Search Results (527)

GM1 gangliosidosis is an autosomal recessive lysosomal storage disorder caused by a deficiency of β-galactosidase due to pathogenic variants in the GLB1 gene. Almost 300 pathogenic or likely pathogenic variants have been identified, associated with a phenotypic spectrum ranging from GM1 gangliosidosis to mucopolysaccharidosis type IVB. Disease severity is largely determined by the extent to which specific variants impair enzymatic catalytic activity, particularly through disruption of substrate recognition and binding within the active site. We report a patient with GM1 gangliosidosis type I harboring two pathogenic missense variants, c.808T>G (p.Tyr270Asp) and c.808T>C (p.Tyr270His), in a compound heterozygous state. To the best of our knowledge, this specific allelic combination has not been previously described. Both variants affect the same codon, resulting in distinct amino acid substitutions at position 270, a residue critically involved in maintaining the structural and functional integrity of the catalytic domain of β-galactosidase. Disruption at this site is expected to severely compromise enzymatic activity. Comparative analysis with previously reported cases carrying variants at the same residue, in either homozygous or compound heterozygous states, demonstrates a possible consistent association with the infantile form of GM1 gangliosidosis, characterized by a rapidly progressive neurodegenerative course and multisystem involvement. Collectively, these findings provide additional support for the hypothesis that codon 270 can be regarded as a critical functional hotspot within GLB1, where even distinct amino acid substitutions can result in profound enzymatic dysfunction and a severe early-onset phenotype. Full article

Background/Objectives: DNAJC3-related syndromic monogenic diabetes is a rare autosomal recessive disorder that presents as juvenile-onset non-autoimmune diabetes; it has been associated with sensorineural hearing loss, hypothyroidism, short stature, and variable degrees of neurological manifestations. A delayed diagnosis occurs frequently because of fragmented subspecialty care and lack of awareness of syndromic monogenic diabetes. Methods: We report a 34-year-old Saudi male from a consanguineous family with insulin-treated diabetes diagnosed during adolescence. He had long-standing sensorineural hearing loss, hypothyroidism, and short stature, which were managed separately. Results: Genetic analysis using whole-exome sequencing identified a homozygous likely pathogenic DNAJC3 variant, c.1177C>T p.(Arg393*), confirming the diagnosis of DNAJC3-related syndromic monogenic diabetes. In addition, he demonstrated no clinically evident neurological manifestations at the time of evaluation, including ataxia, despite reaching adulthood, highlighting the phenotypic variability associated with DNAJC3-related disease. Conclusions: This case adds to the growing evidence supporting phenotypic variability in DNAJC3-related syndromic monogenic diabetes by describing an adult presentation without clinically evident neurological manifestations at the time of evaluation. It highlights how systemic manifestations may remain unrecognized when managed separately across different specialties. In individuals with atypical diabetes accompanied by multisystem involvement, particularly in the setting of consanguinity, early consideration of monogenic diabetes and timely genetic testing may facilitate accurate diagnosis and molecular classification. Establishing a specific genetic diagnosis supports appropriate genetic counseling, informs reproductive decision-making, and may help reduce prolonged diagnostic uncertainty. Full article

Background/Objectives: Arthrochalasia Ehlers–Danlos syndrome (aEDS) is a rare connective tissue disorder characterized by severe joint hypermobility, congenital hip dislocation, skin hyperextensibility, and muscle hypotonia. It is typically caused by heterozygous splice-site variants in COL1A1 or COL1A2, leading to exon 6 skipping. Autosomal recessive forms are extremely rare and have been reported predominantly in families from Saudi Arabia carrying the homozygous COL1A1 missense variant c.2050G>A, p.(Glu684Lys), with clinical presentations ranging from severe to mild. Methods: Clinical and molecular genetic evaluation of the patient was performed. Whole-exome sequencing was carried out, followed by confirmatory Sanger sequencing in the proband and both parents. Results: A 10-month-old boy presented with severe congenital hypotonia, bilateral hip dislocation, generalized joint hypermobility, skin hyperextensibility and craniofacial dysmorphism. A homozygous likely pathogenic variant NM_000088.4:c.2050G>A, p.(Glu684Lys) was identified in exon 31 of COL1A1; both healthy parents were confirmed to be heterozygous carriers of this variant. To our knowledge this is the first reported case in the Russian population and one of the few cases described worldwide of an autosomal recessive arthrochalasia-like EDS phenotype. Conclusions: This case further refines the phenotypic characterization associated with the recurrent homozygous COL1A1 p.(Glu684Lys) variant, demonstrating an arthrochalasia-like EDS phenotype of intermediate severity between the severe neonatal form with respiratory distress and recurrent fractures and the classical EDS. It further highlights the importance of considering collagenopathies in the differential diagnosis of congenital hypotonia, particularly in cases initially suggestive of neuromuscular disorders. Full article

