Shuyuan Li

Background: Rauch‐Steindl syndrome (RAUST) is a rare neurodevelopmental disorder caused by pathogenic variants in NSD2 , a histone methyltransferase gene at 4p16.3. Due to phenotypic overlap with Wolf‐Hirschhorn syndrome (WHS), RAUST is often misdiagnosed. Missense variants in NSD2 are particularly challenging to interpret without functional validation. Methods: Genomic DNA from the proband and her parents was extracted from peripheral blood. Trio‐whole‐exome sequencing (WES) was performed to identify candidate variants based on the clinical phenotype, followed by Sanger sequencing validation. RNA splicing impact was assessed via reverse transcription PCR and TA‐cloning from peripheral blood mononuclear cells. Results: A 7‐year‐8‐month‐old girl mainly presented with intrauterine and postnatal growth restriction, global developmental delay, intellectual disability, epilepsy, short stature, and facial dysmorphism was documented. Trio‐WES identified a novel de novo missense variant in NSD2 (NM_001042424.3: c.2137G>C, p.Gly713Arg), which is located at the last base of exon 11 and was predicted to be highly likely to cause aberrant splicing. Functional analysis revealed this variant causes exon 11 skipping in 53% of transcripts, resulting in a frameshift (p.Leu672Glyfs*20) and premature truncation. Conclusion: This is the first report of an NSD2 missense variant that functionally acts as a splicing mutation leading to protein truncation. Our findings highlight the necessity of RNA‐level functional assays for accurate variant interpretation and reinforce genotype–phenotype distinctions between RAUST and WHS.

A 28-year-old man presenting with multiple osteochondromas was referred to our institution for genetic counseling regarding reproductive risks. The proband (III-12) reported a striking familial history spanning multiple generations, with at least 19 individuals in the extended pedigree suspected to be affected ( Fig. 1A). Physical examination revealed numerous bony exostoses primarily affecting the elbows, knees, and ankles ( Fig. 1B, top). He had a history of several orthopedic interventions to correct joint deformities and improve mobility ( Fig. 1B, bottom).

Background: Radio‐Tartaglia Syndrome (RATARS) is a rare autosomal dominant neurodevelopmental disorder caused by loss‐of‐function (LoF) variants in SPEN . It is characterized by global developmental delay, intellectual disability, distinctive craniofacial features and multisystem involvement. To date, only a limited number of postnatal cases have been reported, and no prenatal case has been documented. Methods: The clinical data of a 17‐week pregnant woman and her affected mother who were suspected with a congenital disorder was comprehensively assessed. To investigate the genetic aetiology, whole‐exome sequencing (WES) was performed to detect candidate pathogenic variants, which were subsequently validated using Sanger sequencing within the family. The proband underwent amniocentesis for prenatal genetic diagnosis of the foetus. Results: The 22‐year‐old pregnant woman presented with neurodevelopmental defects including moderate intellectual disability (ID) and hypotonia, gait abnormalities, behavioural problems, kyphosis and dysmorphic facial features. WES identified a previously unreported heterozygous frameshift variant (c.2417_2418dup, p.Arg807Aspfs*3) in the SPEN gene. Sanger sequencing confirmed the authenticity of the variant and revealed that it was inherited from the mother of the pregnant woman. Compared to the proband, the mother has a milder phenotype, mainly manifested as mild ID. Prenatal ultrasonography during pregnancy revealed no obvious structural abnormalities. However, prenatal genetic testing revealed the foetus harboured the same SPEN pathogenic variant. Conclusions: This family has been diagnosed with RATARS caused by a SPEN variant. Our findings broaden the mutational and phenotypic spectrum of SPEN and characterize the first documented prenatal diagnosis of RATARS. The identification of intrafamilial phenotypic variability highlights the heterogeneous expressivity of RATARS, even among carriers of identical variants.

