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Clin. Genet. [JOURNAL]

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Genetic and Clinical Spectrum of Osteogenesis Imperfecta in an Egyptian Cohort With a High Rate of Lethal Phenotypes.

Elhady G, Amin AK, Iturrate A … +8 more , El-Dessouky S, Nevado J, Campos-Xavier B, Matsa LS, Giunta C, Lapunzina P, Ruiz-Perez VL, Abdalla E

Clin Genet · 2026 Apr · PMID 41090974 · Publisher ↗

Osteogenesis imperfecta (OI) is a genetically heterogeneous connective tissue disorder marked by bone fragility and deformities. This study aimed to define the clinical and molecular characteristics of 21 OI patients fro... Osteogenesis imperfecta (OI) is a genetically heterogeneous connective tissue disorder marked by bone fragility and deformities. This study aimed to define the clinical and molecular characteristics of 21 OI patients from 15 unrelated Egyptian families. Most probands were analyzed by exome sequencing. In three consanguineous cases, variants were identified through SNP array-based homozygosity mapping followed by direct sequencing of a candidate gene. Genotype-phenotype correlations were additionally explored. Parental consanguinity was documented in 66.7% (10/15) of the total cohort and in 100% (8/8) of the families with autosomal recessive OI. Pathogenic or likely pathogenic variants were identified in 14 families, five of which were novel. A variant of uncertain significance was identified in the remaining family. COL1A1 and COL1A2 (n = 7) were the most commonly mutated genes, followed by CRTAP (n = 4), while variants in P3H1, WNT1, CREB3L1, and SEC24D were each identified in a single patient. The present study highlights the molecular heterogeneity of OI. In total, 15 distinct variants in seven OI-related genes were identified. We also report a particularly high number of OI lethal forms affecting 10 patients out of 21. The study adds further evidence for the utility of ES in the genetic diagnosis of OI, which facilitates counseling and personalized care.

ApoE Polymorphism Analysis in Health and Disease of South Asian Populations: A Systematic Review and Meta-Analysis.

Paudel P, Sah A, Paudel P

Clin Genet · 2025 Dec · PMID 41078217 · Publisher ↗

This systematic review and meta-analysis assesses the distribution and health implications of apolipoprotein E (ApoE) ε2, ε3, and ε4 alleles, which play crucial roles in lipoprotein metabolism, in South Asian populations... This systematic review and meta-analysis assesses the distribution and health implications of apolipoprotein E (ApoE) ε2, ε3, and ε4 alleles, which play crucial roles in lipoprotein metabolism, in South Asian populations, with a focus on neurodegenerative diseases, movement disorders, traumatic brain injury, mental health disorders, cardiovascular disorders, metabolic disorders, and trauma-related disorders. A total of 53 studies identified through comprehensive searches in PubMed, Embase, and Google Scholar up to July 31, 2024, were included on the basis of predefined eligibility criteria after Risk of Bias Assessment via the New York Ottawa Scale. ε3/ε3 was found to be the most prevalent genotype, followed by ε3/ε4 and ε2/ε3. ε4-containing genotypes were associated with susceptibility to Alzheimer's disease, coronary artery disease, vascular dementia, and obesity, though high heterogeneity in some associations necessitates cautious interpretation, whereas the ε2/ε3 and ε2 alleles showed protective effects in some conditions. These studies had several limitations, including data gaps for specific health conditions, underrepresentation of some South Asian countries, and heterogeneity in outcomes. Despite gaps in the data for some countries and specific health conditions, this review reveals distinct South Asian patterns in ApoE polymorphism-disease associations, highlighting the need for targeted genetic research and tailored public health strategies to advance personalized medicine and healthcare policies in this region. There was no specific funding for this study. The study was registered in PROSPERO (registration number CRD42024575197).