Background and Clinical Significance: SWI/SNF chromatin remodeling complex-deficient malignancies constitute an aggressive group of undifferentiated tumors defined by inactivation of core subunits including SMARCA4 (BRG1) or SMARCB1 (INI1). In the head and neck, these tumors predominate in the sinonasal tract; oral cavity presentations are exceedingly rare, with reported cases predominantly representing metastatic disease. Peri-implant gingival masses in clinical practice are overwhelmingly reactive, but their occasional malignant nature mandates timely biopsy and thorough pathologic workup. We report the first comprehensively molecularly characterized case of a peri-implant gingival SWI/SNF complex-deficient tumor with confirmed biallelic SMARCA4 inactivation. Case Presentation: A 75-year-old man presented with a one-week history of a rapidly enlarging exophytic erythematous peri-implant gingival mass in the right posterior mandible (region 44–47). Incisional biopsy demonstrated an undifferentiated high-grade tumor with epithelioid, plasmablastoid, and focally rhabdoid morphology with necrosis. Immunohistochemistry showed complete loss of BRG1 (SMARCA4) with retained INI1 (SMARCB1), EMA positivity, Ki-67 of approximately 100%, and negativity across all lineage-specific markers (hematolymphoid, epithelial, melanocytic, endothelial, squamous). Comprehensive next-generation sequencing (Oncomine Comprehensive Assay Plus) confirmed biallelic SMARCA4 inactivation via a truncating nonsense mutation (p.Trp1346Ter; VAF 73.85%) combined with copy number loss, establishing the molecular mechanism underlying BRG1 protein loss. Co-occurring alterations included homozygous CDKN2A/CDKN2B deletion, MTAP loss (9p21.3), clonal TP53 and KEAP1 mutations, and intermediate–high tumor mutational burden (13.3 mutations/Mb) with microsatellite stability. The patient initiated carboplatin–paclitaxel and achieved a partial response at one month with further shrinkage by four months. This case illustrates a rare oral cavity manifestation of SWI/SNF complex deficiency arising in a peri-implant location, with a diagnostic workup that required integration of immunohistochemistry and molecular profiling for definitive characterization. The MTAP deletion co-occurring with homozygous CDKN2A/B loss identifies a potentially actionable synthetic lethal vulnerability to MAT2A and PRMT5 inhibitors currently under clinical investigation. An occult primary site could not be fully excluded due to absence of a dedicated staging workup. Conclusions: Rapidly enlarging peri-implant gingival masses should prompt timely biopsy and SWI/SNF marker testing when histology is high-grade and lineage-ambiguous. NGS-based molecular profiling confirms diagnosis, elucidates mechanism, and reveals actionable targets in this rare tumor class. Full article

