Two compound heterozygous variants in the CLN8 gene are responsible for neuronal cereidolipofuscinoses disorder in a child: a case report.

Background: Neuronal Ceroid Lipofuscinosis (NCL) disorders, recognized as the primary cause of childhood dementia globally, constitute a spectrum of genetic abnormalities. CLN8, a subtype within NCL, is characterized by cognitive decline, motor impairment, and visual deterioration. This study focuses on an atypical case with congenital onset and a remarkably slow disease progression. Methods: Whole-genome sequencing at 30× coverage was employed as part of a national genomics program to investigate the genetic underpinnings of rare diseases. This genomic approach aimed to challenge established classifications (vLINCL and EPMR) and explore the presence of a continuous phenotypic spectrum associated with CLN8. Results: The whole-genome sequencing revealed two novel likely pathogenic mutations in the CLN8 gene on chromosome 8p23.3. These mutations were not previously associated with CLN8-related NCL. Contrary to established classifications (vLINCL and EPMR), our findings suggest a continuous phenotypic spectrum associated with CLN8. Pathological subcellular markers further validated the genomic insights. Discussion: The identification of two previously undescribed likely pathogenic CLN8 gene mutations challenges traditional classifications and highlights a more nuanced phenotypic spectrum associated with CLN8. Our findings underscore the significance of genetic modifiers and interactions with unrelated genes in shaping variable phenotypic outcomes. The inclusion of pathological subcellular markers further strengthens the validity of our genomic insights. This research enhances our understanding of CLN8 disorders, emphasizing the need for comprehensive genomic analyses to elucidate the complexity of phenotypic presentations and guide tailored therapeutic strategies. The identification of new likely pathogenic mutations underscores the dynamic nature of CLN8-related NCL and the importance of individualized approaches to patient management.

Exome Sequencing Reveals Biallelic Mutations in MBTPS1 Gene in a Girl with a Very Rare Skeletal Dysplasia.

The Kondo-Fu type of spondyloepiphyseal dysplasia (SEDKF) is a rare skeletal dysplasia caused by homozygous or compound heterozygous mutations in the MBTPS1 gene. The MBTPS1 gene encodes a protein that is involved in the regulation of cholesterol and fatty acid metabolism. Mutations in MBTPS1 can lead to reduced levels of these lipids, which can have a number of effects on development, including skeletal anomalies, growth retardation, and elevated levels of blood lysosomal enzymes. This work reports the case of a 5-year-old girl with SEDKF. The patient had a severely short stature and a number of skeletal anomalies, including kyphosis, pectus carinatum, and reduced bone mineral density. She also had early onset cataracts and inguinal hernias. Genetic testing revealed two novel compound heterozygous variants in the MBTPS1 gene. These variants are predicted to disrupt the function of the MBTPS1 protein, which is consistent with the patient's clinical presentation. This case report adds to the growing body of evidence that mutations in the MBTPS1 gene are causal of SEDKF. We summarized the features of previous reported cases (with age ranges from 4 to 24 years) and identified that 80% had low stature, 70% low weight, 80% had bilateral cataracts and 70% showed Spondyloepiphyseal dysplasia on X-rays. The findings of this study suggest that SEDKF is a clinically heterogeneous disorder that can present with a variety of features. Further studies are needed to better understand the underlying mechanisms of SEDKF and to develop more effective treatments.

Case Report: Mycosis fungoides as an exclusive manifestation of common variable immunodeficiency in a family with a NFKB2 gene mutation.

Background: Common variable immunodeficiency disorders (CVIDs), which are primary immunodeficiencies characterized by the failure of primary antibody production, typically present with recurrent bacterial infections, decreased antibody levels, autoimmune features, and rare atypical manifestations that can complicate diagnosis and management. Although most cases are sporadic, approximately 10% of the patients may have a family history of immunodeficiency. Genetic causes involving genes related to B-cell development and survival have been identified in only a small percentage of cases. Case presentation: We present the case of a family with two brothers who presented with mycosis fungoides as an exclusive symptom of a common variable immunodeficiency disorder (CVID). Whole-exome sequencing of the index patient revealed a pathogenic variant of the NFKB2 gene. Based on this diagnosis and re-evaluation of other family members, the father and brother were diagnosed with this rare immune and preneoplastic syndrome. All CVID-affected family members presented with mycosis fungoides as their only symptom, which is, to the best of our knowledge, the first case to be reported. Conclusion: This case highlights the importance of high-throughput sequencing techniques for the proper diagnosis and treatment of hereditary hematological disorders.