Genetic Landscape of Robin Sequence: A Systematic Review.

van de Velde S, Mink van der Molen AB, Lachmeijer AMA … +6 more , de Leijer D, Smits JJ, Massink MPG, Versnel SL, van den Boogaard MH, Paes EC

Clin Genet · 2026 Feb · PMID 41077824 · Full text

Robin sequence (RS) is a congenital condition characterized by micrognathia, glossoptosis, and upper airway obstruction, often occurring with cleft palate and syndromic conditions. The genetic basis of RS is heterogeneou... Robin sequence (RS) is a congenital condition characterized by micrognathia, glossoptosis, and upper airway obstruction, often occurring with cleft palate and syndromic conditions. The genetic basis of RS is heterogeneous, including monogenic variants and chromosomal rearrangements. This systematic review synthesizes the current genetic landscape of RS, analyzing data from 107 studies that employed various genetic testing methods, including chromosomal microarray (CMA), targeted sequencing, and whole exome sequencing (WES). A distinction is made between genetic variants identified in isolated versus non-isolated RS. Pathogenic variants in genes as SOX9, SNRPB, SATB2, TGDS, RBM10, COL11A1, and COL2A1 are frequently identified, many of which are linked to non-isolated RS. The most common chromosomal aberrations are deletions of 22q11.2 and 18q. Up-to-date genetic testing is essential to enable accurate diagnosis and personalized clinical care. With the growing use of whole genome sequencing (WGS) in clinical practice, the need for phenotype-driven interpretation tools is increasing. Some platforms can prioritize gene relevance based on Human Phenotype Ontology (HPO) terms. Documenting both known and novel RS-associated genes is therefore crucial to fully realize the diagnostic potential of WGS and support evidence-based clinical decision-making.

Genotype-Phenotype Correlations in Chinese Pediatric Patients With Single Large-Scale Mitochondrial DNA Deletion Disorders.

Wang J, Song M, Liu Z … +7 more , Xu C, Zou Y, Duan X, Liu Y, Zhang W, Li J, Fang F

Clin Genet · 2026 Apr · PMID 41074779 · Publisher ↗

This study investigated clinical and genetic characteristics of Chinese pediatric patients with single large-scale mitochondrial DNA deletions (SLSMD). We analyzed 28 patients (July 2004-March 2025) using long-range PCR... This study investigated clinical and genetic characteristics of Chinese pediatric patients with single large-scale mitochondrial DNA deletions (SLSMD). We analyzed 28 patients (July 2004-March 2025) using long-range PCR and next-generation sequencing. Spearman correlation and ANOVA assessed genotype-phenotype relationships. Patients (mean age 5.52 ± 3.96 years) exhibited multi-organ involvement (5.43 ± 1.87 organs). Common initial presentations included ocular (29%), neurologic, and endocrine dysfunction. Only 14.3% had the classic 4977 bp deletion, and 23 novel deletions were identified in 25 patients. Larger deletions correlated with more deleted MRC complexes (r = 0.516, p = 0.0123) and more deleted tRNAs (r = 0.534, p = 0.0103). Kearns-Sayre syndrome (KSS) patients had later onset (p = 0.0337), larger deletions (p = 0.0263), and greater tRNA/MRC complex (p = 0.0263, p = 0.0319) involvement than non-KSS patients. SLSMD in Chinese children primarily causes KSS, Pearson syndrome (PS), and progressive ophthalmoplegia with multi-organ involvement. Genotype-phenotype correlations exist, particularly between deletion size, onset age, and disease severity. KSS patients show distinct genetic and clinical profiles, suggesting slower progression. This study expands the known SLSMD spectrum and underscores mitochondrial testing in pediatric multi-organ disorders.

Founder Variants of the Turkish.

Kablan A

Clin Genet · 2026 Jan · PMID 41074596 · Publisher ↗

Founder variants-disease-causing genetic variants inherited from a common ancestor-have been extensively documented in isolated populations, shedding light on population history, disease prevalence, and genetic drift. In... Founder variants-disease-causing genetic variants inherited from a common ancestor-have been extensively documented in isolated populations, shedding light on population history, disease prevalence, and genetic drift. In the context of the Turkish population, which lies at the crossroads of Europe and Asia and has experienced a complex demographic history including migration, admixture, a significant number of founder variants have been identified in Türkiye as well as other countries hosting Turkish people. These variants are mostly associated with autosomal recessive disorders and are particularly enriched in subpopulations with high rates of consanguinity. This review aims to compile known founder variations in the Turkish population based on published literature, interpret their historical origins in light of Anatolian population dynamics, and discuss the implications of these variants for genetic counseling, disease gene discovery, and precision medicine. Understanding founder effects in the Turkish population not only provides insight into the nation's population genetics but also supports broader investigations into rare diseases in Middle Eastern and Euro-Asian populations.

