years (OR = 1.42; 95% CI: 0.64-3.15). CONCLUSION: Both maternal and paternal increased age were associated with a higher risk of ASD; however, the association was more pronounced and more consistent with advanced maternal age compared to paternal age.

LHFPL5 mutation: A rare cause of non-syndromic autosomal recessive hearing loss.

Hearing loss is a debilitating disorder that impairs language acquisition, resulting in disability in children and potential isolation in adulthood. Its onset can have a genetic basis, though environmental factors, which are often preventable, can also cause the condition. The genetic forms are highly heterogeneous, and early detection is necessary to arrange appropriate patient support. Here we report the molecular basis of hereditary hearing loss in a consanguineous family with multiple affected members from Oman. Combining homozygosity mapping with whole exome sequencing identified a novel homozygous nucleotide substitution c.575T > C in the lipoma HMGIC fusion partner-like 5 gene (LHFPL5), that converted the 192nd amino acid residue in the protein from a leucine to a proline, p.(Leu192Pro). Sanger sequencing confirmed segregation with the disease phenotype as expected for a recessive condition and the variant was absent in 123,490 subjects from various disease-specific and population genetic studies as well as 150 unrelated individuals and 35 deaf patients of Omani ethnicity. This study, which describes a novel LHFPL5 mutation in a family of Omani origin with hereditary hearing loss, supports previous clinical descriptions of the condition and contributes to the genetic spectrum of mutations in this form of deafness.

Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits.

Recently, with the advancement in next generation sequencing (NGS) along with the improvement of bioinformatics tools, whole exome sequencing (WES) has become the most efficient diagnostic test for patients with intellectual disability (ID). This study aims to estimate the yield of a reanalysis of ID negative exome cases after data reannotation. Total of 50 data files of exome sequencing, representing 50 samples were collected. The inclusion criteria include ID phenotype, and previous analysis indicated a negative result (no abnormality detected). These files were pre-processed and reannotated using ANNOVAR tool. Prioritized variants in the 50 cases studied were classified into three groups, (1) disease-causative variants (2) possible disease-causing variants and (3) variants in novel genes. Reanalysis resulted in the identification of pathogenic/likely pathogenic variants in six cases (12%). Thirteen cases (26%) were classified as having possible disease-causing variants. Candidate genes requiring future functional studies were detected in seven cases (14%). Improvement in bioinformatics tools, update in the genetic databases and literature, and patients' clinical phenotype update were the main reasons for identification of these variants in this study.

Coexistence of Autism Spectrum Disorders Among Three Children with Tuberous Sclerosis Complex: Case reports and review of literature.

Tuberous sclerosis complex (TSC) is a multisystem neurocutaneous disorder inherited in an autosomal dominant manner and characterised by benign tumours in the brain and other vital organs such as the heart, eyes, kidneys, skin and lungs. Links between autism spectrum disorder (ASD) and TSC have been postulated for many decades, with TSC considered to be one of the main syndromic causes of ASD; however, precise confirmation of a relationship between these two disorders required validated diagnostic tools. Fortunately, accurate evaluation of this relationship is now possible with standardised criteria for ASD diagnosis. We report three children who presented to the Sultan Qaboos University Hospital, Muscat, Oman, between 2014 and 2015 with ASD and TSC. These cases demonstrate the spectrum of neuropsychiatric involvement in TSC and highlight the importance of screening children with TSC for ASD features in order to encourage the early enrolment of these children in educational and rehabilitation programmes.

Homozygous single base deletion in TUSC3 causes intellectual disability with developmental delay in an Omani family.

Intellectual disability (ID) is the term used to describe a diverse group of neurological conditions with congenital or juvenile onset, characterized by an IQ score of less than 70 and difficulties associated with limitations in cognitive function and adaptive behavior. The condition can be inherited or caused by environmental factors. The genetic forms are heterogeneous, with mutations in over 500 known genes shown to cause the disorder. We report a consanguineous Omani family in which multiple individuals have ID and developmental delay together with some variably present features including short stature, microcephaly, moderate facial dysmorphism, and congenital malformations of the toes or hands. Homozygosity mapping combined with whole exome next generation sequencing identified a novel homozygous single base pair deletion in TUSC3, c.222delA, p.R74 fs. The mutation segregates with the disease phenotype in a recessive manner and is absent in 60,706 unrelated individuals from various disease-specific and population genetic studies. TUSC3 mutations have been previously identified as causing either syndromic or non-syndromic ID in patients from France, Italy, Iran and Pakistan. This paper supports the previous clinical descriptions of the condition caused by TUSC3 mutations and describes the seventh family with mutations in this gene, thus contributing to the genetic spectrum of mutations. This is the first report of a family from the Arabian peninsula with this form of ID. © 2016 Wiley Periodicals, Inc.

Comorbidity of Learning Disorders and Attention Deficit Hyperactivity Disorder in a Sample of Omani Schoolchildren.

