IntroductionPathogenic variants in the DMD gene maintaining the open reading frame typically cause Becker muscular dystrophy. Here, we report a 7.7-year-old boy exhibiting a severe Duchenne muscular dystrophy phenotype, despite an in-frame deletion of DMD exons 50–51 identified by initial genetic testing, representing a notable exception to the conventional reading-frame rule.MethodsTo elucidate his phenotype-genotype discordance, muscle biopsy and subsequent dystrophin protein and mRNA analyses were conducted, followed by long-read sequencing of DMD gene and splicing analysis.ResultsMuscle biopsy revealed a dystrophic pattern and negative expression of dystrophin-N and dystrophin-C. The dystrophin mRNA analysis identified two out-of-frame DMD transcripts, which were different from the in-frame deletion of DMD exons 50–51 and can explain his severe phenotype. Long-read sequencing uncovered a novel deletion variant (~97kb) in DMD gene, which produced the two out-of-frame transcripts through aberrant splicing.ConclusionThis case underscores the necessity of a stepwise molecular analysis strategy for the interpretation of phenotype-genotype discordance in dystrophinopathy. This stepwise diagnostic approach is essential for accurately characterizing DMD variants, guiding patient management, and genetic counseling.

Thalassemia is a group of inherited blood disorders caused by defects in hemoglobin production, the protein that transports oxygen in red blood cells. These diseases are characterized by either diminished or missing production of one of the globin chains, which are often the alpha or beta chains that comprise hemoglobin. Diagnosis is based on a combination of laboratory tests, including hemoglobin electrophoresis, globin chain chromatography, and genetic analysis. However, diagnosis can become challenging when typical hematological features of thalassemia are not matched by expected biochemical findings. One such situation occurs when HbA2 levels appear normal despite a suspected β-thalassemia trait. This can happen when a β-globin gene variant is present alongside a δ-globin gene pathogenic variant, producing an atypical profile that may mask the true diagnosis. In this case report, we describe a patient carrying a heterozygous β-globin pathogenic variant (HBB c.118C>T; p.Gln40Ter, also known as codon 39) coexisting with a large novel 1.6 kb deletion in the delta-globin gene (HBD) that removes the first two exons. We discuss the diagnostic challenges and clinical implications associated with this rare genetic combination, emphasizing the critical role of comprehensive molecular testing in accurately identifying complex thalassemia cases. This report contributes to the literature by documenting a novel δ-globin deletion in combination with a β-thalassemia variant, providing valuable insights for clinicians and geneticists in the interpretation and management of atypical thalassemia profiles.

BackgroundNon-invasive prenatal testing (NIPT) has emerged as a significant advancement in prenatal screening that offers safer and more accurate detection of chromosomal abnormalities compared to conventional methods. The study aimed to evaluate the status of NIPT adoption in the Kingdom of Saudi Arabia (KSA).MethodsA comprehensive 3-phased study was conducted to examine the status of NIPT in KSA. In Phase I targeted literature review was conducted followed by Phase II and Phase III which involved qualitative interview-based exploration with key stakeholders and round table discussion with key opinion leaders, respectively.ResultsKey stakeholders in KSA underscore NIPT’s clinical value and economic benefits while addressing coverage disparities and the push for national guidelines. In KSA, NIPT prescription is influenced by multiple factors such as logistics, personnel, cost, accessibility, policy, and validation. Addressing these factors is important for the widespread adoption of NIPT as a primary screening test. Key opinion leaders suggest that accurate infrastructure, multidisciplinary care, patient education, and expansion of NIPT’s scope are crucial. To address current challenges, proactive collaboration of both public and private sectors is essential. NIPT usage has increased in KSA over time. It has now been recommended for all pregnant women, leading to an increase in demand for national guidelines to regulate the practice along with awareness campaigns about the value of testing.ConclusionA structured, phased roadmap for implementing NIPT in Saudi Arabia is crucial to ensure cost-effectiveness, cultural and ethical appropriateness, and nationwide access for all pregnant women.