Biochemical Testing Promotes Interpretation of Variants of Uncertain Significance in Prenatal Genetic Disease Testing in Four Organic Acidurias.

Yin K, Qi Q

Clin Genet · 2026 Feb · PMID 41063624 · Full text

Advances in next-generation sequencing (NGS) have revolutionized clinical and translational medicine. NGS is increasingly used in the diagnosis of genetic diseases, including newborn screening, prenatal screening and dia... Advances in next-generation sequencing (NGS) have revolutionized clinical and translational medicine. NGS is increasingly used in the diagnosis of genetic diseases, including newborn screening, prenatal screening and diagnosis, and preimplantation screening. While advancements in sequencing and bioinformatics have facilitated the discovery of novel genes and diseases, the identification of variants continues to outpace our ability to classify them accurately. Variants of uncertain significance (VUS), defined as genetic alterations with insufficient evidence for clinical interpretation, present significant diagnostic challenges. Clinically available functional studies, such as biochemical testing, offer valuable insights for interpreting VUS. This review synthesizes recent literature on amniotic fluid metabolite analysis for prenatal diagnosis and VUS interpretation in four organic acidurias. It aims to guide the application of biochemical testing for inherited metabolic disorders and enhance clinical decision-making regarding VUS classification.

Challenges and Pitfalls in Diagnosing Twins With Discordant BWS Phenotype.

Bellani I, Trevisan V, Viscogliosi G … +6 more , Pomponi MG, Chiurazzi P, Mussa A, Zampino G, Genuardi M, Leoni C

Clin Genet · 2025 Nov · PMID 41054832 · Full text

Accurately diagnosing Beckwith-Wiedemann syndrome (BWS) in twins with discordant phenotypes is essential for personalized oncological monitoring and management. It is advisable to test both twins, even without phenotypic... Accurately diagnosing Beckwith-Wiedemann syndrome (BWS) in twins with discordant phenotypes is essential for personalized oncological monitoring and management. It is advisable to test both twins, even without phenotypic expression, and incorporate prenatal factors like assisted reproduction technologies and twin pregnancies into the diagnostic BWS scoring system.

Genetic Basis of Hypsarrhythmia: Expanding the PHACTR1 Spectrum and Pathway to Targeted Therapy.

Willième K, Dheedene A, Vanlander A … +2 more , Verloo P, Verhelst H

Clin Genet · 2025 Nov · PMID 41054829 · Publisher ↗

We report a 5-month-old girl with a novel PHACTR1 variant, presenting with infantile spasms and hypsarrhythmia. PHACTR1 encodes a protein with a unique actin- and phosphatase-binding structure, interacting with Slack (KC... We report a 5-month-old girl with a novel PHACTR1 variant, presenting with infantile spasms and hypsarrhythmia. PHACTR1 encodes a protein with a unique actin- and phosphatase-binding structure, interacting with Slack (KCNT1-encoded), a Na-activated K-channel linked to epilepsy. This shared pathway may offer a promising avenue to future therapy.

Biallelic Variants in TMEM17 Cause Meckel-Gruber Syndrome Within the Ciliopathy Spectrum.

Pardo LM, Martini J, Zonic E … +22 more , Almeida LS, Iqbal M, Sadagopan M, Reyes AP, León NY, Musambil M, Alfadhel M, Dar FJ, Tahir F, AlSulmi E, Al Qahtani N, Al Taifi HA, Al Hamad M, Alhaddad B, Almubayedh S, Alabdi L, Alkuraya FS, Tabarki B, Tawhari A, Alhashem A, Bauer P, Bertoli-Avella A