X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson's Disease.

BACKGROUND: Sex differences in Parkinson's disease (PD) risk are well-known. However, the role of sex chromosomes in the development and progression of PD is still unclear. OBJECTIVE: The objective of this study was to perform the first X-chromosome-wide association study for PD risk in a Latin American cohort. METHODS: We used data from three admixed cohorts: (1) Latin American Research consortium on the Genetics of Parkinson's Disease (n = 1504) as discover cohort, and (2) Latino cohort from International Parkinson Disease Genomics Consortium (n = 155) and (3) Bambui Aging cohort (n = 1442) as replication cohorts. We also developed an X-chromosome framework specifically designed for admixed populations. RESULTS: We identified eight linkage disequilibrium regions associated with PD. We replicated one of these regions (top variant rs525496; discovery odds ratio [95% confidence interval]: 0.60 [0.478-0.77], P = 3.13 × 10-5 replication odds ratio: 0.60 [0.37-0.98], P = 0.04). rs5525496 is associated with multiple expression quantitative trait loci in brain and non-brain tissues, including RAB9B, H2BFM, TSMB15B, and GLRA4, but colocalization analysis suggests that rs5525496 may not mediate risk by expression of these genes. We also replicated a previous X-chromosome-wide association study finding (rs28602900), showing that this variant is associated with PD in non-European populations. CONCLUSIONS: Our results reinforce the importance of including X-chromosome and diverse populations in genetic studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Fibrodysplasia ossificans progressiva in a 3-year-old female patient.

BACKGROUND: Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disease affecting connective tissue, primarily caused by de novo mutations of the ACVR1 gene. FOP is a disease with congenital malformations of the toes and heterotopic ossification in characteristic patterns that progresses with flare-ups and remissions. Cumulative damage results in disability and, eventually, death. This report aimed to describe a case of FOP to highlight the importance of early diagnosis of this rare condition. CASE REPORT: We describe the case of a 3-year-old female diagnosed with congenital hallux valgus, who initially presented with soft tissue tumors, predominantly in the neck and chest, with partial remission. Multiple diagnostic tests were performed, including biopsies and magnetic resonance imaging, with nonspecific results. We observed ossification of the biceps brachii muscle during evolution. The molecular genetic study found a heterozygous ACVR1 gene mutation that confirmed FOP. CONCLUSIONS: Knowledge of this rare disease by pediatricians is critical for an early diagnosis and for avoiding unnecessary invasive procedures that may promote disease progression. In case of clinical suspicion, performing an early molecular study is suggested to detect ACVR1 gene mutations. The treatment of FOP is symptomatic and focused on maintaining physical function and family support.

INTRODUCCIÓN: La fibrodisplasia osificante progresiva (FOP) es una enfermedad autosómica dominante rara que afecta el tejido conectivo, cuya causa principal son mutaciones de novo del gen ACVR1. Se trata de una enfermedad con malformaciones congénitas de los primeros ortejos y osificación heterotópica en patrones característicos que progresa en empujes y remisiones. El daño acumulativo provoca discapacidad y, eventualmente, la muerte. El objetivo de este trabajo fue describir un caso de FOP para favorecer el diagnóstico precoz de esta enfermedad infrecuente. CASO CLÍNICO: Se describe el caso de una paciente de 3 años, portadora de hallux valgus congénito, que inicialmente presentó tumoraciones dolorosas de tejidos blandos, de predominio en cuello y tórax, con remisión parcial de las mismas. Se realizaron múltiples pruebas diagnósticas, incluyendo biopsias e imágenes de resonancia magnética con resultados inespecíficos. En la evolución se observó osificación de músculo bíceps braquial. El estudio genético molecular encontró una mutación del gen ACVR1 en heterocigosis que confirmó el diagnóstico de FOP. CONCLUSIONES: El conocimiento de esta enfermedad por los pediatras es clave para realizar un diagnóstico precoz y evitar procedimientos invasivos innecesarios que pueden promover la progresión de la enfermedad. Ante la sospecha clínica, se sugiere realizar tempranamente el estudio molecular para detectar mutaciones del gen ACVR1. El tratamiento de la FOP es sintomático, centrado en el mantenimiento de la función física y el apoyo familiar.

X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson Disease.

