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Despite clear technical superiority of genome sequencing (GS) over other diagnostic methods such as exome sequencing (ES), few studies are available regarding the advantages of its clinical application. We analyzed 1007 consecutive index cases for whom GS was performed in a diagnostic setting over a 2-year period. We reported pathogenic and likely pathogenic (P/LP) variants that explain the patients’ phenotype in 212 of the 1007 cases (21.1%). In 245 additional cases (24.3%), a variant of unknown significance (VUS) related to the phenotype was reported. We especially investigated patients which had had ES with no genetic diagnosis (n = 358). For this group, GS diagnostic yield was 14.5% (52 patients with P/LP out of 358). GS should be especially indicated for ES-negative cases since up to 29.6% of them could benefit from GS testing (14.5% with P/LP, n = 52 and 15.1% with VUS, n = 54). Genetic diagnoses in most of the ES-negative/GS-positive cases were determined by technical superiority of GS, i.e., access to noncoding regions and more uniform coverage. Importantly, we reported 79 noncoding variants, of which, 41 variants were classified as P/LP. Interpretation of noncoding variants remains challenging, and in many cases, complementary methods based on direct enzyme assessment, biomarker testing and RNA analysis are needed for variant classification and diagnosis. We present the largest cohort of patients with GS performed in a clinical setting to date. The results of this study should direct the decision for GS as standard second-line, or even first-line stand-alone test.

Purpose Achondroplasia is caused by pathogenic variants in the fibroblast growth factor receptor 3 gene that lead to impaired endochondral ossification. Vosoritide, an analog of C-type natriuretic peptide, stimulates endochondral bone growth and is in development for the treatment of achondroplasia. This phase 3 extension study was conducted to document the efficacy and safety of continuous, daily vosoritide treatment in children with achondroplasia, and the two-year results are reported. Methods After completing at least six months of a baseline observational growth study, and 52 weeks in a double-blind, placebo-controlled study, participants were eligible to continue treatment in an open-label extension study, where all participants received vosoritide at a dose of 15.0 μg/kg/day. Results In children randomized to vosoritide, annualized growth velocity increased from 4.26 cm/year at baseline to 5.39 cm/year at 52 weeks and 5.52 cm/year at week 104. In children who crossed over from placebo to vosoritide in the extension study, annualized growth velocity increased from 3.81 cm/year at week 52 to 5.43 cm/year at week 104. No new adverse effects of vosoritide were detected. Conclusion Vosoritide treatment has safe and persistent growth-promoting effects in children with achondroplasia treated daily for two years.

Background GLUT1 Deficiency Syndrome 1 (GLUT1DS1) is a neurological disorder caused by either heterozygous or homozygous mutations in the Solute Carrier Family 2, Member 1 ( SLC2A1 ) gene. SLC2A1 encodes Glucose transporter type 1 (GLUT1) protein, which is the primary glucose transporter at the blood–brain barrier. A ketogenic diet (KD) provides an alternative fuel for brain metabolism to treat impaired glucose transport. By reanalyzing exome data, we identified a de novo heterozygous SLC2A1 variant in a girl with epilepsy. After reversed phenotyping with neurometabolic tests, she was diagnosed with GLUT1DS1 and started on a KD. The patient's symptoms responded to the diet. Here, we report a patient with GLUT1DS1 with a novel SLC2A1 mutation. She also has a hemangioma which has not been reported in association with this syndrome before. Case presentation A 5-year 8-month girl with global developmental delay, spasticity, intellectual disability, dysarthric speech, abnormal eye movements, and hemangioma. The electroencephalography (EEG) result revealed that she had epilepsy. Magnetic resonance imaging (MRI) showed that non-specific white matter abnormalities. Whole Exome Sequencing (WES) was previously performed, but the case remained unsolved. The re-analysis of WES data revealed a heterozygous splicing variant in the SLC2A1 gene. Segregation analysis with parental DNA samples indicated that the variant occurred de novo. Lumbar puncture (LP) confirmed the diagnosis, and the patient started on a KD. Her seizures responded to the KD. She has been seizure-free since shortly after the initiation of the diet. She also had decreased involuntary movements, her speech became more understandable, and her vocabulary increased after the diet. Conclusions We identified a novel de novo variant in the SLC2A1 gene in a patient who previously had a negative WES result. The patient has been diagnosed with GLUT1DS1. The syndrome is a treatable condition, but the differential diagnosis is not an easy process due to showing a wide range of phenotypic spectrum and the overlapping symptoms with other neurological diseases. The diagnosis necessitates a genomic testing approach. Our findings also highlight the importance of re-analysis to undiagnosed cases after initial WES to reveal disease-causing variants.