The TTN gene (MIM:188840) encodes titin, the largest human protein with exclusive expression in the cardiac and skeletal muscles. Rare variants disrupting the TTN gene are frequent causes of dilated cardiomyopathy and several forms of skeletal myopathy. We report a unique occurrence of two novel, distinct but overlapping intragenic TTN deletions in multiple relatives from a single Czech family with the clinical manifestation of dilated cardiomyopathy (DCM). After clinical exome sequencing using the custom virtual gene panel, two distinct deletions affecting the TTN gene (NM_001267550.2) were detected. The first deletion (3.599 kb in length) encompasses five exons with the breakpoints in exons 326 and 330. The longer one (4.859 kb in length) disrupts exon 326 only. Both deletions segregate with the cardiomyopathy phenotype, and none of the tested individuals carry both. The familial segregation of two distinct intragenic TTN deletions extends the broad spectrum of rare variants in the pathogenesis of DCM. The presence of severely affected carriers of the reported DNA variants and obligatory healthy non-carriers raises the debate on their ancestral origin. Our data demonstrate the clinical benefits of the family cascade screening and molecular genetic analysis in familial DCM, enabling early and effective multidisciplinary medical care.

IntroductionA lack of experience diagnosing and treating rare diseases contributes to delayed or incorrect diagnoses, and optimal clinical treatment is often unachievable. Miller-McKusick-Malvaux syndrome (3M syndrome, also known as dolichospondylic dysplasia) is a rare genetic disorder with unknown prevalence. It is inherited in an autosomal recessive manner and is characterized by severe intrauterine and postnatal growth retardation, dysmorphic facial features, and skeletal abnormalities.MethodsWhole exome sequencing (WES) was performed on the proband using Twist Human Core Exome Plus Kit (Twist Bioscience) and sequenced with Illumina technology (100x depth of mean coverage). Alignment and variant calling were performed with an in-house bioinformatics pipeline. The identified variants were annotated using the Ensembl VEP and multiple databases, including ClinVar, dbSNP, HGMD, and GnomAD. XHMMv1.0.ResultsThis article presents the diagnostic process in siblings diagnosed with 3M syndrome, caused by homozygous variant c.3523C > T (p.His1175Tyr) in the CUL7 gene.DiscussionThis is the first description of a familial syndrome from a local population. Identifying new gene variants has helped expand the spectrum of variations associated with the pathogenesis of 3M syndrome. The expanding database of genetic variants, combined with knowledge of the spectrum and severity of a patient’s clinical symptoms, provides the opportunity to identify genotype-phenotype correlation relevant to medical care.

Background3M syndrome is a rare autosomal recessive genetic disorder characterized by significant intrauterine and postnatal growth restriction. There is limited research on its genetic basis within the Chinese population.MethodsWe performed trio-based whole-exome sequencing to identify the pathogenic gene in the affected child and collected and organized clinical and imaging data. Relevant information was reviewed through a literature search.ResultsIn this study, we present a case involving prenatal diagnostic abnormalities and postnatal confirmation of 3M syndrome, including detailed documentation of clinical features and associated genetic variants. Notably, during prenatal ultrasound examination, the fetus exhibited increased nuchal translucency (NT) and delayed limb development. Postnatally, whole-exome sequencing revealed the compound heterozygous mutations in the CUL7 gene: c.3646–2A>G and c.3355+5G>A. The splicing mutation c.3646–2A>G is a novel pathogenic mutation, while the c.3355+5G>A mutation has been previously reported. In-silico analysis predicted strong pathogenicity for both splicing mutations. Through follow-up, we observed that the patient’s height and weight are below the first percentile, with abnormal skeletal development and distinctive facial features. Based on literature review of reported cases, these mutations disrupt the normal function of CUL7-OBSL1-CCDC8 complex in the ubiquitin-proteasome pathway, leading to impaired growth regulation.DiscussionThis study identified a novel splicing mutation in the CUL7 gene in a patient with 3M syndrome, expanding the genetic spectrum of this disorder and contributing novel insights for clinical diagnosis and management.