Sex differences in Parkinson Disease (PD) risk are well-known. However, it is still unclear the role of sex chromosomes in the development and progression of PD. We performed the first X-chromosome Wide Association Study (XWAS) for PD risk in Latin American individuals. We used data from three admixed cohorts: (i) Latin American Research consortium on the GEnetics of Parkinson's Disease (n=1,504) as discover cohort and (ii) Latino cohort from International Parkinson Disease Genomics Consortium (n = 155) and (iii) Bambui Aging cohort (n= 1,442) as replication cohorts. After developing a X-chromosome framework specifically designed for admixed populations, we identified eight linkage disequilibrium regions associated with PD. We fully replicated one of these regions (top variant rs525496; discovery OR [95%CI]: 0.60 [0.478 - 0.77], p = 3.13 × 10 -5 ; replication OR: 0.60 [0.37-0.98], p = 0.04). rs525496 is an expression quantitative trait loci for several genes expressed in brain tissues, including RAB9B, H2BFM, TSMB15B and GLRA4 . We also replicated a previous XWAS finding (rs28602900), showing that this variant is associated with PD in non-European populations. Our results reinforce the importance of including X-chromosome and diverse populations in genetic studies.

Computational and mitochondrial functional studies of novel compound heterozygous variants in SPATA5 gene support a causal link with epileptogenic encephalopathy.

The SPATA5 gene encodes a 892 amino-acids long protein that has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Several studies have associated homozygous or compound heterozygous mutations in SPATA5 gene to microcephaly, intellectual disability, seizures and hearing loss. This suggests a role of the SPATA5 gene also in neuronal development. Recently, our group presented results validating the use of blood cells for the assessment of mitochondrial function for diagnosis and follow-up of mitochondrial disease, minimizing the need for invasive procedures such as muscle biopsy. In this study, we were able to diagnose a patient with epileptogenic encephalopathy using next generation sequencing. We found two novel compound heterozygous variants in SPATA5 that are most likely causative. To analyze the impact of SPATA5 mutations on mitochondrial functional studies directly on the patients' mononuclear cells and platelets were undertaken. Oxygen consumption rates in platelets and PBMCs were impaired in the patient when compared to a healthy control. Also, a decrease in mitochondrial mass was observed in the patient monocytes with respect to the control. This suggests a true pathogenic effect of the mutations in mitochondrial function, especially in energy production and possibly biogenesis, leading to the observed phenotype.

Fibrodysplasia ossificans progressiva in a 3-year-old female patient / Fibrodisplasia osificante progresiva en una paciente de 3 años

Abstract Background: Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disease affecting connective tissue, primarily caused by de novo mutations of the ACVR1 gene. FOP is a disease with congenital malformations of the toes and heterotopic ossification in characteristic patterns that progresses with flare-ups and remissions. Cumulative damage results in disability and, eventually, death. This report aimed to describe a case of FOP to highlight the importance of early diagnosis of this rare condition. Case report: We describe the case of a 3-year-old female diagnosed with congenital hallux valgus, who initially presented with soft tissue tumors, predominantly in the neck and chest, with partial remission. Multiple diagnostic tests were performed, including biopsies and magnetic resonance imaging, with nonspecific results. We observed ossification of the biceps brachii muscle during evolution. The molecular genetic study found a heterozygous ACVR1 gene mutation that confirmed FOP. Conclusions: Knowledge of this rare disease by pediatricians is critical for an early diagnosis and for avoiding unnecessary invasive procedures that may promote disease progression. In case of clinical suspicion, performing an early molecular study is suggested to detect ACVR1 gene mutations. The treatment of FOP is symptomatic and focused on maintaining physical function and family support.

Resumen Introducción: La fibrodisplasia osificante progresiva (FOP) es una enfermedad autosómica dominante rara que afecta el tejido conectivo, cuya causa principal son mutaciones de novo del gen ACVR1. Se trata de una enfermedad con malformaciones congénitas de los primeros ortejos y osificación heterotópica en patrones característicos que progresa en empujes y remisiones. El daño acumulativo provoca discapacidad y, eventualmente, la muerte. El objetivo de este trabajo fue describir un caso de FOP para favorecer el diagnóstico precoz de esta enfermedad infrecuente. Caso clínico: Se describe el caso de una paciente de 3 años, portadora de hallux valgus congénito, que inicialmente presentó tumoraciones dolorosas de tejidos blandos, de predominio en cuello y tórax, con remisión parcial de las mismas. Se realizaron múltiples pruebas diagnósticas, incluyendo biopsias e imágenes de resonancia magnética con resultados inespecíficos. En la evolución se observó osificación de músculo bíceps braquial. El estudio genético molecular encontró una mutación del gen ACVR1 en heterocigosis que confirmó el diagnóstico de FOP. Conclusiones: El conocimiento de esta enfermedad por los pediatras es clave para realizar un diagnóstico precoz y evitar procedimientos invasivos innecesarios que pueden promover la progresión de la enfermedad. Ante la sospecha clínica, se sugiere realizar tempranamente el estudio molecular para detectar mutaciones del gen ACVR1. El tratamiento de la FOP es sintomático, centrado en el mantenimiento de la función física y el apoyo familiar.

