Search Results (52)

Background: Pathogenic variants in the NEXMIF gene have been linked to a broad neurodevelopmental phenotype, encompassing autism spectrum disorder, intellectual disability, and epilepsy. Among epileptic manifestations, Jeavons Syndrome was observed in 24% of affected females in the largest cohort of NEXMIF-related disorders reported to date, but long-term adult outcomes remain poorly documented. Methods and Results: We report a 25-year-old Italian woman with drug-resistant Jeavons syndrome in which the combined approach of next-generation sequencing and chromosomal microarray analysis allowed us to identify, after a 13-year diagnostic odyssey, a de novo ~350 Kb microdeletion at Xq13.2q13.3 encompassing the entire NEXMIF coding region, with no other OMIM genes involved. To our knowledge, this is the first reported case of a patient harboring a deletion restricted to the entire coding sequence of the NEXMIF gene. The patient presented with moderate intellectual disability and seizure onset at age 10 years. Her epilepsy proved refractory to multiple antiseizure medications. Video-EEG/polygraphic monitoring at age 23 years confirmed epilepsy with eyelid myoclonia, demonstrating characteristic eyelid myoclonia with absences triggered by eye closure. Conclutions: This case provides a detailed clinical description of an adult patient useful for genetic counseling regarding adult outcomes and prognostic expectations. Furthermore, this study underscores the diagnostic value of chromosomal microarray analysis alongside next-generation sequencing in individuals with intellectual disability and drug-resistant epilepsy, in order to expedite the diagnostic pathway and enable timelier and more appropriate patient management. Full article

Mevalonate kinase deficiency (MKD) is a rare autosomal recessive autoinflammatory disorder with marked clinical heterogeneity, frequently leading to delayed diagnosis. We describe a 71-year-old woman with lifelong episodic inflammatory symptoms beginning in infancy, including recurrent fevers, lymphadenopathy, and gastrointestinal and mucocutaneous manifestations, later evolving into intermittent arthralgia, myalgia, and fatigue. A unifying diagnosis was established when genetic testing identified two missense pathogenic MVK variants consistent with compound heterozygous MKD, supported by elevated serum IgD levels and a characteristic clinical phenotype. This case illustrates the essential role of molecular genetic testing in resolving prolonged diagnostic odyssey, in guiding surveillance for complications such as AA amyloidosis, and enabling targeted therapeutic strategies. Full article

Background: Kleefstra syndrome (KS) is a rare neurodevelopmental disorder caused by haploinsufficiency of EHMT1; it is characterized by global developmental delay, intellectual disability, hypotonia, distinctive facial features, and variable congenital anomalies. Autistic features, behavioral abnormalities and severe speech impairment are frequently reported. However, molecularly confirmed cases of KS from Africa remain extremely limited, largely due to restricted access to genomic diagnostic infrastructures. Methods: We describe a 15-month-old patient from Rwanda presenting with neonatal hypotonia, global developmental delay, short stature, and characteristic dysmorphic facial features. Comprehensive clinical evaluation was performed, followed by trio-based exome sequencing to identify the underlying genetic cause of this neurodevelopmental disorder. Results: Exome sequencing identified a de novo heterozygous frameshift variant in EHMT1 (NM_024757.5: c.2871dup; p. Phe958Leufs*219), confirming the diagnosis of KS. Conclusions: This report presents the first molecularly confirmed case of KS in Rwanda. It highlights additional clinical features like bilateral 5th toe clinodactyly, short stature and absence of obesity in KS. There is a need to further delineate the study of EHMT1 and investigate the natural history of KS across different populations for optimal patient management and to reduce diagnostic odyssey. The diagnostic utility of exome sequencing for neurodevelopmental disorders needs to be strengthened, with strong emphasis on expanding genomic medicine to help diagnose rare diseases in resource-limited settings. Full article