Background: Autosomal recessive intellectual developmental disorder-13 (MRT13; OMIM #613192) is a rare neurodevelopmental disorder caused by pathogenic variants in TRAPPC9. Most reported variants are single-nucleotide variants (SNVs), small insertions/deletions, or copy number variants (CNVs), whereas complex structural variants (SVs) remain poorly characterized. Objectives: This study sought to review the clinical and molecular spectrum of TRAPPC9-related disorder, harmonize reported variants, explore genotype–phenotype correlations, and expand the mutational spectrum by reporting a novel patient with a cryptic SV. Methods: We report a novel patient whose diagnostic workup included array-CGH, whole-exome sequencing, karyotyping, and optical genome mapping. Additionally, a systematic literature search was primarily conducted in PubMed/MEDLINE from 2009 to January 2026, with Embase, Web of Science, Google Scholar, Orphanet, OMIM, and ClinVar used as supplementary sources. Patients carrying pathogenic/likely pathogenic TRAPPC9 variants were included. Clinical and molecular data were extracted and descriptively summarized. Genotype–phenotype correlations were explored. Reported variants were re-annotated using MANE Select reference transcripts. Results: The reported patient showed biallelic TRAPPC9 disruption due to two independently inherited structural variants: a maternal ~35 kb intragenic deletion involving exons 10–12, identified by 400K array-CGH, and a paternal balanced translocation t(4;8) disrupting TRAPPC9 within intron 8, characterized by trio-OGM and paired-end whole-genome sequencing (PE-WGS). Thirty-one studies reporting 75 previously published patients were included in the literature review; together with the novel patient described here, the final cohort comprised 76 patients. Intellectual disability was present in 100% of cases, followed by brain MRI abnormalities (95.9%), microcephaly (82.3%), motor delay (71.4%), dysmorphic features (69.8%), obesity (52.8%), behavioral abnormalities/autism spectrum disorder (49.2%/43.8%), and epilepsy (15.9%). Most patients (84.2%) harbored homozygous variants. Thirty-two distinct sequence variants were identified, predominantly loss-of-function. CNVs were identified in 13.2% of patients. No genotype–phenotype correlations were identified. Conclusions: The systematic review provides an updated and harmonized overview of the clinical and molecular spectrum of TRAPPC9-related disorder, supporting the presence of a recognizable phenotype and confirming the predominance of loss-of-function variants. Our case further highlights the contribution of cryptic structural variants to the mutational spectrum of TRAPPC9 and the diagnostic value of advanced genomic approaches. Full article

Inborn errors of immunity, including primary immunodeficiency disorders (PIDs), comprise a heterogeneous group of genetic conditions characterized by immune system dysfunction. One such rare PID is CD137 deficiency, which results from TNFRSF9 mutations. CD137, also known as 4-1BB, plays a pivotal role in immune system regulation and co-stimulation. This literature review explores CD137 deficiency and its implications, emphasizing its association with EBV-associated lymphoproliferative disease and potential therapeutic targets. We present the case of a 21-year-old female patient with CD137 deficiency who experienced recurrent infections, autoimmunity, and lymphoma. Genetic analysis revealed that the patient had a homozygous TNFRSF9 variant. The patient subsequently developed severe Epstein–Barr virus (EBV)-associated lymphoproliferative disease, which is one of the clinical manifestations associated with CD137 deficiency. Additionally, this review discusses similar cases in the literature and details the clinical manifestations and immune abnormalities associated with CD137 deficiency. Understanding the genetic complexity of CD137 deficiency and the immune system dysregulation it causes provides insights into potential therapeutic interventions for affected individuals. This review highlights the role of CD137 as a crucial regulator of immune homeostasis and a potential target for immunotherapy in autoimmune diseases and malignancies. Full article

Background/Objectives: Cardiovascular diseases remain a leading cause of global mortality. The C-X-C motif chemokine ligand 12 (CXCL12) gene has been implicated in atherosclerosis; however, its relationship with lipoprotein subfraction profiles remains unclear. The primary objective of this study was to investigate the association between the CXCL12 rs1801157 C>T single nucleotide polymorphism (SNP) and coronary artery disease (CAD) risk in a Turkish population. The secondary objective was to evaluate the relationship between this polymorphism and LDL and HDL lipoprotein subfraction profiles. Methods: This case–control study included 139 patients with angiographically confirmed CAD and 125 healthy controls. Genotyping was performed using TaqMan real-time polymerase chain reaction (PCR). Low-density lipoprotein (LDL) and high-density lipoprotein (HDL) subfractions were analyzed using the Lipoprint^® polyacrylamide gel electrophoresis system. Multivariable logistic and linear regression analyses were performed, adjusting for age, sex, body mass index (BMI), and major cardiovascular risk factors. Results: No significant differences in rs1801157 genotype or allele distributions were observed between groups (overall χ² = 0.459, p = 0.796). Logistic regression confirmed that the polymorphism was not an independent predictor of CAD risk (CT: OR = 1.396, p = 0.409; TT: OR = 1.458, p = 0.694). HDL-C was an independent protective factor (OR = 0.952, 95% CI: 0.910–0.996; p = 0.029). Notably, TT homozygous carriers exhibited significantly higher large HDL (p = 0.018) and intermediate HDL (p < 0.001) subfraction levels and markedly lower small LDL concentrations (p < 0.001). Multivariable linear regression confirmed these associations were independent of age, sex, and BMI. Conclusions: The CXCL12 rs1801157 variant does not directly influence CAD susceptibility but modulates lipoprotein quality by promoting larger HDL subfractions and reducing atherogenic small LDL particles, suggesting an indirect cardioprotective role through lipid metabolism. Full article