Fetal central nervous system (CNS) anomalies are among the most common congenital malformations, yet the overall prenatal diagnostic yield of current genetic testing remains below 40%. Variants in RNU4‐2 , a non‐coding gene encoding the U4 small nuclear RNA (snRNA), have recently been linked to a novel highly recurrent dominant neurodevelopmental disorder termed ReNU syndrome. While its postnatal phenotype has been well characterized, the contribution of RNU4‐2 to fetal CNS anomalies remains unexplored. In this study, we retrospectively analyzed 148 fetuses with CNS anomalies who had non‐diagnostic results from karyotyping, chromosomal microarray analysis, and exome sequencing. Targeted Sanger sequencing of RNU4‐2 was performed to identify pathogenic variants. Two fetuses harbored the same de novo recurrent variant, n.64_65insT, corresponding to a diagnostic yield of 1.35%. Both cases presented with microcephaly, suggesting that it is a key prenatal feature of ReNU syndrome. Furthermore, molecular confirmation of RNU4‐2 resolved a decade‐long diagnostic odyssey in one family by excluding an inherited Xp22.13 duplication of uncertain significance as the causal variant. In conclusion, this study provides the first systematic prenatal evaluation of RNU4‐2 in fetuses with CNS anomalies, thereby expanding the prenatal phenotypic spectrum of ReNU syndrome. Incorporating RNU4‐2 testing into prenatal genetic workflows may enhance diagnostic yield, enable precise genetic counseling, and support informed reproductive decision‐making.

Background: Noninvasive prenatal screening for aneuploidies and microdeletion/microduplication syndromes (MMS) has gained widespread clinical application. However, the development of noninvasive prenatal diagnosis for monogenic disorders (NIPT-M) has progressed slower. Existing NIPT-M approaches often require specialized designs, are limited to a narrow range of genes, or are expensive and impractical for clinical implementation. Methods: We present HaploNIPD, a universal haplotype-based approach for NIPT-M, utilizing a targeted capture panel that includes 120,000 selected single-nucleotide polymorphisms. Maternal cell-free DNA (cfDNA) and genomic DNA (gDNA) from family members were targeted captured and massively parallel sequenced. Parental haplotypes were phased, and fetal genome-wide haplotypes and copy number profiles were determined. The clinical efficacy of HaploNIPD was assessed in 70 families with monogenic disorders and 152 samples with known fetal karyotypes. Results: Fetal haplotypes were accurately determined in 69 of 70 families (98.57%), with perfect concordance to invasive prenatal diagnosis results. One case was classified as “no call” due to a recombination event within the target region. Compared to fetal haplotypes derived from chorionic villus or amniotic fluid, the deduced fetal haplotypes in maternal plasma by HaploNIPD had an average genome-wide accuracy of 99.74% and 98.23% for paternal and maternal inheritance, respectively. All common aneuploidies (trisomies 13, 18 and 21, monosomy X, XXX, XXY, and XYY) and MMS were accurately identified. Conclusions: Our findings demonstrate the potential of HaploNIPD as a robust and versatile platform for NIPT-M capable of noninvasive genome-wide fetal haplotyping and simultaneous detection of aneuploidies and MMS, offering a scalable solution for comprehensive prenatal genetic diagnosis.