Two mutations in the SBDS gene reveal a diagnosis of Shwachman-Diamond syndrome in a patient with atypical symptoms.

We present the case of a 53-yr-old woman with an inherited bone marrow failure coexisting with uncommon extrahematological symptoms, such as cirrhosis and skin abnormalities. Whole-exome sequencing revealed a diagnosis of Shwachman-Diamond syndrome (SDS) with an atypical presentation. Unexpected was the age of disease expression, normally around the pediatric age, with a predominantly median survival age of 36 yr. To our knowledge, she was the first adult patient with a molecular diagnosis of Shwachman-Diamond in Uruguay. The patient was referred to our service when she was 43-yr-old with a history of bone marrow failure with anemia and thrombocytopenia. All secondary causes of pancytopenia were excluded. Bone marrow aspirate and biopsy specimens were hypocellular for the patient's age. Numerous dysplastic features were observed in the three lineages. She had a normal karyotype and normal chromosomal fragility. A diagnosis of low-risk hypoplastic MDS was made. Dermatological examination revealed reticulate skin pigmentation with hypopigmented macules involving the face, neck, and extremities; nail dystrophy; premature graying; and thin hair. Extrahematological manifestations were present (e.g., learning difficulties, short stature). Last, she was diagnosed with cryptogenic liver cirrhosis CHILD C. This rules out all other possible causes of chronic liver disease. This clinical presentation initially oriented the diagnosis toward telomeropathy, so we did a telomeropathy NGS panel that came up negative. Finally, we did an exome sequencing that confirmed the diagnosis of SDS. Using whole-exome sequencing, we were able to find two compound heterozygous mutations in the SBDS gene that were responsible for the phenotype of a patient that was undiagnosed for 10 years. An earlier genetic diagnosis could have influenced our patient's outcome.

Novel frameshift mutation in LIS1 gene is a probable cause of lissencephaly: a case report.

BACKGROUND: Lissencephaly (LIS) is a cortical malformation, characterized by smooth or nearly smooth cerebral surface and a shortage of gyral and sulcal development, which is caused by deficient neuronal migration during embryogenesis. Neuronal migration involves many gene products, among which is the product of the PAFAH1B1 gene, associated with this disease. LIS is a rare disease, characterized by low population frequency, and with non-specific clinical symptoms such as early epilepsy, developmental delay or cerebral palsy-like motor problems. Given that high-throughput sequencing techniques have been improving diagnosis, we have chosen this technique for addressing this patient. CASE PRESENTATION: We present the case of a seven years old male patient with an undiagnosed rare disease, with non-specific clinical symptoms possibly compatible with lissencephaly. The patient was enrolled in a study that included the sequencing of his whole genome. Sequence data was analyzed following a bioinformatic pipeline. The variants obtained were annotated and then subjected to different filters for prioritization. Also mitochondrial genome was analyzed. A novel candidate frameshift insertion in known PAFAH1B1 gene was found, explaining the index case phenotype. The assessment through in silico tools reported that it causes nonsense mediated mechanisms and that it is damaging with high confidence scores. The insertion causes a change in the reading frame, and produces a premature stop codon, severely affecting the protein function and probably the silencing of one allele. The healthy mother did not carry the mutation, and the unaffected father was not available for analysis. CONCLUSIONS: Through this work we found a novel de novo mutation in LIS1/PAFAH1B1 gene, as a likely cause of a rare disease in a young boy with non-specific clinical symptoms. The mutation found correlates with the phenotype studied since the loss of function in the gene product has already been described in this condition. Since there are no other variants in the PAFAH1B1 gene with low population frequency and due to family history, a de novo disease mechanism is proposed.

Polygenic risk prediction and SNCA haplotype analysis in a Latino Parkinson's disease cohort.

