Congenital Disorders of Glycosylation in Portugal-Two Decades of Experience.

OBJECTIVE: To describe the clinical, biochemical, and genetic features of both new and previously reported patients with congenital disorders of glycosylation (CDGs) diagnosed in Portugal over the last 20 years. STUDY DESIGN: The cohort includes patients with an unexplained multisystem or single organ involvement, with or without psychomotor disability. Serum sialotransferrin isoforms and, whenever necessary, apolipoprotein CIII isoforms and glycan structures were analyzed. Additional studies included measurement of phosphomannomutase (PMM) activity and analysis of lipid-linked oligosaccharides in fibroblasts. Sanger sequencing and massive parallel sequencing were used to identify causal variants or the affected gene, respectively. RESULTS: Sixty-three individuals were diagnosed covering 14 distinct CDGs; 43 patients diagnosed postnatally revealed a type 1, 14 a type 2, and 2 a normal pattern on serum transferrin isoelectrofocusing. The latter patients were identified by whole exome sequencing. Nine of them presented also a hypoglycosylation pattern on apolipoprotein CIII isoelectrofocusing, pointing to an associated O-glycosylation defect. Most of the patients (62%) are PMM2-CDG and the remaining carry pathogenic variants in ALG1, ATP6AP1, ATP6AP2, ATP6V0A2, CCDC115, COG1, COG4, DPAGT1, MAN1B1, SLC35A2, SRD5A3, RFT1, or PGM1. CONCLUSIONS: Portuguese patients with CDGs are presented in this report, some of them showing unique clinical phenotypes. Among the 14 genes mutated in Portuguese individuals, 8 are shared with a previously reported Spanish cohort. However, regarding the mutational spectrum of PMM2-CDG, the most frequent CDG, a striking similarity between the 2 populations was found, as only 1 mutated allele found in the Portuguese group has not been reported in Spain.

Functional analysis of splicing mutations in the IDS gene and the use of antisense oligonucleotides to exploit an alternative therapy for MPS II.

Mucopolysaccharidosis II is a lysosomal storage disorder caused by mutations in the IDS gene, including exonic alterations associated with aberrant splicing. In the present work, cell-based splicing assays were performed to study the effects of two splicing mutations in exon 3 of IDS, i.e., c.241C>T and c.257C>T, whose presence activates a cryptic splice site in exon 3 and one in exon 8, i.e., c.1122C>T that despite being a synonymous mutation is responsible for the creation of a new splice site in exon 8 leading to a transcript shorter than usual. Mutant minigene analysis and overexpression assays revealed that SRSF2 and hnRNP E1 might be involved in the use and repression of the constitutive 3' splice site of exon 3 respectively. For the c.1122C>T the use of antisense therapy to correct the splicing defect was explored, but transfection of patient fibroblasts with antisense morpholino oligonucleotides (n=3) and a locked nucleic acid failed to abolish the abnormal transcript; indeed, it resulted in the appearance of yet another aberrant splicing product. Interestingly, the oligonucleotides transfection in control fibroblasts led to the appearance of the aberrant transcript observed in patients' cells after treatment, which shows that the oligonucleotides are masking an important cis-acting element for 5' splice site regulation of exon 8. These results highlight the importance of functional studies for understanding the pathogenic consequences of mis-splicing and highlight the difficulty in developing antisense therapies involving gene regions under complex splicing regulation.

Cost-effective control of plant disease when epidemiological knowledge is incomplete: modelling Bahia bark scaling of citrus.