Interest in the genomic sequencing of healthy newborns has raised a discussion on whether this technology should be introduced into existing newborn screening (NBS) programs. This qualitative study explores a multi-stakeholder perspective on the future of genomic sequencing in NBS. Semi-structured interviews were conducted with 26 professionals involved in NBS or in clinical genome sequencing in the Netherlands. Participants highlighted opportunities such as the possibility to use one test for a wide range of genetic conditions, reducing diagnostic odyssey, expanding the scope of NBS, and increasing program efficiency. Challenges were raised regarding genetic variant interpretation, expected increased parental anxiety, data privacy issues, difficulties with information provision, and high costs. Three areas of tension between participants’ perspectives were identified: screening strategy, screening performance, and roles and responsibilities. It was emphasized that implementing genomic sequencing should not risk reducing the current high NBS participation, and that enhancing knowledge, communication, and collaboration between all stakeholders is needed. Although most participants did not believe genomic sequencing as a first-tier test is currently desirable and feasible, they acknowledged it has a role to play in the future of NBS. Future decision-making should consider the potential impact on the participation rate, program quality, and balancing benefits and harms. Full article

Background: Niemann–Pick type C is a lysosomal storage disorder that results from pathogenic variants in the NPC1 gene or in some cases from NPC2 pathogenic alterations. The disease presents a remarkable clinical variability that in some cases resembles common diseases, often resulting in a diagnostic odyssey or at least delaying proper diagnosis. In addition, the NPC1 gene is highly polymorphic, and consequently, when missense variants are identified after gene sequencing, accurate classification of their pathogenicity is essential to ensure appropriate access to available therapies and to provide reliable genetic counseling. Objectives: To get insights into the pathogenicity of a novel variant in NPC1, p.Cys800Ser, we created stable cell lines expressing this variant, in parallel with cell lines expressing the NPC1 wild-type and NPC1 pathogenic variants. Methods: We leveraged an isogenic cell line in which the NPC1 gene was knocked down and subsequently infected it with retroviruses carrying NPC1-WT and NPC1 variants C-terminally fused with an mNeonGreen tag. Three different NPC1 variants were included in this study: two known pathogenic variants, p.Ala1035Val and p.Pro1007Ala, and the novel p.Cys800Ser, whose significance was unknown. Results: We observed in the stable cell line expressing NPC1 p.Cys800Ser that the mutated NPC1 protein is transported to the lysosome similarly to the p.Pro1007Ala variant and affects lysosomal distribution. Conclusions: Using this approach, we could analyze the pathogenicity of each variant separately and these cell lines could be used for personalized medicine-based approaches and multi-omic studies. Full article

Genetic variation in ATP Binding Cassette Subfamily C Member 6 (ABCC6) can cause both pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI). There are 930 distinct missense variants in ABCC6 reported, 87% of which are of uncertain clinical significance (VUS). New approaches are needed to mechanistically interpret and classify these VUS. We developed 3D protein models of ABCC6 in three functionally relevant conformations to calculate the structural effects of variants. We also used three-dimensional (3D) hotspot detection and developed a mechanistic ontology for critical structure-based functions of ABCC6, enabling us to categorize genomic variants. We identified two 3D hotspots and six specific functions of ABCC6 which variants impact. From this, we propose a mechanism for pathogenicity for 41% of VUS according to their impacted function. We propose that 33 of these variants could be reclassified as Likely Pathogenic with the addition of these structure-based evidence. The mechanistic information we present will guide future research to better address calcification disorders and understand genetic variants. This work emphasizes the benefits of thorough, holistic, and protein-based approaches to genetic interpretation. Further, our VUS reclassification approach will improve the diagnosis of ABCC6-driven diseases, shortening diagnostic odysseys. We believe that computational structural genomics approaches will soon take prominence in genomics data interpretation and variant classification. Full article