Introduction: Congenital myasthenic syndrome (CMS) is a rare hereditary disorder of the neuromuscular junction caused by pathogenic variants that affect acetylcholine transmission. We report three pediatric cases with CMS, including a rare homozygous CHRNE mutation previously described only once, a novel CHRNE compound heterozygous variant, and two novel DPAGT1 variants associated with limb-girdle CMS (LG-CMS), thereby expanding the known genetic and phenotypic spectrum of the disorder. Case presentation: The first patient, a 4-year-old girl born to consanguineous parents, presented with bilateral ptosis and fatigable weakness since infancy. Whole-genome sequencing revealed a homozygous CHRNE variant, c.991C>T. The second patient, a 4-year-old boy born to non-consanguineous parents, presented with congenital bilateral ptosis and ophthalmoplegia without generalized weakness. Genetic analysis identified compound heterozygous CHRNE variants, c.905C>G and c.1040T>C. Both patients demonstrated marked improvement with pyridostigmine therapy. The third patient, a 3-year-old girl born to non-consanguineous parents, presented with severe limb weakness requiring assistance in walking and performing daily activities with minimal ocular involvement, suggesting a diagnosis of LG-CMS. Genetic testing identified two novel variants in the DPAGT1 gene in the compound heterozygous form, c.710G>T and c.858C>A. The initial response to pyridostigmine diminished over time. Conclusions: These cases underscore the phenotypic heterogeneity of CMS, even within the same genetic subtype, and expand the existing mutational spectrum of CHRNE and DPAGT1 genes. This study also highlights the essential role of molecular diagnosis in distinguishing CMS from other neuromuscular disorders. Early genetic confirmation facilitates genotype-targeted therapy, prevents inappropriate immunosuppression, and enables informed reproductive counseling. Full article

Background: Vitamin D receptor (VDR) polymorphisms have been widely investigated as genetic determinants of neurodegenerative diseases, yet findings remain inconsistent and population-dependent. Evidence from the Middle East, North Africa, and Türkiye (MENA&T) regions, which is characterized by widespread vitamin D deficiency and distinct genetic backgrounds, has not been comprehensively synthesized. Methods: We conducted a systematic review and meta-analysis evaluating associations between four common VDR polymorphisms (ApaI rs7975232, FokI rs2228570, TaqI rs731236, and BsmI rs1544410) and the risk of multiple sclerosis (MS), Parkinson’s disease (PD), and Alzheimer’s disease (AD) in MENA&T populations. Six databases were searched from inception to November 2025. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated using fixed- and random-effects models across multiple genetic contrasts. Subgroup analyses by ethnicity were conducted for MS. Study quality was assessed using the Newcastle–Ottawa Scale (NOS), and the certainty of evidence was assessed using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE). Results: Nineteen unique case–control studies (20 reports), including 4744 participants, were included. For MS, the ApaI polymorphism showed consistent associations with increased risk across genetic models (random-effects ORs = 1.4–1.9), with stronger effects in Arab and Iranian populations and no association in Turkish cohorts. FokI showed associations with MS under selected genetic models, particularly recessive and homozygous contrasts, although findings were not consistent across all analytical approaches. TaqI showed model-dependent associations with substantial heterogeneity, while BsmI showed no significant association. For AD, a meta-analysis of two studies showed no significant associations. For PD, ApaI showed associations with increased risk across several models without heterogeneity; however, these findings were based on a limited number of studies. Overall certainty of evidence ranged from very low to moderate. Conclusions: In MENA&T populations, VDR ApaI polymorphism shows consistent evidence of association with MS susceptibility, while FokI may be associated under specific genetic models; evidence for AD and PD remains limited and should be considered exploratory. These findings highlight population-specific genetic heterogeneity and underscore the need for further large-scale studies to confirm these associations. These population-specific genetic associations underscore the importance of incorporating VDR genotyping into precision medicine frameworks for neurodegenerative disease risk stratification in MENA&T populations, where vitamin D deficiency is highly prevalent. Full article