A spatially-explicit, stochastic model is developed for Bahia bark scaling, a threat to citrus production in north-eastern Brazil, and is used to assess epidemiological principles underlying the cost-effectiveness of disease control strategies. The model is fitted via Markov chain Monte Carlo with data augmentation to snapshots of disease spread derived from a previously-reported multi-year experiment. Goodness-of-fit tests strongly supported the fit of the model, even though the detailed etiology of the disease is unknown and was not explicitly included in the model. Key epidemiological parameters including the infection rate, incubation period and scale of dispersal are estimated from the spread data. This allows us to scale-up the experimental results to predict the effect of the level of initial inoculum on disease progression in a typically-sized citrus grove. The efficacies of two cultural control measures are assessed: altering the spacing of host plants, and roguing symptomatic trees. Reducing planting density can slow disease spread significantly if the distance between hosts is sufficiently large. However, low density groves have fewer plants per hectare. The optimum density of productive plants is therefore recovered at an intermediate host spacing. Roguing, even when detection of symptomatic plants is imperfect, can lead to very effective control. However, scouting for disease symptoms incurs a cost. We use the model to balance the cost of scouting against the number of plants lost to disease, and show how to determine a roguing schedule that optimises profit. The trade-offs underlying the two optima we identify-the optimal host spacing and the optimal roguing schedule-are applicable to many pathosystems. Our work demonstrates how a carefully parameterised mathematical model can be used to find these optima. It also illustrates how mathematical models can be used in even this most challenging of situations in which the underlying epidemiology is ill-understood.

Infestation dynamics of Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) in citrus orchards as affected by edaphic and climatic variables.

Brevipalpus phoenicis (Geijskes) is a cosmopolitan and polyphagous mite that transmits important phytoviruses, such as coffee ringspot virus, passion fruit green spot virus and Citrus leprosis virus C. To characterise the dynamics of the probability and the rate of B. phoenicis infestation in response to edaphic and climatic factors, monthly inspections were performed in nine orchards in a citrus region of the State of Bahia, Brazil, for 35 months. Three fruits per plant were examined using a magnifying glass (10×) on 21 plants distributed along a "W"-shaped path in each orchard. Meteorological data were collected from a conventional station. To determine the correlations among the climatic variables, the data were analysed using Spearman correlations. Variables were selected by principal component analysis, and those that contributed the most to differentiate the groups were evaluated via a Mann-Whitney test. Using the quantile-quantile method, the limit values for the following climatic variables were determined: temperature (24.5 °C), photoperiod (12 h), relative humidity (83%), evapotranspiration (71 mm) and rainy days (14 days). The combination of longer days, higher temperatures, lower relative humidity levels and lower evapotranspiration increased the probability of B. phoenicis infestation, whereas successive rain events decreased that risk. Infestation rates were negatively affected by relative humidity levels above 83% and were positively affected by a decreasing available soil-water fraction and increasing insolation and photoperiod.

Understanding Hypertriglyceridemia: Integrating Genetic Insights.

Hypertriglyceridemia is an exceptionally complex metabolic disorder characterized by elevated plasma triglycerides associated with an increased risk of acute pancreatitis and cardiovascular diseases such as coronary artery disease. Its phenotype expression is widely heterogeneous and heavily influenced by conditions as obesity, alcohol consumption, or metabolic syndromes. Looking into the genetic underpinnings of hypertriglyceridemia, this review focuses on the genetic variants in LPL, APOA5, APOC2, GPIHBP1 and LMF1 triglyceride-regulating genes reportedly associated with abnormal genetic transcription and the translation of proteins participating in triglyceride-rich lipoprotein metabolism. Hypertriglyceridemia resulting from such genetic abnormalities can be categorized as monogenic or polygenic. Monogenic hypertriglyceridemia, also known as familial chylomicronemia syndrome, is caused by homozygous or compound heterozygous pathogenic variants in the five canonical genes. Polygenic hypertriglyceridemia, also known as multifactorial chylomicronemia syndrome in extreme cases of hypertriglyceridemia, is caused by heterozygous pathogenic genetic variants with variable penetrance affecting the canonical genes, and a set of common non-pathogenic genetic variants (polymorphisms, using the former nomenclature) with well-established association with elevated triglyceride levels. We further address recent progress in triglyceride-lowering treatments. Understanding the genetic basis of hypertriglyceridemia opens new translational opportunities in the scope of genetic screening and the development of novel therapies.