Progressive pseudorheumatoid dysplasia (PPD) is a rare autosomal recessive cartilage disorder caused by biallelic variants in CCN6, which encodes the matricellular protein WISP3. Although WISP3 is thought to contribute to extracellular matrix (ECM) homeostasis, its precise molecular role in PPD remains unclear. To elucidate how disease-associated CCN6 variants affect chondrocyte function, we overexpressed four variants—p.Cys52*, p.Tyr109*, p.Gly83Glu, and p.Cys114Trp—all located within the IGFBP domain, and evaluated their impact on parameters including redox balance, ER stress, ECM remodeling, gene expression, and protein–protein interactions. The p.Cys52* variant resulted in rapid degradation of WISP3, indicating a complete loss-of-function. The p.Tyr109* variant disrupted ECM regulation, markedly reducing protein interaction capacity, which was correlated with elevated mitochondrial ROS (mtROS) levels and triggered a strong response that led to programmed cell death. Although both missense variants yielded full-length proteins, their effects diverged significantly: p.Gly83Glu induced minor cellular alterations, whereas p.Cys114Trp caused severe protein destabilization, increased ROS accumulation, and high levels of ER stress. Proteomic analysis revealed that p.Cys114Trp acquired novel interaction partners, suggesting a potential gain-of-function mechanism. Collectively, these findings demonstrate that the functional consequences of CCN6 variants depend not only on variant type or domain location but also on their positional and structural context. The distinct cellular responses elicited by each variant underscore the importance of functional validation in modeling PPD pathogenesis and offer valuable biological and therapeutic perspectives.

Cas Simons, Ryan Taft and colleagues report the identification of KCNH1 mutations in six individuals with Temple-Baraitser syndrome (TBS). Electrophysiological measurements of cells expressing mutant KCNH1 channels show decreased activation thresholds and slower deactivation in comparison to wild-type channels, suggesting that these mutations lead to gain of function of KCNH1. Temple-Baraitser syndrome (TBS) is a multisystem developmental disorder characterized by intellectual disability, epilepsy, and hypoplasia or aplasia of the nails of the thumb and great toe 1 , 2 . Here we report damaging de novo mutations in KCNH1 (encoding a protein called ether à go-go, EAG1 or K V 10.1), a voltage-gated potassium channel that is predominantly expressed in the central nervous system (CNS), in six individuals with TBS. Characterization of the mutant channels in both Xenopus laevis oocytes and human HEK293T cells showed a decreased threshold of activation and delayed deactivation, demonstrating that TBS-associated KCNH1 mutations lead to deleterious gain of function. Consistent with this result, we find that two mothers of children with TBS, who have epilepsy but are otherwise healthy, are low-level (10% and 27%) mosaic carriers of pathogenic KCNH1 mutations. Consistent with recent reports 3 , 4 , 5 , 6 , 7 , 8 , this finding demonstrates that the etiology of many unresolved CNS disorders, including epilepsies, might be explained by pathogenic mosaic mutations.