BACKGROUND: Large-scale Parkinson's disease (PD) genome-wide association studies (GWAS) have, until recently, only been conducted on subjects with European-ancestry. Consequently, polygenic risk scores (PRS) constructed using PD GWAS data are likely to be less predictive when applied to non-European cohorts. METHODS: Using GWAS data from the largest study to date, we constructed a PD PRS for a Latino PD cohort (1497 subjects from LARGE-PD) and tested it for association with PD status and age at onset. We validated the PRS performance by testing it in an independent Latino cohort (448 subjects) and by repeating the analysis in LARGE-PD with the addition of 440 external Peruvian controls. We also tested SNCA haplotypes for association with PD risk in LARGE-PD and a European-ancestry PD cohort. RESULTS: The GWAS-significant PD PRS had an area under the receiver-operator curve (AUC) of 0.668 (95% CI: 0.640-0.695) in LARGE-PD. The inclusion of external Peruvian controls mitigated this result, dropping the AUC 0.632 (95% CI: 0.607-0.657). At the SNCA locus, haplotypes differ by ancestry. Ancestry-specific SNCA haplotypes were associated with PD status in both LARGE-PD and the European-ancestry cohort (p-value < 0.05). These haplotypes both include the rs356182 G-allele, but only share 14% of their variants overall. CONCLUSION: The PD PRS has potential for PD risk prediction in Latinos, but variability caused by admixture patterns and bias in a European-ancestry PD PRS data limits its utility. The inclusion of diverse subjects can help elucidate PD risk loci and improve risk prediction in non-European cohorts.

Tracing the Distribution of European Lactase Persistence Genotypes Along the Americas.

In adulthood, the ability to digest lactose, the main sugar present in milk of mammals, is a phenotype (lactase persistence) observed in historically herder populations, mainly Northern Europeans, Eastern Africans, and Middle Eastern nomads. As the -13910∗T allele in the MCM6 gene is the most well-characterized allele responsible for the lactase persistence phenotype, the -13910C > T (rs4988235) polymorphism is commonly evaluated in lactase persistence studies. Lactase non-persistent adults may develop symptoms of lactose intolerance when consuming dairy products. In the Americas, there is no evidence of the consumption of these products until the arrival of Europeans. However, several American countries' dietary guidelines recommend consuming dairy for adequate human nutrition and health promotion. Considering the extensive use of dairy and the complex ancestry of Pan-American admixed populations, we studied the distribution of -13910C > T lactase persistence genotypes and its flanking haplotypes of European origin in 7,428 individuals from several Pan-American admixed populations. We found that the -13910∗T allele frequency in Pan-American admixed populations is directly correlated with allele frequency of the European sources. Moreover, we did not observe any overrepresentation of European haplotypes in the -13910C > T flanking region, suggesting no selective pressure after admixture in the Americas. Finally, considering the dominant effect of the -13910∗T allele, our results indicate that Pan-American admixed populations are likely to have higher frequency of lactose intolerance, suggesting that general dietary guidelines deserve further evaluation across the continent.

Blood cell respiration rates and mtDNA copy number: A promising tool for the diagnosis of mitochondrial disease.

Human mitochondrial diseases are a group of heterogeneous diseases caused by defects in oxidative phosphorylation, due to mutations in mitochondrial (mtDNA) or nuclear DNA. The diagnosis of mitochondrial disease is challenging since mutations in multiple genes can affect mitochondrial function, there is considerable clinical variability and a poor correlation between genotype and phenotype. Herein we assessed mitochondrial function in peripheral blood mononuclear cells (PBMCs) and platelets from volunteers without known metabolic pathology and patients with mitochondrial disease. Oxygen consumption rates were evaluated and respiratory parameters indicative of mitochondrial function were obtained. A negative correlation between age and respiratory parameters of PBMCs from control individuals was observed. Surprisingly, respiratory parameters of PBMCs normalized by cell number were similar in patients and young controls. Considering possible compensatory mechanisms, mtDNA copy number in PBMCs was quantified and an increase was found in patients with respect to controls. Hence, respiratory parameters normalized by mtDNA copy number were determined, and in these conditions a decrease in maximum respiration rate and spare respiratory capacity was observed in patients relative to control individuals. In platelets no decay was seen in mitochondrial function with age, while a reduction in basal, ATP-independent and ATP-dependent respiration normalized by cell number was detected in patients compared to control subjects. In summary, our results offer promising perspectives regarding the assessment of mitochondrial function in blood cells for the diagnosis of mitochondrial disease, minimizing the need for invasive procedures such as muscle biopsies, and for following disease progression and response to treatments.

Characterizing the Genetic Architecture of Parkinson's Disease in Latinos.