A Case of Amyloid Goitre in Heavy Chain Amyloidosis: Diagnostic Challenges and Clinical Implications.

Immunoglobulin heavy chain amyloidosis (AH amyloidosis) is an extremely rare subtype of immunoglobulin-derived amyloidosis and there is limited literature on how to diagnose and manage this disorder. We describe a rare case of AH amyloidosis with amyloid goitre and the importance of mass spectrometry in the identification of the different types of amyloids. While additional studies are needed, several observations suggest important practical implications, including differences in clinical picture, prognosis, and pathologic diagnosis. LEARNING POINTS: Immunoglobulin heavy chain amyloidosis is an extremely rare subtype of immunoglobulin-derived amyloidosis and amyloid goitre is even rarer.There is limited literature on how to diagnose and manage this disorder.This case portrays one of these cases - one of the few existing in the literature - and reinforces the diagnostic complexity of this entity.

Severe Hypertriglyceridemia: A 10-Year Review in a Portuguese Hospital.

INTRODUCTION: Severe hypertriglyceridemia (SHTG) is a rare condition associated with serious complications, such as acute pancreatitis (AP), and the best treatment is still a matter of discussion. The aim of this study is to outline the demographics, management, and outcomes (recurrence and mortality) of complications in patients with SHTG. MATERIAL AND METHODS: A retrospective, observational, and analytical study was carried out by obtaining clinical data from the electronic health records of patients with SHTG admitted to the Internal and Intensive Medicine units from the 1st of January 2009 to the 31st of December 2020 in a university hospital. RESULTS: The cohort included 17 patients. The most common complication was AP (13/17 = 76.5%). Admission to the intensive care unit (ICU) was observed in 84.2%. Among patients with AP, the most commonly administered therapies were insulin (82.4%) and fibrates (76.5%). Plasmapheresis was used in 58.8%, and the criteria for using this technique were mainly based on clinical and laboratory abnormalities. There were no deaths. The readmission rate at 30 days was 36.3%. CONCLUSION: This study shows the morbidity profile associated with SHTG, with a high level of ICU admissions and also a high level of the use of plasmapheresis. In our population, this approach had good results, and this should be highlighted as there are no clear international guidelines for this intervention. Distinguishing between patients with familial chylomicronemia syndrome or with multifactorial chylomicronemia is important as recent specific therapy for lipoprotein lipase (LPL) genetic deficit is available. In the near future, the performance of a genetic study should be considered in patients with SHTG as an attempt to avoid the high recurrence rate of complications of this disease.

Primary Squamous Cell Carcinoma of the Renal Pelvis: A Rare Complication of Xanthogranulomatous Pyelonephritis.

Xanthogranulomatous pyelonephritis is a rare disease resulting from chronic inflammation and infection of the renal parenchyma. It usually arises as a consequence of obstructive chronic pyelonephritis. Primary squamous cell carcinoma of the renal pelvis is a distinct pathology, very rare in clinical practice, with a well-established association with xanthogranulomatous pyelonephritis. The authors present the case of a 57-year-old woman with chronic pyelonephritis containing xanthogranulomatous features. Subsequent workup revealed a concomitant, unsuspected, primary squamous cell carcinoma of the renal pelvis. With this case, the authors intend to emphasize and reinforce the need to be alert to an uncommon association between two rare diseases due to its diagnostic, therapeutic, and prognostic implications.

Impact of Structural GLA Protein Changes on Peripheral GLA Activity and Substrate Accumulation in Fabry Disease Patients.