Acromesomelic dysplasia type Maroteaux (AMDM, OMIM #602875) is an autosomal recessive disorder characterized by severe short stature, shortened middle and distal segments of the limbs, redundant skin of fingers, radial head subluxation or dislocation, large great toes and cranium, and normal intelligence. Only the skeletal system appears to be consistently affected. AMDM is caused by biallelic loss-of-function variants in the natriuretic peptide receptor B (NPRB or NPR2, OMIM #108961) which is involved in endochondral ossification and longitudinal growth of limbs and vertebrae. In this study, we investigated 26 AMDM patients from 22 unrelated families and revealed their genetic etiology in 20 families, via Sanger sequencing or exome sequencing. A total of 22 distinct variants in NPR2 (14 missense, 5 nonsense, 2 intronic, and 1 one-amino acid deletion) were detected, among which 15 were novel. They were in homozygous states in 19 patients and in compound heterozygous states in four patients. Parents with heterozygous NPR2 variants were significantly shorter than the control. Extra-skeletal abnormalities, including global developmental delay/intellectual disability, nephrolithiasis, renal cyst, and oligodontia were noted in the patient cohort. The high parental consanguinity rate might have contributed to these findings, probably associated with other gene variants. This study represents the largest cohort of AMDM from Turkey and regional countries and further expands the molecular and clinical spectrum of AMDM.

[LANGUAGE=”English”]Xeroderma pigmentosum (XP) is a rare autosomal recessive genodermatosis caused by mutations in the DNA repair system, leading to impaired repair of ultraviolet (UV) radiation-induced damage. XP is classified into seven nucleotide excision repair-deficient types (XPA to XPG) and a variant type (XPV). Diagnosis can be made at a later age in the XPV subtype, where sunburn reactions are known to be less severe. In this case, a 33-year-old male patient with a history of freckling that began at age 10 and basal cell carcinoma and squamous cell carcinoma in the head and neck region over the past 5 years presented with a suspicious non-pigmented 6 mm nodular lesion in the left subauricular region. Pathological examination revealed a diagnosis of malignant melanoma (MM). Concurrent genetic analysis revealed a homozygous c.491-6T>G mutation in the POLH gene, confirming a diagnosis of XPV. The mild clinical features of XP in our patient made the XPV diagnosis challenging, and the atypical dermoscopic features of the lesion complicated the clinical diagnosis of MM. It is reported that the age of onset of malignant skin tumors in XPV patients is later than in other groups, and the frequency of MM is higher. This case highlights the frequent delay in diagnosis and the diagnostic challenges of skin tumors in XPV patients.[LANGUAGE=”Turkish”]Kseroderma pigmentozum (XP), DNA onarım sistemindeki mutasyonlar nedeniyle ultraviyole ışınlarına bağlı hasarın tamirinin bozulduğu nadir bir otozomal resesif genodermatozdur. XP, yedi nükleotid eksizyon onarım eksikliği tipi (XPA’dan XPG’ye) ve bir varyant tip (XPV) olarak sınıflandırılır. Güneş yanığı reaksiyonunun daha az olduğu bilinen XPV alt tipinde tanı daha geç yaşta konulabilmektedir. Sunulmakta olan 10 yaşında başlayan çillenme, son 5 yıldır baş ve boyun bölgesinde ortaya çıkan bazal hücreli karsinom ve skuamöz hücreli karsinom öyküleri olan 33 yaşındaki erkek olguda sol subaurikular bölgede pigmente olmayan 6 mm çapında şüpheli nodüler lezyon tespit edilmiş, patolojik inceleme sonucunda malign melanom (MM) tanısı konulmuştur. Beraberinde yapılan genetik incelemede POLH geninde homozigot c.491- 6T>G mutasyonu tespit edilmiş ve hastaya XPV tanısı da konulmuştur. Olgumuzun XP’ye ait hafif klinik bulguları XPV tanısını, lezyonun atipik dermatoskopik özellikleri de klinik olarak MM tanısını zorlu kılmıştır. XPV hastalarında malign deri tümörlerinin görülme yaşı diğer gruplara göre daha geç, MM görülme sıklığının ise daha yüksek olduğu bildirilmektedir. Bu olgu, XPV hastalarında tanının gecikme sıklığını ve deri tümörlerinin tanısal zorluklarını vurgulamaktadır.