PurposeX-linked severe combined immunodeficiency (X-SCID) is an inherited immune disorder caused by pathogenic variants in the IL2RG gene, leading to recurrent infections. Identifying these variants and elucidating their pathogenic mechanisms are crucial for precise diagnosis and treatment, prenatal diagnosis, and preimplantation genetic testing (PGT). This study aimed to identify candidate variants in four families with suspected immunodeficiency, assess their pathogenicity, elucidate their pathogenic mechanisms, and provide a basis for precise treatment, prenatal diagnosis, and PGT.Patients and MethodsFour families with suspected immunodeficiency were recruited from the Reproductive and Genetic Hospital of CITIC-Xiangya. Whole exome sequencing (WES) was used to identify the genetic etiology. Functional experiments were performed to assess the pathogenicity of the identified IL2RG variants, and to elucidate their pathogenic mechanisms.ResultsWES identified four IL2RG variants: three hemizygous (c.569G>C:p.R190P, c.515T>C:p.L172P, c.217A>C:p.T73P) and one heterozygous (c.1091C>T:p.T364I) variants. Three of these variants were novel. Initially three variants (p.R190P, p.T73P, and p.T364I) were classified as variants of uncertain significance (VUS) and one (p.L172P) was likely pathogenic (LP) according to ACMG/AMP guidelines. Functional analyses revealed reduced STAT5 phosphorylation and transcriptional activity across all variants, supporting the reclassification of three variants (p.R190P, p.L172P, and p.T73P) as likely pathogenic (LP), and one variant (p.T364I) as VUS with a Bayesian score of 5. Furthermore, IP-MS analysis revealed that the mutant IL2RG resulted in reduced cell-surface expression and abnormal nuclear localization. Therefore, the identified IL2RG variants impair IL-2-induced STAT5 phosphorylation and transcriptional activity to cause X-linked severe combined immunodeficiency in these families.ConclusionThis study highlights the critical role of functional analysis in clarifying variant pathogenicity and provides a clear example of pathogenicity assessment for IL2RG variants. Integrating genomic and functional data enhance diagnostic precision and informs precise treatment strategies, genetic counseling, prenatal diagnosis, and PGT for X-SCID.

Zellweger syndrome (ZS) is a heterogeneous group of clinical conditions that commonly manifest with neurodevelopmental delay, multiple neurological abnormalities, visual and auditory impairments, and adrenocortical dysfunction. ZS is an autosomal recessive peroxisomal disorder resulting from mutations in one of over 13 identified genes. We report the case of a male child with episodic seizures starting at 18 days of life, followed by neurodevelopmental delay and neuroimaging findings of asymmetric polymicrogyria and cortical abnormalities. His healthy parents were consanguineous, and notably, a brother, who passed away at the age of 5 years-old, had epilepsy and adrenoleukodystrophy. Exome sequencing allowed the identification of a novel stop-loss homozygous variant in the PEX5 gene in the index case. The phenotype associated to this gene, Zellweger syndrome, as well as the inheritance mechanism, is consistent with that observed in both the patient and his brother.

Familial Mediterranean fever (FMF) is an inherited autoinflammatory disorder resulting in recurrent fever, polyserositis, and arthralgias. It is caused by mutations in the MEFV (Mediterranean Fever) gene. We report a Lebanese pediatric patient with typical FMF symptoms and unique triple homozygous variations E148Q-P369S-R408Q in the MEFV gene. This is the second-ever reported case with this specific triple homozygous variation.

ObjectiveAllo-HSCT is a well-established treatment for several hematological malignancies. Relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains a significant problem and is associated with a poor prognosis and low overall survival. Chimerism analysis is one of the tools applied in post-transplant monitoring, as an increasing fraction of recipient cells after HSCT has been linked to a higher risk of relapse.Study DesignIn this retrospective, single-centre study we have analysed the data of patients treated with allo-HSCT for a range of hematological malignancies in the Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, Poland, between years 2002–2018.ResultsFor all 103 patients 3-years OS was 72.6 (95% CI: 64.3–82.0) and 3-years EFS was 72.0 (95% CI: 63.5–81.6). There were no differences in 3-years OS and EFS in group of patients who achieved FDC <14 and >14 days: 67.9 (95% CI: 57.4–80.3) vs 81.9 (95% CI: 69.7–96.2), p = 0.220 and 66.0 (95% CI: 55.3–78.7) vs 84.1 (95% CI: 72.3–97.9), p = 0.073, respectively. Early FDC achievement was not significantly associated with risk of relapse, p = 0.181. Based on multivariate Cox regression analysis AML/MDS increased risk of relapse 3x compared to ALL, HR = 2.72, CI95 [1.24–5.98], p = 0.013; PB/CB increased the risk nearly 3x compared to cells from BM, HR = 2.52, CI95 [1.12–5.65], p = 0.025.ConclusionIn presented study, achieving early FDC was not associated with lower risk of relapse and had no impact on overall and event-free survival. However, the study presents a unique data of very early chimerism in a large cohort of paediatric patients with haematological malignancies treated within a single unit. Possible extensions to this study, to include analysing more data from a larger patient cohort, may allow us to determine the exact prognostic value of very early chimerism analysis to establish relevant cutoff values and risk thresholds for intervention.