Clin Genet · 2025 Nov · PMID 41054827 · Publisher ↗

TMEM17 encodes a transition zone protein essential for ciliary function. Three cases with homozygous variants in TMEM17 in primary ciliopathies (Joubert and Oral-Facial-Digital syndrome) have been reported. We investigat... TMEM17 encodes a transition zone protein essential for ciliary function. Three cases with homozygous variants in TMEM17 in primary ciliopathies (Joubert and Oral-Facial-Digital syndrome) have been reported. We investigated whether biallelic TMEM17 variants contribute to primary ciliopathies. We queried our Biodatabank and evaluated the gene-disease relationship (GDR) according to the ClinGen recommendations. Four unrelated patients (four families) were identified with a clinical diagnosis of Meckel-Gruber syndrome (MGS) and novel homozygous variants: NM_198276.3:c.4del p.(Glu2Serfs*58); NM_198276.3:c.366dup p.(Pro123Thrfs*9); and NM_198276.3:c.368C>G p.(Pro123Arg). A fifth family lost three foetuses with MGS phenotype, both parents are heterozygote carriers (NM_198276.3:c.4del p.(Glu2Serfs*58)) but biological material from the foetuses was not available. The cases in this study had a severe prenatal phenotype, including encephalocele, polycystic kidney dysplasia, and polydactyly, leading to early lethality. This study strengthens the gene-disease association of TMEM17, upgrading it from "limited" to "moderate." We expand the phenotypic spectrum, ranging from MGS-with prenatal onset and early lethality-to Oral-Facial-Digital and Joubert syndromes. Our findings indicate that loss-of-function variants may underlie the most severe TMEM17 ciliopathy manifestations, suggesting a potential genotype-phenotype correlation.

Three New Cases of Autosomal Recessive Stickler Syndrome due to Biallelic Variants in the LOXL3 Gene.

Sánchez CMD, Soler MJS, Del Carmen Martínez Romero M … +2 more , Calvo DD, Martínez MJB

Clin Genet · 2026 Apr · PMID 41052910 · Publisher ↗

Stickler syndrome (SS) is clinically and genetically heterogeneous. Autosomal recessive Stickler syndrome (ARSS) is characterized by sensorineural hearing loss, myopia, retinal degeneration, vitreous anomalies, and epiph... Stickler syndrome (SS) is clinically and genetically heterogeneous. Autosomal recessive Stickler syndrome (ARSS) is characterized by sensorineural hearing loss, myopia, retinal degeneration, vitreous anomalies, and epiphyseal dysplasia. It may also include midfacial hypoplasia, cleft palate, and skeletal manifestations. Currently, only 40 ARSS cases have been described, and just 4 are linked to pathogenic variants in the LOXL3 gene. A 20-year-old woman was referred to Medical Genetics due to Pierre Robin sequence, myopia, hearing loss, and distinct features. She was evaluated in early childhood with her sisters but was discharged without a specific genetic diagnosis. Polyhydramnios was detected in prenatal ultrasounds. Delivery occurred at 35 weeks. At birth, Pierre Robin sequence was evident, and she was admitted due to apnea. Complementary tests included karyotype, FISH 22q11, and screening for associated anomalies (cardiology, ophthalmology, ABR, and abdominal and cranial ultrasounds), all of which were normal. She had delayed speech development. She presents high myopia and bilateral conductive hearing loss, as well as nonspecific joint pain. She has two sisters with overlapping phenotypes. Both had cleft palate repair (one also with Pierre Robin sequence) and high-degree myopia. The first had a ventricular septal defect that spontaneously closed at age 5, and the second has conductive hearing loss. The physical examination highlights: microcephaly (head circumference < p1, -2.5 SD), downward-slanting palpebral fissures, midfacial and nasal ala hypoplasia, flat nasal bridge, elongated and flat philtrum, high-arched palate, absent uvula, joint hypermobility, shortening of third-fifth metacarpals and metatarsals, wide feet, and bilateral hallux valgus. Targeted sequencing of SS-associated genes revealed a likely pathogenic variant c.1735C>T and a variant of uncertain significance c.956G>A in the LOXL3 gene. Affected sisters carry both variants; both parents are healthy carriers. We report three new cases of SS due to previously undescribed biallelic variants in the LOXL3 gene. The clinical features are similar to those observed in other SS patients; however, digital anomalies and microcephaly have not been previously reported in patients with LOXL3 variants, thus expanding the phenotypic spectrum. This case highlights the importance of re-evaluating patients in light of ongoing advances in genetic diagnostics.