Periventricular nodular heterotopia (PVNH) is a genetically heterogeneous malformation of cortical development with variable neurological outcomes. Among recessive forms, ARFGEF2-related disorder is uniquely characterised by the association of diffuse PVNH and progressive microcephaly. We describe a two-year-old boy born to consanguineous parents who presented with severe developmental delay, hypotonia, progressive microcephaly, and infantile-onset epileptic spasms with developmental regression. Brain MRI showed extensive bilateral PVNH associated with callosal hypoplasia and ventriculomegaly. EEG revealed dysmature background activity with multifocal epileptiform discharges and runs of asynchronous fast activity during sleep. Genetic testing identified a novel homozygous nonsense variant in ARFGEF2. The clinical course was characterised by drug-resistant epilepsy and multisystemic involvement, including feeding difficulties and recurrent respiratory infections. To contextualise this case, we performed a comprehensive review of previously reported patients, further delineating the clinical, neuroradiological, and electroclinical spectrum of ARFGEF2-related disorder. This case highlights progressive microcephaly as a key distinguishing feature of ARFGEF2-related PVNH and underscores the importance of early genetic diagnosis to guide targeted surveillance for extra-CNS complications and multidisciplinary care. Full article

The genomic landscape of myelodysplastic syndromes/neoplasms (MDS), a heterogeneous group of myeloid malignancies defined by bone marrow cell dysplasia with ineffective hematopoiesis, includes somatic and, less frequently, germline mutations in hematopoietic stem and progenitor cells, along with chromosomal abnormalities. The latest World Health Organization 2022 classification of myeloid neoplasms, as well as stratification in lower-risk (LR) and higher-risk (HR) MDS using either the Revised International Prognostic Scoring System (IPSS-R) or the Molecular International Prognostic Scoring System (IPSS-M), guide prognostic assessment and risk-adjusted therapy. We report the case of an 81-year-old patient diagnosed with LR-MDS according to IPSS-R that exhibited direct progression to acute myeloid leukemia. The retrospective analysis of paired DNA samples from MDS and leukemic phases, obtained four months apart, using both targeted next-generation sequencing and single nucleotide polymorphism array, indicated swift alterations in the genomic profile, being suggested that the leukemic clone emerged from the clone harboring homozygous TET2 and heterozygous SRSF2 variants that acquired RUNX1, BCOR, BCORL1 likely pathogenic mutations and trisomy 13. By employing IPSS-M for prognostic evaluation at the MDS phase, the patient would have been assigned to the HR-MDS category with a possible benefit from hypomethylating agent therapy. Risk stratification is of pivotal importance in a patient-centered approach to MDS treatment being significantly improved by incorporating the molecular genetic findings. Full article

Objectives: Oculocutaneous albinism (OCA), a group of inherited disorders characterized by deficient melanin synthesis, leads to hypopigmentation of the skin, hair, and eyes. OCA type 2 (OCA2) is caused by mutations in OCA2. This study aimed to characterize the comprehensive clinical and genetic spectrum of OCA2, and to identify the key ocular determinants of visual acuity. Methods: We enrolled 90 probands clinically diagnosed with albinism. Whole-exome sequencing and comprehensive ophthalmic examinations were performed. Results: OCA2 was confirmed in 29 probands (32.2%). Visual impairment was distributed as mild/no impairment (30.8%), moderate (53.8%), and severe/blindness (15.4%). All patients exhibited nystagmus and photophobia. Ocular phenotype grading showed distinct distributions: iris translucency (n = 25) was 68% grade 3, 20% grade 2, 8% grade 1, and 4% grade 4; fundus hypopigmentation (n = 26) was 42.3% grade 1, 30.8% grade 2, and 26.9% grade 3; and foveal hypoplasia (n = 20) was 70% grade 4, 25% grade 3, and 5% grade 1. We identified 33 OCA2 variants (26 compound heterozygous and 3 homozygous), with missense variants accounting for 62.1% of alleles. Five variants were identified to be novel. The severity of foveal hypoplasia demonstrated a strong, statistically significant negative correlation with visual acuity (r = −0.71, p < 0.001). Conclusions: OCA2 accounts for 32.2% of albinism cases, with moderate visual impairment being the most common (53.8%). Graded phenotyping demonstrated moderate-to-severe iris translucency (88%), mild fundus hypopigmentation (42.3%), and severe (grade 4) foveal hypoplasia (70%). The severity of foveal hypoplasia emerged as an important determinant of visual acuity. Full article