INTRODUCTION: Fabry disease is an X-linked lysosomal storage disorder caused by pathogenic variants in the GLA gene, leading to decreased/absent α-galactosidase activity. In clinical practice, enzyme activity and substrate/byproduct accumulation play a role in diagnosis and disease-monitoring biomarkers. However, interpreting biomarker levels is not straightforward and can change according to the underlying GLA protein abnormality. OBJECTIVE: Our goals were to understand how disrupting specific protein regions changes biomarker behaviour and to establish specific patterns for individual variants. METHODOLOGY: We analysed data from the Biochemical Genetics Laboratory regarding GLA variants, GLA enzyme activity (in dried blood spots, plasma or white blood cells), plasma LysoGb3 accumulation, and urinary Gb3 excretion. We assessed correlations, trends, and potential predictor models of biomarker behaviour. RESULTS: We assessed 169 hemizygous male and 255 heterozygous female patients. For both groups, substrate accumulation correlates inversely with GLA activity. Variants affecting residues buried within the protein core or the active site were associated with more severe biomarker changes, while those affecting residues that establish disulfide bonds or are glycosylated were similar to other variants. For each non-truncating variant, we also established specific profiles of biomarker behaviour. Finally, we also designed predictor models of biomarker behaviour based on structural variant information. This study provides the groundwork for the impact of GLA protein variation on GLA activity and substrate accumulation. CONCLUSION: This knowledge is of extreme relevance for diagnostic labs and clinicians, as some genetic variants are challenging to interpret regarding pathogenicity. Assessing whether biomarker changes are in the expected range for a specific variant may help diagnostic evaluation. This study also contributes to recognising non-disease-causing variants, considering their overall biochemical impact, and providing a comparative reference for biomarker discovery studies. In the future, the correlation of these findings with disease severity may be of great relevance for diagnosis and monitoring progression.

Maturity-onset diabetes of the young in a large Portuguese cohort.

AIMS: Monogenic forms of diabetes that develop with autosomal dominant inheritance are classically aggregated in the Maturity-Onset Diabetes of the Young (MODY) categories. Despite increasing awareness, its true prevalence remains largely underestimated. We describe a Portuguese cohort of individuals with suspected monogenic diabetes who were genetically evaluated for MODY-causing genes. METHODS: This single-center retrospective cohort study enrolled patients with positive genetic testing for MODY between 2015 and 2021. Automatic sequencing and, in case of initial negative results, next-generation sequencing were performed. Their clinical and molecular characteristics were described. RESULTS: Eighty individuals were included, 55 with likely pathogenic/pathogenic variants in one of the MODY genes and 25 MODY-positive family members, identified by cascade genetic testing. The median age at diabetes diagnosis was 23 years, with a median HbA1c of 6.5%. The most frequently mutated genes were identified in HNF1A (40%), GCK (34%) and HNF4A (13%), followed by PDX1, HNF1B, INS, KCNJ11 and APPL1. Thirty-six unique variants were found (29 missense and 7 frameshift variants), of which ten (28%) were novel. CONCLUSIONS: Our data highlights the importance of genetic testing in the diagnosis of MODY and the establishment of its subtypes, leading to more personalized treatment and follow-up strategies.

Dorfman-Chanarin Syndrome: A Rare Cause of Metabolic Associated Fatty Liver Disease Related to Homozygosity of the Nonsense Mutation c.934C>T (p.R312*).

Metabolic associated fatty liver disease became the most common form of chronic liver disease, in the vast majority of the cases related to increased insulin resistance or metabolic dysregulation. Yet, other causes may be implied. We report the late diagnosis of Dorfman-Chanarin syndrome in a non-alcoholic steatohepatitis previously labeled cirrhotic middle-aged man, with consanguineous parents, complicated with hepatocellular carcinoma. Congenital ichthyosis, neurosensory hearing loss and elevated muscular enzymes hit on the track of Dorfman-Chanarin syndrome. The genetic analysis uncovered a first-time described homozygotic nonsense mutation in the ABHD5 gene, responsible for coding the ABHD5 protein. The patient was successfully submitted to liver transplantation. Inborn errors of metabolism are a rare cause of metabolic associated fatty liver disease, but they need to be kept in consideration in all patients who present with atypical clinical features. This shall raise the awareness of physicians to rare forms of presentation since it may imply not only a different prognosis, but also other actions, like particular therapies as liver transplantation due to related complications of cirrhosis, or familial screening.