Reduced Penetrance and Variable Expression of Dilated Cardiomyopathy Associated With Homozygous Truncating Variants in NRAP Gene.

Alqahtani A, Tulbah S, Alruwaili N … +10 more , Takroni S, Alkorashy M, Manea W, Albert Brotons DC, Alwadai A, Alburaiki J, Alkuraya F, Al-Hashmi N, Zarroug S, Al-Hassnan ZN

Clin Genet · 2026 Mar · PMID 41033658 · Publisher ↗

Dilated Cardiomyopathy (DCM) is a genetically heterogeneous condition of left ventricular dilation and systolic dysfunction, leading to heart failure. It is mostly inherited in a dominant pattern. Recessive inheritance h... Dilated Cardiomyopathy (DCM) is a genetically heterogeneous condition of left ventricular dilation and systolic dysfunction, leading to heart failure. It is mostly inherited in a dominant pattern. Recessive inheritance has been rarely encountered. This study aims to outline the clinical and genetic characteristics associated with recessively inherited NRAP truncating variants in our highly consanguineous population. Twenty-three cases from 12 unrelated consanguineous families were recruited. Cardiological evaluation and genetic testing with exome sequencing (ES) were conducted in all cases, followed by segregation analysis of first-degree relatives. Genetic analysis with ES identified five unique homozygous truncating variants in NRAP in the affected cases. The segregation analysis detected a total of 23 homozygous and 21 heterozygous individuals. Out of the total homozygous cases, three were asymptomatic, while 20 exhibited symptoms with remarkable inter- and intrafamilial variability of the age of onset (range: 9 months to 47 years, median 10 years), seven of whom died (range: 9 months to 28 years, median 7 years). None of the heterozygous individuals showed symptoms. Of note, three homozygous cases underwent heart transplantation. Our findings show that truncating variants in NRAP are associated with reduced penetrance and clinical variability, suggesting a complex mechanism beyond simple Mendelian inheritance.

MINPP1 -Related Pontocerebellar Hypoplasia in Five New Patients: Identification of Three Novel Variants and Further Phenotype Delineation.

Abdel-Ghafar SF, Ahmed AE, Mohammed ET … +3 more , Abdel-Salam GMH, Zaki MS, Abdel-Hamid MS

Clin Genet · 2026 Apr · PMID 41025723 · Publisher ↗

MINPP1-related pontocerebellar hypoplasia (PCH) is a rare neurodevelopmental disorder characterized by microcephaly, profound developmental delay, and a distinct neuroimaging pattern. To date, only 21 patients from 13 un... MINPP1-related pontocerebellar hypoplasia (PCH) is a rare neurodevelopmental disorder characterized by microcephaly, profound developmental delay, and a distinct neuroimaging pattern. To date, only 21 patients from 13 unrelated families have been reported. Herein, we describe five patients from four Egyptian families with homozygous MINPP1 variants. All patients presented with global developmental delay, microcephaly, hypotonia, nystagmus, severe motor impairment, seizures, and intellectual disability. Interestingly, all patients exhibited dysmorphic facies, characterized by a high forehead, long philtrum, smooth philtrum, thin upper lip vermilion, broad chin, and low-set ears. Additional variable findings were optic atrophy, strabismus, feeding difficulties, and genital anomalies. Brain MRI showed cerebellar and pontine hypoplasia, thin corpus callosum, cortical atrophic changes, white matter signal, enlarged ventricles, and striking basal ganglia hypoplasia. Exome sequencing identified four MINPP1 variants, including three novel variants (p.Trp68Ter, p.Trp141Ter, and p.Val434_Gln435dup). All variants are localized within functionally critical domains of the protein and were either absent or extremely rare in public databases. Our study increases the number of affected individuals with MINPP1 variants and reinforces the clinical and brain imaging features of the disorder. In addition, the specific facial gestalt noted in our patients along with the basal ganglia changes appear characteristic and might point to the diagnosis of this type of PCH.