Background Collection of real-world evidence (RWE) is important in achondroplasia. Development of a prospective, shared, international resource that follows the principles of findability, accessibility, interoperability, and reuse of digital assets, and that captures long-term, high-quality data, would improve understanding of the natural history of achondroplasia, quality of life, and related outcomes. Methods The Europe, Middle East, and Africa (EMEA) Achondroplasia Steering Committee comprises a multidisciplinary team of 17 clinical experts and 3 advocacy organization representatives. The committee undertook an exercise to identify essential data elements for a standardized prospective registry to study the natural history of achondroplasia and related outcomes. Results A range of RWE on achondroplasia is being collected at EMEA centres. Whereas commonalities exist, the data elements, methods used to collect and store them, and frequency of collection vary. The topics considered most important for collection were auxological measures, sleep studies, quality of life, and neurological manifestations. Data considered essential for a prospective registry were grouped into six categories: demographics; diagnosis and patient measurements; medical issues; investigations and surgical events; medications; and outcomes possibly associated with achondroplasia treatments. Conclusions Long-term, high-quality data are needed for this rare, multifaceted condition. Establishing registries that collect predefined data elements across age spans will provide contemporaneous prospective and longitudinal information and will be useful to improve clinical decision-making and management. It should be feasible to collect a minimum dataset with the flexibility to include country-specific criteria and pool data across countries to examine clinical outcomes associated with achondroplasia and different therapeutic approaches.

Purpose: The Ehlers–Danlos syndrome (EDS), dermatosparaxis type, is a recessively inherited connective tissue disorder caused by deficient activity of ADAMTS-2, an enzyme that cleaves the aminoterminal propeptide domain of types I, II, and III procollagen. Only 10 EDS dermatosparaxis patients have been reported, all presenting a recognizable phenotype with characteristic facial gestalt, extreme skin fragility and laxity, excessive bruising, and sometimes major complications due to visceral and vascular fragility. Methods: We report on five new EDS dermatosparaxis patients and provide a comprehensive overview of the current knowledge of the natural history of this condition. Results: We identified three novel homozygous loss-of-function mutations (c.2927_2928delCT, p.(Pro976Argfs*42); c.669_670dupG, p.(Pro224Argfs*24); and c.2751-2A>T) and one compound heterozygous mutation (c.2T>C, p.? and c.884_887delTGAA, p.(Met295Thrfs26*)) in ADAMTS2 in five patients from four unrelated families. Three of these displayed a phenotype that was strikingly milder than that of previously reported patients. Conclusion: This study expands the clinical and molecular spectrum of the dermatosparaxis type of EDS to include a milder phenotypic variant and stresses the importance of good clinical criteria. To address this, we propose an updated set of criteria that accurately captures the multisystemic nature of the dermatosparaxis type of EDS. Genet Med 18 9, 882–891.

In this article, we report a 21-gestational-week fetus diagnosed with congenital cataract by ultrasonography. The parents decided to terminate the pregnancy and asked for examination of the fetus. An amniocentesis was performed for fetal karyotyping. After termination of the pregnancy, fetal autopsy was conducted. Whole exome sequencing (Trio-WES) analysis of the mother and father was done from peripheral blood samples. In the pathologic autopsy report, bilateral anterior and posterior subcapsular cataracts were confirmed. Whole exome sequencing analysis revealed a previously unreported class 3 variant of uncertain significance (c755A>G [PLys252Arg]) of the CRYBB1 gene, which is associated with congenital cataract, that was homozygous in the fetus and heterozygous in the parents. The obtained result is consistent with a genetic diagnosis of isolated autosomal recessive cataract. Keywords: Class 3 variant of uncertain significance (c755A>G [PLys252Arg]), congenital cataract, autosomal recessive inheritance