A doença hepática gorda dismetabólica tornou-se a forma mais comum de doença hepática crónica, estando mais vezes relacionada com o aumento da insulinorresistência ou desregulação metabólica. Contudo, outras causas podem estar também implicadas. Apresentamos o caso clínico de um doente com um diagnóstico de síndrome de Dorfman-Chanarin estabelecido tardiamente num homem de meia-idade com um diagnóstico prévio de cirrose associada a esteatohepatite não alcoólica, com pais consanguíneos, e complicada de carcinoma hepatocelular. A presença de ictiose congénita, a perda de audição neurosensorial, e a elevação de enzimas musculares, colocaram na pista de diagnóstico de síndrome de Dorfman-Chanarin. O estudo genético demonstrou a presença de uma mutação nonsense descrita pela primeira vez em homozigotia no gene ABHD5, responsável pela codificação da proteína ABHD5. O doente foi submetido a transplante hepático com sucesso. Os erros inatos do metabolismo são uma causa rara de doença hepática gorda, mas necessitam de ser tidos em consideração em todos os doentes que se apresentem com características clínicas atípicas. Isto deve aumentar a consciencialização dos médicos para formas raras de apresentação, uma vez que pode implicar não apenas um prognóstico diferente, mas também outras ações, como o transplante hepático por complicações associadas à cirrose, ou despiste familiar.

The Man of a Thousand Pustules: A Case About Acute Generalized Exanthematous Pustulosis.

Acute generalized exanthematous pustulosis (AGEP) is a rare entity characterized by fever associated with the sudden appearance of erythematous lesions, on which multiple sterile, non-follicular pustules develop. We describe a case of a 44-year-old healthy male who developed fever and multiple erythematous and edematous lesions with progressive generalization to the entire body, associated with multiple small non-follicular pustules three days after having started flucloxacillin for the treatment of a furuncle. Considering the characteristics of the exanthema, fever, and association with aminopenicillin initiation, AGEP was considered. A skin biopsy revealed subcorneal and superficial epidermal pustules, with foci of spongiosis, papillary edema, and a superficial, perivascular inflammatory cell infiltrate with neutrophils and eosinophils, consistent with the clinical diagnosis of AGEP. The culprit drug was suspended, and prednisolone was started, considering the rash extension, with progressive and complete improvement. Although it is a rare condition, the hypothesis of AGEP should be considered in acute febrile conditions with disseminated pustules. It resolves spontaneously after discontinuation of the offending drug, and the diagnosis is based on clinical presentation and skin biopsy.

MODY probability calculator utility in individuals' selection for genetic testing: Its accuracy and performance.

INTRODUCTION: MODY probability calculator (MPC) represents an easy-to-use tool developed by Exeter University to help clinicians prioritize which individuals should be oriented to genetic testing. We aimed to assess the utility of MPC in a Portuguese cohort with early-onset monogenic diabetes. METHODS: This single-centre retrospective study enrolled 132 participants submitted to genetic testing between 2015 and 2020. Automatic sequencing and, in case of initial negative results, generation sequencing were performed. MODY probability was calculated using the probability calculator available online. Positive and negative predictive values (PPV and NPV, respectively), accuracy, sensitivity and specificity of the calculator were determined for this cohort. RESULTS: Seventy-three individuals were included according to inclusion criteria: 20 glucokinase (GCK-MODY); 16 hepatocyte nuclear factor 1A (HNF1A-MODY); 2 hepatocyte nuclear factor 4A (HNF4A-MODY) and 35 DM individuals with no monogenic mutations found. The median probability score of MODY was significantly higher in monogenic diabetes-positive subgroup (75.5% vs. 24.2%, p < .001). The discriminative accuracy of the calculator, as expressed by area under the curve, was 75% (95% CI: 64%-85%). In our cohort, the best cut-off value for the MODY calculator was found to be 36%, with a PPV of 74.4%, NPV of 73.5% and corresponding sensitivity and specificity of 76.2% and 71.4%, respectively. CONCLUSIONS: In a highly pre-selected group of probands qualified for genetic testing, the Exeter MODY probability calculator provided a useful tool in individuals' selection for genetic testing, with good discrimination ability under an optimal probability cut-off of 36%. Further geographical and population adjustments are warranted for general use.

Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies.

Neuromuscular diseases are genetically highly heterogeneous, and differential diagnosis can be challenging. Over a 3-year period, we prospectively analyzed 268 pediatric and adult patients with a suspected diagnosis of inherited neuromuscular disorder (INMD) using comprehensive gene-panel analysis and next-generation sequencing. The rate of diagnosis increased exponentially with the addition of genes to successive versions of the INMD panel, from 31% for the first iteration (278 genes) to 40% for the last (324 genes). The global mean diagnostic rate was 36% (97/268 patients), with a diagnostic turnaround time of 4-6 weeks. Most diagnoses corresponded to muscular dystrophies/myopathies (68.37%) and peripheral nerve diseases (22.45%). The most common causative genes, TTN, RYR1, and ANO5, accounted for almost 30% of the diagnosed cases. Finally, we evaluated the utility of the differential diagnosis tool Phenomizer, which established a correlation between the phenotype and molecular findings in 21% of the diagnosed patients. In summary, comprehensive gene-panel analysis of all genes implicated in neuromuscular diseases facilitates a rapid diagnosis and provides a high diagnostic yield.

Case Report: Diffuse Polymicrogyria Associated With a Novel ADGRG1 Variant.

Pathogenic variants of the ADGRG1 gene are associated with bilateral frontoparietal polymicrogyria, defined radiologically by polymicrogyria with an anterior-posterior gradient, pontine and cerebellar hypoplasia and patchy white matter abnormalities. We report a novel homozygous ADGRG1 variant with atypical features. The patient presented at 8 months of age with motor delay, esotropia, hypotonia with hyporeflexia and subsequently developed refractory epilepsy. At the last assessment, aged 12 years, head control, sitting and language were not acquired. Magnetic resonance imaging revealed diffuse polymicrogyria with relative sparing of the anterior temporal lobes, without an anterior-posterior gradient, diffuse hypomyelination and pontine and cerebellar hypoplasia. A panel targeting brain morphogenesis defects yielded an unreported homozygous ADGRG1 nonsense variant (dbSNP rs746634404), present in the heterozygous state in both parents. We report a novel ADGRG1 variant associated with diffuse polymicrogyria without an identifiable anterior-posterior gradient, diffuse hypomyelination and a severe motor and cognitive phenotype. Our case highlights the phenotypic diversity of ADGRG1 pathogenic variants and the clinico-anatomical overlap between recognized polymicrogyria syndromes.

Utility of Gene Panels for the Diagnosis of Inborn Errors of Metabolism in a Metabolic Reference Center.

Next-generation sequencing (NGS) technologies have been proposed as a first-line test for the diagnosis of inborn errors of metabolism (IEM), a group of genetically heterogeneous disorders with overlapping or nonspecific phenotypes. Over a 3-year period, we prospectively analyzed 311 pediatric patients with a suspected IEM using four targeted gene panels. The rate of positive diagnosis was 61.86% for intermediary metabolism defects, 32.84% for complex molecular defects, 19% for hypoglycemic/hyperglycemic events, and 17% for mitochondrial diseases, and a conclusive molecular diagnosis was established in 2-4 weeks. Forty-one patients for whom negative results were obtained with the mitochondrial diseases panel underwent subsequent analyses using the NeuroSeq panel, which groups all genes from the individual panels together with genes associated with neurological disorders (1870 genes in total). This achieved a diagnostic rate of 32%. We next evaluated the utility of a tool, Phenomizer, for differential diagnosis, and established a correlation between phenotype and molecular findings in 39.3% of patients. Finally, we evaluated the mutational architecture of the genes analyzed by determining z-scores, loss-of-function observed/expected upper bound fraction (LOEUF), and haploinsufficiency (HI) scores. In summary, targeted gene panels for specific groups of IEMs enabled rapid and effective diagnosis, which is critical for the therapeutic management of IEM patients.