Novel MBTPS1 Variants and Cutis Laxa Phenotype in the 8th Reported Case of Spondyloepiphyseal Dysplasia, Kondo-Fu Type.

Lucas-Castro E, Diaz-González F, Modamio-Høybjor S … +7 more , Parrón-Pajares M, Pajares S, Gort L, Nevado J, Lapunzina P, Leiva-Gea A, Heath KE

Clin Genet · 2026 Apr · PMID 41024587 · Publisher ↗

Spondyloepiphyseal dysplasia, Kondo-Fu (SEDKF) type is a rare skeletal dysplasia caused by biallelic variants in MBTPS1. To date, only seven SEDKF cases have been reported in the literature. Here, we report the eighth, a... Spondyloepiphyseal dysplasia, Kondo-Fu (SEDKF) type is a rare skeletal dysplasia caused by biallelic variants in MBTPS1. To date, only seven SEDKF cases have been reported in the literature. Here, we report the eighth, a 20-year-old male presenting with severe disproportionate short stature, spondyloepiphyseal dysplasia, and the previously unreported feature of cutis laxa, which led to the clinical suspicion of geroderma osteodysplasica. Whole exome sequencing identified compound heterozygosity for a predicted splicing variant and a complete gene deletion in the patient. Functional validation using RNA splicing assays confirmed aberrant splicing, establishing the molecular diagnosis of SEDKF. This case broadens the clinical and molecular spectrum of MBTPS1-related disorders by presenting a novel combination of variants and phenotypic features.

Clinical, Biochemical and Molecular Characterisation of Newborns With Fatty Acid β-Oxidation Disorders: Novel Variants in the ACADM , ACADVL and SLC22A5 Genes.

Hidalgo Mayoral I, Herranz Cecilia A, Rodríguez-Jiménez C … +5 more , Carazo Álvarez A, Bergua Martínez A, Andrade Guerrero JD, Moráis López A, Rodríguez-Nóvoa S

Clin Genet · 2026 Apr · PMID 41022664 · Publisher ↗

In this study, we aimed to assess clinical, laboratory and molecular features of newborns with clinical suspicion for systemic primary carnitine deficiency (CUD), medium-chain acyl-CoA dehydrogenase deficiency (MCADD) an... In this study, we aimed to assess clinical, laboratory and molecular features of newborns with clinical suspicion for systemic primary carnitine deficiency (CUD), medium-chain acyl-CoA dehydrogenase deficiency (MCADD) and very long-chain acyl-CoA dehydrogenase deficiency (VLCADD). The implementation of newborn screening programs for fatty acid β-oxidation disorders (FAODs) has changed the natural course of these diseases, facilitating the initiation of preventive or therapeutic measures for affected newborns shortly after birth. This study included 94 newborns who were admitted between 2016 and 2023 because of biochemical signs of CUD, MCADD and VLCADD, and provided clinical, biochemical and genotypic data. Definitive molecular diagnosis confirmed that 16/94 newborns (17%) were true positives of the NBS, and 17 novel variants were detected in SLC22A5, ACADM and ACADVL genes. We assessed the clinical evolution of patients over time. This study expands the genotypic spectrum of SLC22A5, ACADM and ACADVL and highlights the role of genetics in identifying and correctly characterising FAODs.

The Genetic Defects of N-DRC in Male Infertility.