Fanconi anemia (FA) is a rare inherited disorder associated with impaired DNA repair, characterized by congenital anomalies, bone marrow failure, and a significantly increased risk of developing malignancies, particularly squamous cell carcinoma (SCC) of the head and neck. Treatment options for advanced SCC in FA are limited due to hypersensitivity to DNA-damaging agents. This article presents a unique case of SCC that developed in a 17-year-old patient with FA caused by a homozygous mutation in the FANCA gene. At the age of 10, he received a bone marrow transplant from a compatible related donor. Conditioning therapy included busulfan, thymoglobulin, and fludarabine, while graft-versus-host disease (GvHD) prophylaxis was administered with rituximab, methotrexate, and cyclosporine A. Nevertheless, he developed chronic cutaneous GVHD, which was treated for four years with ruxolitinib and tacrolimus, achieving only partial control. During this period, locally advanced cutaneous SCC (T3N0M0, stage III) manifested on the face. Surgery, radiation therapy, and immunotherapy with pembrolizumab led only to an initial partial response. This first pediatric case of immunotherapy for SCC in FA highlights the challenges of treating this rare patient group. Nevertheless, combining radiation therapy with immunotherapy may represent a possible option for disease control. Full article

Spinal muscular atrophy 5q (5q SMA) is one of the most prevalent autosomal recessive disorders globally. The underlying cause of 5q SMA is attributed to variants in SMN1. To date, there are no reported cases of gene-based therapy in rare patients with 5q SMA caused by subtle SMN1 variants of unknown clinical significance. We included 10 patients with the clinical manifestations of 5q SMA associated with intragenic variants in combination with a heterozygous SMN1 deletion in this retrospective study. Previously reported pathogenic or likely pathogenic variants were identified (e.g., c.*3+1del, c.815A>G (p.Tyr272Cys), and c.821C>T (p.Thr274Ile)). Variants of unknown clinical significance were also found, including a recurrent, previously unreported variant c.80A>C (p.Gln27Pro). We also report detailed molecular genetic and clinical data on 9 patients with 5q SMA. In addition, we provide results from the cohort of patients with gene-based therapy, consistent with data from patients with a homozygous SMN1 deletion. Full article

Calanthe aristulifera is a critically endangered orchid species of profound horticultural and ecological significance. However, establishing its species integrity is complicated by frequent natural introgression with sympatric relatives, such as C. sieboldii and C. discolor. Because phenotypic plasticity and complex hybrid swarms often confound traditional floral phenotyping, establishing an accurate molecular diagnostic system is imperative for conservation. In this study, we developed and validated high-throughput Kompetitive Allele-Specific PCR (KASP) and rapid Sequence-Characterized Amplified Region (SCAR) markers utilizing Genotyping-by-Sequencing (GBS) data from 64 Calanthe individuals—the same dataset reported in a companion population genomic study—re-analyzed using a more stringent marker-development pipeline. From 853,301 SNPs and 55,857 InDels initially identified, we filtered 62,231 high-quality SNPs and 1271 InDels to mine fixed homozygous alleles specific to C. aristulifera. This process isolated 179 SNP and 107 InDel loci to design three KASP markers (Ca-KASP1–3) and two SCAR markers (Ca-SCAR1–2). The KASP assays demonstrated a concordance of 98.4% (63/64 individuals; 95% CI: 91.6–99.7%) with morphological pre-classification. The single discordant case (Sample 52) was independently confirmed as a heterozygous hybrid by GBS-based population genomic analysis of the same individuals, providing molecular ground truth entirely independent of morphological assessment. The combined SCAR marker system yielded 96.9% concordance (62/64; 95% CI: 89.3–99.1%). Our findings provide an essential molecular framework for assessing species integrity and guiding the restoration of endangered C. aristulifera populations. Full article