Genotype-phenotype correlations and BH4 estimated responsiveness in patients with phenylketonuria from Rio de Janeiro, Southeast Brazil.

BACKGROUND: Genetic heterogeneity and compound heterozygosis give rise to a continuous spectrum of phenylalanine hydroxylase deficiency and metabolic phenotypes in phenylketonuria (PKU). The most used parameters for evaluating phenotype in PKU are pretreatment phenylalanine (Phe) levels, tolerance for dietary Phe, and Phe overloading test. Phenotype can vary from a "classic" (severe) form to mild hyperphenylalaninemia, which does not require dietary treatment. A subset of patients is responsive to treatment by the cofactor tetrahydrobiopterin (BH4 ). Genotypes of PKU patients from Rio de Janeiro, Brazil, were compared to predicted and observed phenotypes. Genotype-based estimations of responsiveness to BH4 were also conducted. METHODS: Phenotype was defined by pretreatment Phe levels. A standard prediction system based on arbitrary assigned values was employed to measure genotype-phenotype concordance. Patients were also estimated as BH4 -responders according to the responsiveness previously reported for their mutations and genotypes. RESULTS: A 48.3% concordance rate between genotype-predicted and observed phenotypes was found. When the predicted phenotypes included those reported at the BIOPKU database, the concordance rate reached 77%. A total of 18 genotypes from 30 patients (29.4%) were estimated as of potential or probable BH4 responsiveness. Inconsistencies were observed in genotypic combinations including the common "moderate" mutations p.R261Q, p.V388M, and p.I65T and the mild mutations p.L48S, p.R68S, and p.L249F. CONCLUSION: The high discordance rate between genotype-predicted and observed metabolic phenotypes in this study seems to be due partially to the high frequency of the so-called "moderate" common mutations, p.R261Q, p.V388M, and p.I65T, which are reported to be associated to erratic or more severe than expected metabolic phenotypes. Although our results of BH4 estimated responsiveness must be regarded as tentative, it should be emphasized that genotyping and genotype-phenotype association studies are important in selecting patients to be offered a BH4 overload test, especially in low-resource settings like Brazil.

Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients.

In order to characterize the genetic architecture of epilepsy in a pediatric population from the Iberian Peninsula (including the Canary Islands), we conducted targeted exome sequencing of 246 patients with infantile-onset seizures with or without neurodevelopmental delay. We detected 107 variants in 48 different genes, which were implicated in neuronal excitability, neurodevelopment, synaptic transmission, and metabolic pathways. In 104 cases (42%) we detected variant(s) that we classified as pathogenic or likely pathogenic. Of the 48 mutated genes, 32 were dominant, 8 recessive and 8 X-linked. Of the patients for whom family studies could be performed and in whom pathogenic variants were identified in dominant or X-linked genes, 82% carried de novo mutations. The involvement of small copy number variations (CNVs) is 9%. The use of progressively updated custom panels with high mean vertical coverage enabled establishment of a definitive diagnosis in a large proportion of cases (42%) and detection of CNVs (even duplications) with high fidelity. In 10.5% of patients we detected associations that are pending confirmation via functional and/or familial studies. Our findings had important consequences for the clinical management of the probands, since a large proportion of the cohort had been clinically misdiagnosed, and their families were subsequently able to avail of genetic counseling. In some cases, a more appropriate treatment was selected for the patient in question, or an inappropriate treatment discontinued. Our findings suggest the existence of modifier genes that may explain the incomplete penetrance of some epilepsy-related genes. We discuss possible reasons for non-diagnosis and future research directions. Further studies will be required to uncover the roles of structural variants, epimutations, and oligogenic inheritance in epilepsy, thereby providing a more complete molecular picture of this disease. In summary, given the broad phenotypic spectrum of most epilepsy-related genes, efficient genomic tools like the targeted exome sequencing panel described here are essential for early diagnosis and treatment, and should be implemented as first-tier diagnostic tools for children with epilepsy without a clear etiologic basis.