Qin J, Wang J, Li D … +1 more , Li F

Clin Genet · 2026 Jan · PMID 41022581 · Publisher ↗

The nexin-dynein regulatory complex (N-DRC) is a large protein complex composed of at least 11 subunits (DRC1-DRC11) and plays a crucial role in ciliary and flagellar motility. It links adjacent doublets of microtubules... The nexin-dynein regulatory complex (N-DRC) is a large protein complex composed of at least 11 subunits (DRC1-DRC11) and plays a crucial role in ciliary and flagellar motility. It links adjacent doublets of microtubules (DMTs) between A and B microtubules, regulating dynein motor activity. Genetic defects in N-DRC subunits lead to primary ciliary dyskinesia (PCD) and abnormal flagellar motility. In recent years, an increasing number of genetic mutations in N-DRC subunits have been reported, associated with male infertility, characterized by multiple morphological abnormalities of the flagella (MMAF) and asthenozoospermia. Therefore, genetic diagnosis of N-DRC defects in male infertility is of significant clinical importance, impacting the reproductive health of patients and the well-being of their offspring. In this review, we summarize the gene mutations of N-DRC subunits reported in the literature concerning male infertility, analyze the phenotypes of affected patients, and outline the functions and mechanisms of N-DRC in sperm flagellar motility. Furthermore, we provide an overview of gene knockout (KO) mouse models of N-DRC and their associated phenotypes. Finally, we summarize the outcomes of assisted reproductive technology (ART) in both patients and KO mice, offering references for the diagnosis and treatment of clinical male infertility caused by N-DRC genetic factors.

RAD51 -Related Fanconi Anemia: Expanding the Phenotypic Spectrum and Strong Association With VACTERL.

Altintas B, Stacy A, Gettinger K … +2 more , Wilson DB, Shinawi MS

Clin Genet · 2026 Mar · PMID 41017074 · Publisher ↗

Fanconi anemia (FA) is a multiorgan disease caused by pathogenic variants in genes involved in the FA/BRCA DNA repair pathway. We report a 10-year-old female who presented with multiple congenital anomalies consistent wi... Fanconi anemia (FA) is a multiorgan disease caused by pathogenic variants in genes involved in the FA/BRCA DNA repair pathway. We report a 10-year-old female who presented with multiple congenital anomalies consistent with VACTERL (Vertebral anomalies, Anal atresia, Cardiac anomalies, Tracheoesophageal fistula, Esophageal/duodenal atresia, and Renal and Limb anomalies) and PHENOS (abnormal Pigmentation, small Head, small Eyes, central Nervous system anomalies, Otological anomalies, short Stature), and later exhibited global developmental delay. She tested positive for a de novo likely pathogenic variant in RAD51 and had inconclusive chromosomal breakage studies. This case provides evidence for a common association between RAD51-related FA and VACTERL and expands its genotypic and phenotypic spectra.

Mapping the Prevalence of Lynch Syndrome in the Ceará-Northeast of Brazil.

Dos Santos Luciano MC, de Barros Silva PG, de Sant'Ana RO … +6 more , de Albuquerque CGP, Oliveira FFB, da Silveira Bitencourt F, de Lima Silva Fernandes IJ, Moura JFB, Bezerra MJB

Clin Genet · 2026 Apr · PMID 41014487 · Full text

Lynch syndrome (LS) is an autosomal dominant hereditary disorder that increases the risk of various cancers, especially colorectal (CRC) and endometrial cancer (EC). It results from pathogenic variants in mismatch repair... Lynch syndrome (LS) is an autosomal dominant hereditary disorder that increases the risk of various cancers, especially colorectal (CRC) and endometrial cancer (EC). It results from pathogenic variants in mismatch repair (MMR) genes-primarily MLH1, MSH2, MSH6, and PMS2. Population-specific variant frequencies emphasize the need for localized genetic studies. Methods This study investigated LS prevalence in Ceará, Northeast Brazil, analyzing 150 patients: 130 with CRC, 13 with endometrial cancer, and 7 with other tumors but a family history of LS-associated cancers. Researchers used next-generation sequencing (NGS) to examine 131 genes linked to hereditary cancer syndromes. Variants were classified as Lynch-syndrome associated (MMR genes) or non-Lynch-associated (non-MMR genes). Detection rates varied from 1.18 to 5.07 per 100,000 people; pathogenic variant prevalence ranged from 0 to 1.96 per 100,000 across microregions. Overall, the prevalence of MMR variants was 0.56 per 100,000, and 0.34 for non-MMR variants. MSH2 showed the highest number of pathogenic or likely pathogenic variants, followed by MSH6, PMS2, and MLH1. The study found a particular geographic distribution of LS-related variants. One novel MSH6 variant and two unreported non-Lynch variants (APC and SMAD4) were identified. Conclusions These findings highlight three novel variants in MSH6, APC, and SMAD4, and indicate that Ceará has a higher diversity and a unique spectrum of variants. This reinforces the importance of regional genetic screening and suggests the need to expand testing access, especially in high-risk areas, to improve the early detection and prevention of hereditary cancers in Northeast Brazil.