OBJECTIVES: The estimated worldwide prevalence of learning disorders (LDs) is approximately 2-10% among school-aged children. LDs have variable clinical features and are often associated with other disorders. This study aimed to examine the comorbidity of LDs and attention deficit hyperactivity disorder (ADHD) among a sample of schoolchildren in Oman. METHODS: This study was conducted between January 2014 and January 2015 at the Sultan Qaboos University, Muscat, Oman. The Learning Disabilities Diagnostic Inventory (LDDI) and the 28-item version of the Conners' Teacher Rating Scale was completed by classroom teachers to determine the existence of LD and ADHD symptoms in 321 children in grades 1-4 who had been referred to a learning support unit for LDs from elementary schools in Muscat. RESULTS: The mean age of the students was 8.5 years. Among the cohort, 30% were reported to have symptoms of ADHD, including conduct problems (24%), hyperactivity (24%) and inattentive-passive behaviours (41%). Male students reportedly exhibited greater conduct problems and hyperactivity than females. However, there were no gender differences noted between LDDI scores. CONCLUSION: This study suggests that Omani schoolchildren with LDs are likely to exhibit signs of ADHD. The early identification of this disorder is essential considering the chronic nature of ADHD. For interventional purposes, multidisciplinary teams are recommended, including general and special educators, clinical psychologists, school counsellors, developmental or experienced general paediatricians and child psychiatrists.

De Novo Duplication of 7p21.1p22.2 in a Child with Autism Spectrum Disorder and Craniofacial Dysmorphism.

The duplication of the short arm of chromosome 7 as de novo is extremely rare. The phenotype spectrum varies depending on the region of duplication. We report a case of de novo duplication of chromosomal region 7p21.1p22.2 in a three-year-old male child with autism who presented to the Sultan Qaboos University Hospital in Muscat, Oman, in January 2012. The patient was diagnosed with craniofacial dysmorphism, global developmental delay, hypotonia and bilateral cryptorchidism. The duplication was detected by conventional G-banded karyotype analysis/fluorescence in situ hybridisation and confirmed by array comparative genomic hybridisation. To the best of the authors' knowledge, this is the first report of chromosomal region 7p21.1 involvement in an autistic patient showing features of a 7p duplication phenotype. Identifying genes in the duplicated region using molecular techniques is recommended to promote characterisation of the phenotype and associated condition. It may also reveal the possible role of these genes in autism spectrum disorder.

Incidence and Risk Factors of Parenteral Nutrition-Associated Cholestasis in Omani Neonates: Single centre experience.

OBJECTIVES: Parenteral nutrition-associated cholestasis (PNAC) is one of the most challenging complications of prolonged parenteral nutrition (PN) in neonates. There is a lack of research investigating its incidence in newborn infants in Oman and the Arab region. Therefore, this study aimed to assess the incidence of PNAC and its risk factors in Omani neonates. METHODS: This retrospective study took place between January and April 2014. All neonates who received PN for ≥14 days during a four-year period (June 2009 to May 2013) at the neonatal intensive care unit (NICU) in Sultan Qaboos University Hospital, Muscat, Oman, were enrolled. RESULTS: A total of 1,857 neonates were admitted to the NICU over the study period and 135 neonates (7.3%) received PN for ≥14 days. Determining the incidence of PNAC was only possible in 97 neonates; of these, 38 (39%) had PNAC. The main risk factors associated with PNAC were duration of PN, duration of enteral starvation, gastrointestinal surgeries, blood transfusions and sepsis. Neonates with PNAC had a slightly higher incidence of necrotising enterocolitis in comparison to those without PNAC. CONCLUSION: This study found a PNAC incidence of 39% in Omani neonates. There were several significant risk factors for PNAC in Omani neonates; however, after logistic regression analysis, only total PN duration remained statistically significant. Preventive strategies should be implemented in NICUs so as to avoid future chronic liver disease in this population.

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.

Consanguinity, endogamy and inborn errors of metabolism in Oman: a cross-sectional study.

The Sultanate of Oman, like many other Arab countries, has relatively high rates of consanguinity. Reports suggest that the incidence of inborn errors of metabolism (IEM) is also high in Oman. This retrospective cross-sectional study was designed to evaluate the number of patients with IEM being followed at the only two tertiary centers in Oman treating such patients, and to calculate the consanguinity rates among these families. The electronic medical records of all patients were reviewed for demographic and clinical characteristics. A total of 285 patients with IEM were being followed at the 2 centers involved; 162 (56.8%) were male and 123 (43.2%) were female. The history of consanguinity was documented or available for 241 patients: 229 patients (95%) were born to consanguineous parents related as second cousins or closer. First-cousin marriages were reported in 191 families (79.3%), while 31 patients (12.9%) were born to second cousins. The parents of 5 patients (2%) were related as double first cousins, and 2 patients (1%) were born to first cousins once removed. The average coefficient of inbreeding (F) in our study was 0.081. Seventeen patients (6%) had associated comorbid conditions other than IEM. Our study highlights the clinical burden of IEM in Oman and emphasizes the high consanguinity rates among the parents of affected patients.