Background: Duchenne and Becker muscular dystrophies are X-linked neuromuscular disorders caused by mutations in the dystrophin gene (DMD). Duplications account for approximately 10% of pathogenic variants, but their structural complexity and variable clinical impact present significant challenges in pathogenicity interpretation. Methods: We retrospectively analyzed whole exome sequencing and multiplex ligation-dependent probe amplification data from 3842 individuals, identifying 39 patients with DMD duplications. These patients underwent whole genome sequencing (WGS) to characterize duplication patterns, breakpoint features, and haplotype structures. Optical genome mapping (OGM) was additionally performed in WGS-unresolved cases to identify exact haplotypes. We also compared the diagnostic performance of different platforms and further investigated genotype–phenotype correlations. Results: DMD duplications exhibited substantial structural heterogeneity and were characterized into 4 major patterns: tandem duplication (58%), duplication-normal-duplication (16%), duplication-inversion-duplication (16%), and intricate duplication (10%). Recurrent complex arrangements were associated with high-homology repeats and often extended beyond DMD, complicating haplotype interpretation. WGS alone failed to resolve haplotypes in 34% (13/38) of cases, while OGM missed certain exon duplications and small fragments in 33% of cases (2/6). Integration of WGS and OGM enabled precise haplotype reconstruction and improved genotype–phenotype correlation. Conclusions: Our findings broaden the molecular spectrum of DMD duplications, highlight their widespread structural complexity, and emphasize the importance of integrating multiple technologies to precisely delineate duplication haplotype structures and assess the pathogenicity of variants with uncertain significance. These findings provide valuable insights for DMD duplication detection, pathogenicity evaluation, and genetic counseling.

The molecular etiology of more than half of neurodevelopment disorders remains unknown. In this study, we identified recessive variants in the TMPRSS7 gene in a fetus from a non-consanguineous Chinese family with a history of recurrent central nervous system (CNS) malformations, as the likely genetic cause of a neurodevelopmental disorder. TMPRSS7 encodes matriptase-3, a type II transmembrane serine protease (TTSP) that becomes active when its catalytic domain is released outside the cell. During the proteolytic process, the canonical RV(I)V(I)G motif is cleaved, converting the inactive single-chain zymogen into its active form. This activation is closely temporally coupled with TTSPs shedding and ultimately leads to the release of the catalytic domain into the extracellular space to exert its function. The patient carrying compound heterozygous variants in the TMPRSS7 gene, p.R479H and p.S685Kfs*26, exhibited impaired synthesis of the matriptase-3 protease zymogen and defective shedding of the functional serine protease domain. Tmprss7 homozygous knockout (KO) mice exhibited dysregulated synaptic dendritic spine density, function, and dendritic elongation in the cerebral cortex and hippocampus. In addition, the KO animals displayed neurobehavioral deficits, including impairments in spatial learning, anxiety-like behavior, and a reduced preference for social novelty. Multi-omics analysis discovered enrichment of pathways related to synaptic signaling disruptions in both the cerebral cortex and hippocampus. Collectively, our findings identify TMPRSS7 as a candidate gene essential for normal neurodevelopment, highlighting its potential role in the molecular pathogenesis of neurodevelopmental disorders.

Background: To identify the genetic variants underlying neurofibromatosis type 1 (NF1) and to investigate genotype-phenotype correlations. Methods: Thirty-three patients from 27 Chinese pedigrees with suspected NF1 phenotypes underwent genetic analysis. The impact of splicing variant on NF1 mRNA processing was determined by cDNA direct sequencing. Additional NF1 patients with detailed clinical and molecular data were extracted from the literature for performing genotype-phenotype correlation analysis. Results: Genetic analysis identified 24 distinct NF1 variants: nine frameshift, four nonsense, four missense, six splice site, and one exon deletion. Among them, 10 were previously unreported in the literature. A functional study showed that the canonical splicing variant (c.3497–2 A > G) resulted in an in-frame deletion of two amino acids, which may not affect protein function. Finally, 22 variants were classified as pathogenic or likely pathogenic. After evaluation of the clinical data and genetic evidence, the diagnoses of 31 patients from 25 families were confirmed. Genotype–phenotype correlation analysis from the cohort, consisting of 28 patients in this study and 235 published cases, showed that the onset of neurofibromas and bone lesions exhibited an age-dependent association, with 79.8% and 73.8% probability of developing in patients older than 23.5 years or 20.5 years, respectively. No association was found between the location or type of NF1 variants and any specific features. Conclusions: We comprehensively described the clinical and genetic data of a Chinese NF1 cohort and emphasized the necessity of further functional analysis on splicing variants. Neurofibromas and bone lesions are age-dependent disease complications that exhibit progressive tendencies with increasing age in patients with NF1.