Background/Objectives: X-linked intellectual disability (XLID) is a highly heterogeneous disorder accounting for ~10% of all males with ID. Next-generation sequencing (NGS) has revolutionized the discovery of causal XLID genes and variants; however, many cases remain unresolved. We present a four-generation syndromic XLID family with multiple males exhibiting variable degree of ID, focal dystonia and epilepsy. Methods: Extensive cytogenetic and targeted genetic testing was initially performed, followed by whole-exome sequencing (WES) and short-read whole-genome sequencing (WGS). Apart from the routine NGS analysis pipelines, sequencing data was revisited by focusing on poorly covered/mapped regions on chromosome X (chrX), to potentially reveal unidentified clinically relevant variants. Candidate variant validation and family segregation analysis were performed with Sanger sequencing. Results: All initial diagnostic testing was negative. Subsequently, 300 previously reported “dark” chrX coding DNA sequences, overlapping 97 genes, were cross-checked against 29 chrX genes highly associated (p < 0.05) with ID and focal dystonia, according to Phenomizer. Manual inspection of the existing NGS data in two low-coverage regions, chrX:25013469-25013696 and chrX:111744737-111744820 (hg38), revealed a recurrent pathogenic ARX variant NM_139058.3:c.441_464dup p.(Ala148_Ala155dup) (ARXdup24) associated with non-syndromic or syndromic XLID, including Partington syndrome. Sanger sequencing confirmed ARXdup24 in all affected males, with carrier status in their unaffected mothers, and absence in other unaffected relatives. Conclusions: After several years of diagnostic odyssey, the pathogenic ARXdup24 variant was unmasked, supporting a genotype–phenotype correlation in the first Partington syndrome family in Cyprus. This study highlights that re-examining underrepresented genomic regions and using phenotype-driven tools can provide critical diagnostic insights in unresolved XLID cases. Full article

Background: Rare pediatric neurological diseases (RPND) often remain undiagnosed for years, creating prolonged and costly diagnostic odysseys. Combining Human Phenotype Ontology (HPO)-based deep phenotyping with exome sequencing (ES) and reverse phenotyping offers the potential to improve diagnostic yield, accelerate diagnosis, and support sustainable healthcare in resource-limited settings. Objectives: To evaluate the diagnostic yield and clinical impact of an integrated approach combining deep phenotyping, ES, and reverse phenotyping in children with suspected RPNDs. Methods: In this multicenter observational study, eighty-one children from eleven hospitals in South Kazakhstan were recruited via the Central Asian and Transcaucasian Rare Pediatric Neurological Diseases Consortium. All patients underwent standardized HPO-based phenotyping and ES, with variant interpretation following ACMG guidelines. Reverse phenotyping and interdisciplinary discussions were used to refine clinical interpretation. Results: A molecular diagnosis was established in 34 of 81 patients (42%) based on pathogenic or likely pathogenic variants. Variants of uncertain significance (VUS) were identified in an additional 9 patients (11%), but were reported separately and not included in the diagnostic yield. Reverse phenotyping clarified or expanded clinical features in one-third of genetically diagnosed cases and provided supportive evidence in most VUS cases, although their classification remained unchanged. Conclusions: Integrating deep phenotyping, ES, and reverse phenotyping substantially improved diagnostic outcomes and shortened the diagnostic odyssey. This model reduces unnecessary procedures, minimizes delays, and provides a scalable framework for advancing equitable access to genomic diagnostics in resource-constrained healthcare systems. Full article

Background: The COX20 gene encodes a critical assembly factor for cytochrome C oxidase (complex IV), and biallelic loss-of-function variants in this gene cause mitochondrial complex IV deficiency, typically presenting in infancy or childhood with hypotonia, ataxia, neuropathy, or dystonia. Methods: This study describes an adult male patient with a broad clinical spectrum of central and peripheral nervous system involvement. Different medical genetic tests were performed for the patient, and only whole-genome trio sequencing identified pathogenic variants in the COX20 gene. A review of previously reported cases was conducted to compare clinical and imaging findings. Results: Two compound heterozygous COX20 variants in were identified: a known missense variant (c.41A>G; p.Lys14Arg) disrupting splicing, and a novel start-loss variant (c.2T>C; p.Met1?). The patient exhibited progressive ataxia, pyramidal signs, and peripheral neuropathy, accompanied by cervical spinal cord atrophy on spinal cord MRI and lower leg muscle fat infiltration on muscle MRI, an imaging feature not previously emphasized in COX20-related disease. Conclusions: A review of previously reported cases underscores broad clinical variability of the COX20-associated disorder, which may contribute to a prolonged diagnostic odyssey. Full article