SIGMAR1 gene mutation causing Distal Hereditary Motor Neuropathy in a Portuguese family.

SIGMAR1 gene encodes a non-opioid endoplasmic reticulum (ER) protein which is involved in a large diversity of cell functions and is expressed ubiquitously in both central and peripheral nervous systems. Alterations of its normal function may contribute to two different phenotypes: juvenile amyotrophic lateral sclerosis (ALS 16) and distal hereditary motor neuropathies (dHMN). We present the case of a female patient, of 37-years-old, with distal muscle weakness and atrophy beginning in childhood and slowly progressive in the first two decades of life. Neurological examination revealed a symmetrical severe muscle wasting and weakness in distal lower and upper limbs, with claw hands, footdrop with equinovarus deformity and hammer toes, generalized areflexia and normal sensory examination. The electrodiagnostic study revealed a pure chronic motor peripheral nerve involvement without signs of demyelination. The molecular study found the deletion c.561_576del on exon 4 and a deletion of all exon 4, in the SIGMAR1 gene.

Mutation analysis of the PAH gene in phenylketonuria patients from Rio de Janeiro, Southeast Brazil.

BACKGROUND: Phenylketonuria (PKU) is an autosomal recessive disease resulting from mutations in the PAH gene. Most of the patients are compound heterozygotes, and genotype is a major factor in determining the phenotypic variability of PKU. More than 1,000 variants have been described in the PAH gene. Rio de Janeiro's population has a predominance of Iberian, followed by African and Amerindian ancestries. It is expected that most PKU variants in this Brazilian state have originated in the Iberian Peninsula. However, rare European, African or pathogenic variants that are characteristic of the admixed population of the state might also be found. METHODS: A total of 102 patients were included in this study. Genomic DNA was isolated from dried blood spots. Sanger sequencing was used for PAH gene variant identification. Deletions and duplications were also screened using MLPA analysis. Haplotypes were also determined. RESULTS: Nine (8.8%) homozygous and 93 (91.2%) compound heterozygous patients were found. The spectrum included 37 causative mutations. Missense, nonsense, and splicing pathogenic variants corresponded to 63.7%, 2.9%, and 22.6% of the mutant alleles, respectively. Large (1.5%), and small deletions, inframe (5.4%) and with frameshift (3.9%), comprised the remainder. The most frequent pathogenic variants were: p.V388M (12.7%), p.R261Q (11.8%), IVS10-11G>A (10.3%), IVS2+5G>C (6.4%), p.S349P (6.4%), p.R252W (5.4%), p.I65T (4.4%), p.T323del (4.4%), and p.P281L (3.4%). One novel variant was detected: c.934G>T (p.G312C) [rs763115697]. CONCLUSION: The three most frequent pathogenic variants in our study (34.8% of the alleles) were also the most common in other Brazilian states, Portugal, and Spain (p.V388M, p.R261Q, IVS10-11G>A), corroborating that the Iberian Peninsula is the major source of PAH mutations in Rio de Janeiro. Pathogenic variants that have other geographical origins, such IVS2+5G>C, p.G352Vfs*48, and IVS12+1G>A were also detected. Genetic drift and founder effect may have also played a role in the mutation spectrum we observed.