OBJECTIVE: This work was undertaken in order to identify Parkinson's disease (PD) risk variants in a Latino cohort, to describe the overlap in the genetic architecture of PD in Latinos compared to European-ancestry subjects, and to increase the diversity in PD genome-wide association (GWAS) data. METHODS: We genotyped and imputed 1,497 PD cases and controls recruited from nine clinical sites across South America. We performed a GWAS using logistic mixed models; variants with a p-value <1 × 10-5 were tested in a replication cohort of 1,234 self-reported Latino PD cases and 439,522 Latino controls from 23andMe, Inc. We also performed an admixture mapping analysis where local ancestry blocks were tested for association with PD status. RESULTS: One locus, SNCA, achieved genome-wide significance (p-value <5 × 10-8 ); rs356182 achieved genome-wide significance in both the discovery and the replication cohorts (discovery, G allele: 1.58 OR, 95% CI 1.35-1.86, p-value 2.48 × 10-8 ; 23andMe, G allele: 1.26 OR, 95% CI 1.16-1.37, p-value 4.55 × 10-8 ). In our admixture mapping analysis, a locus on chromosome 14, containing the gene STXBP6, achieved significance in a joint test of ancestries and in the Native American single-ancestry test (p-value <5 × 10-5 ). A second locus on chromosome 6, containing the gene RPS6KA2, achieved significance in the African single-ancestry test (p-value <5 × 10-5 ). INTERPRETATION: This study demonstrated the importance of the SNCA locus for the etiology of PD in Latinos. By leveraging the demographic history of our cohort via admixture mapping, we identified two potential PD risk loci that merit further study. ANN NEUROL 2021;90:353-365.

CBG Montevideo: A Clinically Novel SERPINA6 Mutation Leading to Haploinsufficiency of Corticosteroid-binding Globulin.

Corticosteroid-binding globulin (CBG) is the main transport protein for cortisol, binding up to 90% in a 1:1 ratio. CBG provides transport of cortisol within the circulation and targeted cortisol tissue delivery. Here, we describe the clinically novel "CBG Montevideo" a SERPINA6 pathogenic variant that results in a 50% reduction in plasma CBG levels. This was associated with low serum total cortisol and clinical features of hypoglycemia, exercise intolerance, chronic fatigue, and hypotension in the proband, a 7-year-old boy, and his affected mother. Previous reports of 9 human CBG genetic variants affecting either CBG concentrations or reduced CBG-cortisol binding properties have outlined symptoms consistent with attenuated features of hypocortisolism, fatigue, and hypotension. Here, however, the presence of hypoglycemia, despite normal circulating free cortisol, suggests a specific role for CBG in effecting glucocorticoid function, perhaps involving cortisol-mediated hepatic glucose homeostasis and cortisol-brain communication.

Whole genome sequencing reveals a frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease.

BACKGROUND: Rare diseases are pathologies that affect less than 1 in 2000 people. They are difficult to diagnose due to their low frequency and their often highly heterogeneous symptoms. Rare diseases have in general a high impact on the quality of life and life expectancy of patients, which are in general children or young people. The advent of high-throughput sequencing techniques has improved diagnosis in several different areas, from pediatrics, achieving a diagnostic rate of 41% with whole genome sequencing (WGS) and 36% with whole exome sequencing, to neurology, achieving a diagnostic rate between 47 and 48.5% with WGS. This evidence has encouraged our group to pursue a molecular diagnosis using WGS for this and several other patients with rare diseases. RESULTS: We used whole genome sequencing to achieve a molecular diagnosis of a 7-year-old girl with a severe panvascular artery disease that remained for several years undiagnosed. We found a frameshift variant in one copy and a large deletion involving two exons in the other copy of a gene called YY1AP1. This gene is related to Grange syndrome, a recessive rare disease, whose symptoms include stenosis or occlusion of multiple arteries, congenital heart defects, brachydactyly, syndactyly, bone fragility, and learning disabilities. Bioinformatic analyses propose these mutations as the most likely cause of the disease, according to its frequency, in silico predictors, conservation analyses, and effect on the protein product. Additionally, we confirmed one mutation in each parent, supporting a compound heterozygous status in the child. CONCLUSIONS: In general, we think that this finding can contribute to the use of whole genome sequencing as a diagnosis tool of rare diseases, and in particular, it can enhance the set of known mutations associated with different diseases.

Novel frameshift mutation in PURA gene causes severe encephalopathy of unclear cause.

