Jin Wang

Weyers acrofacial dysostosis (WAD) is a rare autosomal dominant ciliopathy caused by heterozygous pathogenic variants in the EVC2 gene. The classic phenotype includes short stature, dental anomalies, and nail dysplasia. To date, all reported causative variants are truncating mutations located within the last exon (exon 22). In contrast, pathogenic variants in other regions, particularly splice-site variants, remain poorly characterized. The co-occurrence of WAD and epilepsy has rarely been documented. We performed exome sequencing in a proband with comorbid developmental and epileptic encephalopathy (DEE) and WAD features. A candidate splice-site variant was further investigated using an in vitro minigene splicing assay. Exome sequencing identified a de novo heterozygous splice-site variant in EVC2 (c.451-1G > T). Minigene analysis confirmed that this variant causes complete skipping of exon 4, predicted to lead to an in-frame deletion (p.Tyr151_Leu173del). To our knowledge, this is the first report of a pathogenic splice-site variant in this region of EVC2 associated with WAD and DEE. Our study expands the mutational spectrum of EVC2. It underscores the utility of exome sequencing coupled with functional assays for diagnosing complex cases.

Duchenne/Becker muscular dystrophy (DMD/BMD) is caused by variants in the X‐linked DMD gene—most commonly deletions, duplications, or point mutations, and only rarely by complex chromosomal rearrangements (CCRs). In this study, structural variant sequencing (SVseq) was applied to a 14‐year‐old male patient with DMD. Although the patient exhibited typical symptoms, conventional tests—including karyotype analysis, gene panel, whole‐exome sequencing (WES), and multiplex ligation–dependent probe amplification (MLPA)—were all negative. SVseq identified a novel complex rearrangement on the X chromosome, comprising a 974,456 bp inversion spanning the 5 ^′ UTR and Exons 1–2 of the DMD gene, flanked by two microdeletions of 7285 and 6468 bp (NC_000023.11:g.[32865334_32872619del;32872619_33847075inv33847075_33853543del]). This rearrangement disrupts the DMD coding sequence and is classified as a pathogenic variant. Short tandem repeat (STR) analysis confirmed the familial relationship, whereas PCR and Sanger sequencing precisely mapped the breakpoints, establishing that the mutation arose de novo in his mother and was maternally inherited. Reproductive interventions—including preimplantation genetic testing for monogenic disorders (PGT‐M) and second‐trimester prenatal diagnosis—enabled the successful birth of a healthy male child. SVseq demonstrated clear advantages over standard methods for detecting CCRs, highlighting its value in genetically elusive cases. We recommend SVseq as a complementary diagnostic tool for unresolved DMD cases where conventional testing does not explain the findings. This approach can enhance diagnostic yield and support informed family planning.

Intellectual disability (ID) significantly impacts individual development and imposes a societal burden. Although mild ID accounts for approximately 85% of total cases, research into its genetic etiology remains relatively limited. We investigated a two-generation pedigree exhibiting varying degrees of global developmental delay (GDD) and ID. We collected clinical data from the proband and her parents, identified the genetic etiology through testing, investigated pathogenic mechanisms, and provided family genetic counseling. Peripheral blood samples were collected from pedigree members for chromosomal karyotyping and genomic DNA extraction. Trio exome sequencing (Trio-ES) was performed on the DNA samples. Candidate variants identified were validated using Sanger sequencing, and their pathogenicity was assessed in accordance with the standards and guidelines of the American College of Medical Genetics and Genomics (ACMG). The proband, a 2-year-old female, presented with GDD. Her father exhibited borderline intellectual disability, while her mother had mild intellectual disability. ES analysis revealed: Exome sequencing identified a unknown inheritance heterozygous variant (NM_001202543.2[CUX1]: c.2637G > A [p.Trp879*]) in both the proband and her father, classified as likely pathogenic. The mother carried an 8.60 Mb deletion (seq[hg19]del(9)(p24.3p24.1), which was classified as a pathogenic copy number variant (CNV). Our findings expand the spectrum of genetic variations associated with CUX1-related disorders. The conclusive molecular diagnosis established through genetic testing not only facilitated accurate genetic counseling but also reduced the time and economic burdens associated with the diagnostic odyssey.

Vulto-van Silfhout-de Vries syndrome (VSVS; MIM 615828) is an extremely rare autosomal dominant disorder with unknown incidence. It is always caused by de novo heterozygous pathogenic variants in the DEAF1 gene, which encodes deformed epidermal autoregulatory factor-1 homology. VSVS is characterized by mild to severe intellectual disability (ID) and/or global developmental delay (GDD), seriously limited language expression, behavioral abnormalities, somnipathy, and reduced pain sensitivity. In this study, we present a Chinese boy with moderate GDD and ID, severe expressive language impairment, behavioral issues, autism spectrum disorder (ASD), sleeping dysfunction, high pain threshold, generalized seizures, imbalanced gait, and recurrent respiratory infections as clinical features. A de novo heterozygous pathogenic missense variant was found in the 5th exon of DEAF1 gene, NM_021008.4 c.782G>C (p. Arg261Pro) variant by whole exome sequencing (WES). c.782G>C had not been previously reported in genomic databases and literature. According to the ACMG criteria, this missense variant was considered to be “Likely Pathogenic”. We diagnosed the boy with VSVS both genetically and clinically. At a follow-up of 2.1 years, his seizures were well controlled after valproic acid therapy. In addition, the child’s recurrent respiratory infections improved at 3.5 years of age, which has not been reported in previous individuals. Maybe the recurrent respiratory infections like sleep problems reported in the literature are not permanent but may improve naturally over time. The literature review showed that there were 35 individuals with 28 different de novo pathogenic variants of DEAF1-related VSVS. These variants were mostly missense and the clinical manifestations were similar to our patient. Our study expands the genotypic and phenotypic profiles of de novo DEAF1.