Background and Objectives: Many diagnostic methods exist for identifying thyroid malignancy, but most of them resemble an odyssey, as the journey from palpating a nodule to receiving a definitive diagnose is often long and costly. The aim of the present study is to investigate the role of Sestamibi scintigraphy in the characterization of cytological indeterminate thyroid nodules. Materials and Methods: A focused literature review was conducted, emphasizing the comparison between Fine Needle Aspiration Biopsy (FNAB), the main diagnostic method for thyroid cancer, and Sestamibi. Results: It is widely accepted that Sestamibi is the primary alternative for patients with non-diagnostic FNAB. As shown in the literature, Sestamibi has a high negative predictive value in excluding thyroid malignancy. Conclusions: Much like Odysseus’ adventurous 10-year journey returning to Ithaca, the path to diagnosing thyroid cancer is not straightforward. Molecular imaging with 99mTc-Sestamibi may serve as a valuable adjunct in evaluating thyroid nodules with inconclusive cytological findings. Full article

Background/Objectives: Rare diseases are predominantly genetic in etiology and characterized by a prolonged ‘diagnostic odyssey’. Advances in genetic testing (GT) have helped shorten the time to diagnosis for rare/undiagnosed conditions. We aimed to synthesize the evidence on psychosocial factors related to GT for rare diseases to inform more person-centered approaches to care. Methods: We conducted a systematic literature search in six databases using structured terms (September 2024). Retrieved articles underwent independent dual review. Data were extracted and collated in tables for analysis. Thematic analysis was used to identify promoters/barriers to GT for patients and families. Findings were validated by a patient advocate and were reported using PRISMA-ScR guidelines. Synthesized findings were mapped to the Theory of Planned Behavior to inform intervention development. Results: Of 1730 retrieved articles, 32 were included for data extraction/synthesis. Studies employed qualitative (n = 19), quantitative (n = 10), and mixed-methods (n = 3) approaches. Nearly all (29/32, 91%) were non-interventional, reporting on decision-making cognitions/processes (19/32, 59%), attitudes/preferences (15/32, 47%), psychosocial impact (6/32, 19%), and knowledge/awareness (4/32, 8%) of pre-conception/prenatal/diagnostic GT and carrier screening. Promoters included understanding GT, ending the diagnostic odyssey, actionable outcomes, personal/family history, altruism, and reproductive decision-making. Barriers included logistical (e.g., distance, cost), psychological burden, perceived lack of benefit, and discrimination/social stigma concerns. Conclusions: Some psychosocial factors related to GT for rare diseases overlap with those in literature on GT for common conditions. Identified factors represent targets for theory-informed, person-centered interventions to support high-quality GT decisions that are informed and aligned with patient/family values and preferences. Full article

Background: Genetic causes of chronic diseases, once considered rare in adult-onset disease, now account for between 10 and 20% of cases of chronic kidney disease (CKD). Confirming a genetic diagnosis can influence disease management; however, the utility of genetic testing in older adults remains poorly understood, partly due to age-based restrictions on testing access. To better evaluate the diagnostic yield and clinical utility of genetic testing in this population, we analyzed data from adults aged ≥50 years with CKD who were assessed in a specialized kidney genetics clinic. Methods: We studied a cohort of 125 adults with CKD aged ≥50 years at the time of genetic testing. Genetic testing included gene panels targeting disease-related genes based on clinical phenotype, and/or exome sequencing for additional monogenic causes if the initial panel testing was inconclusive. Results: Pathogenic variants in disease-related genes were identified in 38% of patients. The highest diagnostic yield (48%) was in patients aged 50–54 years. The most common diagnosis post-testing was glomerulopathies (32%). Clinical utility, shown through the case series, included modifications to treatment and clinical management, as well as a reduction in the diagnostic odyssey. Conclusions: Our findings from a dedicated Kidney Genetics Clinic show that genetic testing in adults ≥50 years with CKD has significant diagnostic and clinical utility. These results support guideline recommendations that there should be no upper age limit for genetic testing. Future research in unselected CKD populations is needed to establish the broader applicability and feasibility of genetic testing in older adults. Full article