BACKGROUND: The etiology of many genetic diseases is challenging. This is especially true for developmental disorders of the central nervous system, since several genes can be involved. Many of such pathologies are considered rare diseases, since they affect less than 1 in 2000 people. Due to their low frequency, they present several difficulties for patients, from the delay in the diagnosis to the lack of treatments. Next-generation sequencing techniques have improved the search for diagnosis in several pathologies. Many studies have shown that the use of whole-exome/genome sequencing in rare Mendelian diseases has a diagnostic yield between 30% and 50% depending on the disease. METHODS: Here, we present the case of an undiagnosed 6-year-old boy with severe encephalopathy of unclear cause, whose etiological diagnosis was achieved by whole-genome sequencing. RESULTS: We found a novel variant that has not been previously reported in patients nor it has been described in GnomAD. Segregation analysis supports a de novo mutation, since it is not present in healthy parents. The change is predicted to be harmful to protein function, since it falls in the first quarter of the protein producing an altered reading frame and generating a premature stop codon. Additionally, the variant is classified as pathogenic according to ACMG criteria (PVS1, PM2, and PP3). Furthermore, there are several reported frameshift mutations in nearby codons as well as nonsense mutations that are predicted as pathogenic in other studies. CONCLUSION: We found a novel de novo frameshift mutation in the PURA gene (MIM number 600473), c.151_161del, with sufficient evidence of its pathogenicity.

Genome-Wide Analysis of Copy Number Variation in Latin American Parkinson's Disease Patients.

BACKGROUND: Parkinson's disease is the second most common neurodegenerative disorder and affects people from all ethnic backgrounds, yet little is known about the genetics of Parkinson's disease in non-European populations. In addition, the overall identification of copy number variants at a genome-wide level has been understudied in Parkinson's patients. The objective of this study was to understand the genome-wide burden of copy number variants in Latinos and its association with Parkinson's disease. METHODS: We used genome-wide genotyping data from 747 Parkinson's disease patients and 632 controls from the Latin American Research Consortium on the Genetics of Parkinson's disease. RESULTS: Genome-wide copy number burden analysis showed that patients were significantly enriched for copy number variants overlapping known Parkinson's disease genes compared with controls (odds ratio, 3.97; 95%CI, 1.69-10.5; P = 0.018). PRKN showed the strongest copy number burden, with 20 copy number variant carriers. These patients presented an earlier age of disease onset compared with patients with other copy number variants (median age at onset, 31 vs 57 years, respectively; P = 7.46 × 10-7 ). CONCLUSIONS: We found that although overall genome-wide copy number variant burden was not significantly different, Parkinson's disease patients were significantly enriched with copy number variants affecting known Parkinson's disease genes. We also identified that of 250 patients with early-onset disease, 5.6% carried a copy number variant on PRKN in our cohort. Our study is the first to analyze genome-wide copy number variant association in Latino Parkinson's disease patients and provides insights about this complex disease in this understudied population. © 2020 International Parkinson and Movement Disorder Society.

Epilepsy and Electroencephalographic Abnormalities in SATB2-Associated Syndrome.

BACKGROUND: Seizures are an under-reported feature of the SATB2-associated syndrome phenotype. We describe the electroencephalographic findings and seizure semiology and treatment in a population of individuals with SATB2-associated syndrome. METHODS: We performed a retrospective review of 101 individuals with SATB2-associated syndrome who were reported to have had a previous electroencephalographic study to identify those who had at least one reported abnormal result. For completeness, a supplemental survey was distributed to the caregivers and input from the treating neurologist was obtained whenever possible. RESULTS: Forty-one subjects were identified as having at least one prior abnormal electroencephalography. Thirty-eight individuals (93%) had epileptiform discharges, 28 (74%) with central localization. Sleep stages were included as part of the electroencephalographies performed in 31 individuals (76%), and epileptiform activity was recorded during sleep in all instances (100%). Definite clinical seizures were diagnosed in 17 individuals (42%) with a mean age of onset of 3.2 years (four months to six years), and focal seizures were the most common type of seizure observed (42%). Six subjects with definite clinical seizures needed polytherapy (35%). Delayed myelination and/or abnormal white matter hyperintensities were seen on neuroimaging in 19 individuals (61%). CONCLUSIONS: Epileptiform abnormalities are commonly seen in individuals with SATB2-associated syndrome. A baseline electroencephalography that preferably includes sleep stages is recommended during the initial evaluation of all individuals with SATB2-associated syndrome, regardless of clinical suspicion of epilepsy.