Objective. The current study aimed to compare the characteristics of chromosome abnormalities detected by conventional G-banding karyotyping, chromosome microarray analysis (CMA), or fluorescence in situ hybridization (FISH)/CNVplex analysis and further explore the application value of combined karyotype analysis and CMA in prenatal diagnosis with a larger sample size. Methods. From March 2019 to March 2021, 3710 amniocentesis samples were retrospectively collected from women who accepted prenatal diagnosis at 16 to 22+6 weeks of pregnancy. The pregnant women underwent karyotype analysis and CMA. In the case of fetal chromosomal mosaicism, FISH or CNVplex analysis was utilized for validation. Results. In total, 3710 G-banding karyotype results and CMA results from invasive prenatal diagnosis were collected. Of these, 201 (5.41) fetuses with an abnormal karyotype were observed. The CMA analysis showed that the abnormality rate was 9.14 (340/3710). The detection rate of CMA combined with karyotype analysis was 0.35 higher than that of CMA alone and 4.08 higher than that of karyotyping alone. Additionally, 12 cases had abnormal karyotype analysis, despite normal CMA results. To further detect the chromosome mosaicism, we used FISH analysis to correct the karyotype results of case 1. Correspondingly, a total of 157 cases showed abnormal CMA results but normal karyotype analysis. We also found chromosomal mosaicism in 4 cases using CMA. Moreover, CNVplex and CMA demonstrated that representative case 15 was mosaicism for trisomy 2. Conclusions. Conventional G-banding karyotyping and CMA have their own advantages and limitations. A combination of karyotype analysis and CMA can increase the detection rate of chromosome abnormalities and make up for the limitation of signal detection.

Hydrocephalus due to aqueductal stenosis (HSAS; Online Mendelian Inheritance in Man #307000) is a rare X‑linked, recessively‑inherited disease characterized by severe hydrocephaly and occasionally adducted thumbs, in addition to intellectual disability and spasticity in surviving individuals. The present study described two fetuses with severely enlarged ventricles of the brain. The clinical diagnosis of HSAS was made on the basis of family history and sonographic findings. Molecular testing of the L1 cell adhesion molecule (L1CAM) gene revealed two novel hemizygous L1CAM variants, c.998C>T(p.Pro333Leu) and c.2362G>T(p.Val788Phe). The variants affect the highly conserved amino acids which are located in the key domains of the protein (the fourth Ig domain and second FnIII domain, respectively). The two variants were predicted to be 'disease causing' by a number of prediction tools, and have been classified as likely pathogenic following the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. The present study highlights the importance of combining family history, prenatal ultrasonography and molecular testing in the diagnosis of HSAS. The novel variants expand the mutational spectrum of L1CAM gene in the Chinese population, and could be used in genetic counseling, carrier testing of female relatives, and prenatal, as well as preimplantation genetic diagnosis.

Osteogenesis imperfecta (OI) is a rare congenital disorder characterized by bone fragility and fractures, and associated with bone deformity, short stature, dentin, ligament and blue‑gray eye sclera. OI is caused by a heterozygous mutation in collagen α‑1(I) chain (COL1A1) or collagen α‑2(I) chain (COL1A2) genes that encode α chains of type I collagen. Collagen α chain peptide contains an N‑propeptide, which has a role in assembly and processing of collagen. Point mutations in the N‑propeptide domain appear to trigger OI. In the present study, a novel heterozygous missense mutation, c.281T>A (p.Val94Asp), was identified in the von Willebrand C domain of N‑terminal of type I collagen in an individual with type IV OI. The majority of N‑terminal mutations are associated with OI/Ehlers‑Danlos syndrome (EDS); however, in the present study, the affected individual did not suffer from EDS and the level of serum phosphorus of the patient was low (0.67 mmol/l). A number of clinical phenotypes were observed at the same variation site or in the same region on the polypeptide chain of COL1A, which suggests that additional genetic and environmental factors may influence the severity of OI. The present study may provide insight into the phenotype‑genotype association in collagen-associated diseases and improve clinical diagnosis of OI.

The aim of this study is to assess the disease incidence and mutation spectrum of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Guangxi, China, and to determine an optimal cutoff value to identify heterozygous female neonates. A total of 130, 635 neonates were screened from the year of 2013 to 2017. Neonates suspected for G6PD deficiency were further analyzed by quantitatively enzymatic assay and G6PD mutation analysis. The overall incidence of G6PD deficiency was 7.28%. A total of 14 G6PD mutations were identified, and different mutations lead to varying levels of G6PD enzymatic activities. The best cut-off value of G6PD activity in male subjects is 2.2 U/g Hb, same as conventional setting. In female population, however, the cut-off value is found to be 2.8 U/g Hb (sensitivity: 97.5%, specificity: 87.7%, AUC: 0.964) to best discriminate between normal and heterozygotes, and 1.6 U/g Hb (sensitivity: 82.2%, specificity: 85.9%, AUC: 0.871) between heterozygotes and deficient subjects. In conclusion, we have conducted a comprehensive newborn screening of G6PD deficiency in a large cohort of population from Guangxi, China, and first established a reliable cut-off value of G6PD activity to distinguish heterozygous females from either normal or deficient subjects.