High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.

Birnbaum R, Slovik M, Zenvirt S … +11 more , Livyatan I, Altman I, Gershon S, Rips J, Daum H, Rosenbluh C, Elpeleg O, Meiner V, Frumkin A, Mor-Shaked H, Harel T

Clin Genet · 2026 Mar · PMID 41014177 · Full text

Exome sequencing (ES), originally developed to detect single nucleotide variants (SNVs), has been increasingly leveraged to detect copy number variants (CNVs) through read-depth analysis, enhancing diagnostic yield with... Exome sequencing (ES), originally developed to detect single nucleotide variants (SNVs), has been increasingly leveraged to detect copy number variants (CNVs) through read-depth analysis, enhancing diagnostic yield with minimal computational overhead. However, chromosomal microarray (CMA) testing remains widely used. To evaluate the utility of ES as a first-tier clinical diagnostic test, we compared the sensitivity of CNV detection by ES to that of CMA in individuals who underwent both tests, and developed triploidy screening based on ES data. ES identified most clinically relevant CNVs, with a 98.91% concordance for regions adequately captured. A retrospective analysis of CNVs detected from ES over a ~3-year period, comprising 1563 prenatal and 4884 postnatal cases, revealed CNVs in 3.8% of prenatal and 4.4% of postnatal samples. The relatively low percentage stems from the fact that most cases underwent CMA before ES. Pathogenic or likely pathogenic variants constituted 78.7% and 78.0% of these subgroups, with the remainder classified as variants of unknown significance. We highlight clinically relevant examples of CNVs across a range of sizes, including cases involving both CNVs and SNVs. The high consanguinity rate of the cohort allowed for systematic analysis of homozygous CNVs. Additionally, we demonstrate that ES can capture other diagnostic utilities traditionally associated with CMA, specifically uniparental disomy (UPD) and triploidy. Overall, our findings support ES as a robust, cost-effective alternative to CMA and advocate for its broader use as a first-tier diagnostic test for neurodevelopmental delay and congenital malformations, particularly until whole genome sequencing becomes more accessible and affordable.

A Further Case Supporting BORCS8 as a Cause of an Infantile-Onset Neurodegenerative Disorder.

Abdel-Hamid MS, ElKhayat SH, Abdel-Salam GMH

Clin Genet · 2026 Feb · PMID 40993886 · Publisher ↗

We describe a new patient with the recently described BORCS8-related neurodevelopmental disorder. The clinical and brain imaging features are similar to the previous report and reinforce BORCS8 as a molecule fundamental... We describe a new patient with the recently described BORCS8-related neurodevelopmental disorder. The clinical and brain imaging features are similar to the previous report and reinforce BORCS8 as a molecule fundamental to normal human development.

HYPK-Related Neurodevelopmental Syndrome: Case Report of Intellectual Disability, Developmental Delay, and Dysmorphic Features.

Patel R, Makwana R, Marchi E … +8 more , Fan Z, Falsey E, Menendez B, Giampietro P, Wentzensen IM, Hsieh TC, Shan SO, Lyon GJ

Clin Genet · 2026 Feb · PMID 40986405 · Full text

HYPK is a critical modulator and inhibitor of the NatA complex. Here, we report a male proband with a de novo HYPK variant presenting with developmental delay, autism, and facial dysmorphia. Biochemical analyses show tha... HYPK is a critical modulator and inhibitor of the NatA complex. Here, we report a male proband with a de novo HYPK variant presenting with developmental delay, autism, and facial dysmorphia. Biochemical analyses show that this pathogenic variant enhances the inhibitory activity of HYPK on NatA-mediated N-terminal protein acetylation. Our findings provide the first phenotypic characterization of a pathogenic HYPK variant and elucidate its molecular basis, which will facilitate future diagnosis and management in similar cases worldwide.
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