Síndrome branquio-oto-renal. Presentación de un caso / Branchio-oto-renal syndrome. Case study / Síndrome brânquio-otorrenal. Relato de caso

Resumen: El síndrome branquio-oto-renal (BOR) es un trastorno hereditario autosómico dominante, poco frecuente, que se presenta con expresividad variable y penetrancia reducida, con gran heterogeneidad clínica inter e intrafamiliar. Es causado por alteraciones del desarrollo del oído, riñones y de los segundos arcos branquiales, estructura que en el embrión en desarrollo da origen a tejidos del cuello. Los hallazgos clínicos más comunes son las fístulas o quistes en el cuello, déficit auditivo, malformaciones del oído externo con apéndices u hoyuelos preauriculares y afectación renal uni o bilateral que va de moderada a severa. El síndrome es causado principalmente por mutaciones en el gen EYA1 que actúa como regulador transcripcional durante la embriogénesis, las cuales se detectan en el 40% de los pacientes. Presentamos un caso ilustrativo de síndrome de BOR que se mostró con hallazgos clínicos sugestivos como fositas preauriculares, fístulas branquiales, hipoacusia severa con anomalías anatómicas del oído, compromiso renal y antecedentes familiares. En este paciente se encontró una variante patogénica en el gen EYA1: c.1081C>T (p.Arg361TER). Esta es considerada una variante nula, ya que provoca un codón de terminación prematuro que conduce a una pérdida de la función de la proteína. Dada la expresividad variable del síndrome de BOR, el diagnóstico molecular cobra importancia para evitar errores diagnósticos, iniciar el seguimiento familiar en cascada con el fin de identificar familiares afectados y para implementar medidas preventivas tendientes a disminuir la morbilidad y mortalidad causadas por este síndrome.

Summary: The branchio-oto-renal syndrome (BOR) is an uncommon autosomal dominant genetic disorder with variable expressivity, reduced penetrance and significant clinical and intra-familial heterogeneity. It is caused by alterations in the development of the ears, kidneys and second branchial arches, a structure that in developing embryos produces neck tissue. The most common clinical findings are neck fistulas or cysts, hearing loss, malformations of the outer ear with appendices and/or pre-auricular dimples and unilateral or bilateral moderate to severe renal involvement. The syndrome is mainly caused by mutations in the EYA1 gene that acts as a transcriptional regulator during embryogenesis, and which are detected in 40% of patients. We hereby introduce a representative case of BOR syndrome that showed suggestive clinical findings such as preauricular holes, branchial fistulas, severe hearing loss with anatomical anomalies of the ear, and renal impairment. In this case, we found a pathogenic variant in the EYA1 gene: c.1081C>T (p.Arg361TER). This is considered a null variant, since it causes a premature stop codon that leads to protein function loss. Given the BOR Syndrome variable expressivity, molecular diagnosis is relevant to prevent diagnostic errors, initiate familial cascade screening in order to identify affected relatives and to implement preventive measures aimed at reducing the morbidity and mortality caused by this syndrome.

Resumo: A síndrome branquio-oto-renal (BOR) é uma desordem genética autossômica dominante incomum com expressividade variável, penetrância reduzida e significativa heterogeneidade clínica e intrafamiliar. É causada por alterações no desenvolvimento das orelhas, rins e segundos arcos branquiais, as quais durante o desenvolvimento do embrião produzem tecido no pescoço. Os achados clínicos mais comuns são fístulas ou cistos no pescoço, déficit auditivo, malformações da orelha externa com apêndices e / ou seios pré-auriculares e comprometimento renal moderado a grave unilateral ou bilateral. A síndrome é causada principalmente por mutações no gene EYA1, que atua como regulador da transcrição durante a embriogênese e é detectada em 40% dos pacientes. Introduzimos aqui um caso representativo da síndrome BOR que apresentou achados clínicos sugestivos, como fossas pré-auriculares, fístulas branquiais, perda auditiva grave com anomalias anatômicas da orelha e comprometimento renal. Nesse caso, encontramos uma variante patogênica no gene EYA1: c.1081C> T (p.Arg361TER). Isso é considerado uma variante nula, pois causa um códon de parada prematuro que leva a uma perda da função da proteína. Dada a expressividade variável da síndrome do ROR, o diagnóstico molecular é relevante para evitar erros de diagnóstico, iniciar o rastreamento em cascata familiar, a fim de identificar os familiares afetados e implementar medidas preventivas destinadas a reduzir a morbimortalidade causada pela síndrome.