Background and Clinical Significance: Ciliopathies are a heterogeneous group of diseases caused by damage to the primary cilium. Disorders of ciliary motility can lead to a wide range of clinical manifestations, including infertility, lateralization defects, lung infections, and more. Some ciliopathies associated with kidney disease include nephronophthisis, polycystic disease, and renal cell carcinoma. Since they are clinically and genetically diverse, their diagnosis may require a longer time and one or more genetic assays. Case presentation: We present the case of a 43-year-old man with a wide anamnesis, including unexplained nephrolithiasis, bronchiectasis, recurrent otitis media since infancy, appendicular lithiasis, and infertility. After a long history of various clinical examinations and consultations with diverse specialists, he was referred to genetic counseling. Whole exome sequencing (WES) revealed a homozygous pathogenic variant in the RSPH3 gene—NM_031924.8:c.205-2A>G—which was later confirmed through Sanger sequencing. It is classified as pathogenic in widely used databases and is associated with primary ciliary dyskinesia. This condition can present nontypically, and the patients might suffer from an extensive diagnostic odyssey. Being mindful of its clinical and genetic heterogeneity can shorten the period until diagnosis. Conclusions: It is essential to have this condition included in differential diagnosis and involve specialists from the medical/clinical genetic department in a multidisciplinary team. Genetic confirmation through WES or another molecular genetic method is crucial for the therapeutic approach and to adequately perform genetic counseling for patients and their families. Full article

(1) Background: Most rare disease patients endure long delays in obtaining a correct diagnosis, the so-called “diagnostic odyssey”, due to a combination of the rarity of their disorder and the lack of awareness of rare diseases among both primary care professionals and specialists. Next-generation sequencing (NGS) techniques that target genes underlying diverse phenotypic traits or groups of diseases are helping reduce these delays; (2) Methods: We used a combination of biochemical (thin-layer chromatography and high-performance liquid chromatography-tandem mass spectrometry), NGS (resequencing gene panels) and splicing assays to achieve a complete diagnosis of three patients with suspected metachromatic leukodystrophy, a neurologic lysosomal disorder; (3) Results: Affected individuals in each family were homozygotes for harmful variants in the ARSA gene, one of them novel (c.854+1dup, in family 1) and the other already described (c.640G>A, p.(Ala214Thr), in family 2). In addition, both affected individuals in family 2 were carriers of a known pathogenic variant in an additionallysosomal disease gene, GNPTAB (for mucolipidosis III). This additional variant may modify the clinical presentation by increasing lysosomal dysfunction. (4) Conclusions: We demonstrated the deleterious effect of the novel variant c.854+1dup on the splicing of ARSA transcripts. We also confirmed the involvement of variant c.640G>A in metachromatic leukodystrophy. Our results show the power of diagnostic approaches that combine deep phenotyping, NGS, and biochemical and functional techniques. Full article

Biochemical phenotyping has been the milestone for diagnosing and managing patients affected by inborn errors of intermediary metabolism (IEiM); however, identifying the genotype responsible for these monogenic disorders greatly contributes to achieving these goals. Herein, whole-exome sequencing (WES) was used to determine the genotypes of 95 unrelated Mexican pediatric patients suspected of having IEiM. They were classified into those bearing specific biochemical abnormalities (Group 1), and those presenting unspecific biochemical profiles (Group 2). The overall concordance between the initial biochemical diagnosis and final genotypic diagnoses was 72.6% (N = 69/95 patients), with the highest concordance achieved in Group 1 (91.3%, N = 63/69), whereas the concordance was limited in Group 2 (23.07%). This finding suggests that previous biochemical phenotyping correlated with the high WES diagnostic success. Concordance was high for urea cycle disorders (94.1%) and organic acid disorders (77.4%). The identified mutational spectrum comprised 83 IEiM-relevant variants (pathogenic, likely pathogenic, and variants of uncertain significance or VUS), including three novel ones, distributed among 29 different genes responsible for amino acid, organic acid, urea cycle, carbohydrate, and lipid disorders. Inconclusive WES results (7.3%, N = 7/95) relied on monoallelic pathogenic genotypes or those involving two VUS for autosomal-recessive IEiMs. A second monogenic disease was observed in 10.5% (N = 10/95) of the patients. According to the WES results, modifications in treatment had to be made in 33.6% (N = 32/95) of patients, mainly attributed to the presence of a second monogenic disease, or to an actionable trait. This study includes the largest cohort of Mexican patients to date with biochemically suspected IEiM who were genetically diagnosed through WES, underscoring its importance in medical management. Full article