Systematic genotype-phenotype mapping and transcriptomic analyses highlight SEMA6A as a candidate for neuronal migration defects in 5q22-q23 deletions.
Aug 2026· Journal of Human Genetics· 0 citations· 46 references
Medicine
TL;DR
Re-analysis of human fetal cortex single-cell RNA sequencing data demonstrated that SEMA6A and FLNA are significantly co-expressed in apical radial glia and newborn excitatory neurons, suggesting that SEMA6A is a candidate contributor to neuronal migration defects in 5q22.3-q23.3 deletions.
Current knowledge on the genotypic and phenotypic spectra of SET-NDD is expanded, and pinpoints a smaller 9q34.11 critical region excluding upstream NDD-associated genes, STXBP1 and SPTAN1, implicating SET as a significant NDD-associated gene.
Angelo Condell, Elaine Zhang, Tim Sikora et al.· Clinical Genetics· 0 citations
Cleidocranial dysplasia (CCD) is a genetic disorder characterized by delayed cranial suture closure, hypoplastic clavicles, and dental anomalies, with varying severity. Most cases are linked to RUNX2 variants; however, rare CCD‐like phenotypes can arise from other genetic alterations, including variants in MSX2, a critical skeletal development gene. Here, we describe two patients with persistent anterior fontanelles and microduplications upstream of MSX2, a region previously associated with CCD‐like phenotypes. Microarray analysis revealed narrower duplication ranges in these patients than in two earlier reported cases. To elucidate the underlying mechanisms, we performed in silico analyses using publicly available datasets. Epigenetic characterization of the minimal overlapping duplicated region (chr5:173848716–173888281) identified two transcriptionally active subregions showing high chromatin accessibility in osteoblasts. These findings suggest a regulatory role in osteogenic differentiation. Differential chromatin accessibility analysis using ATAC‐seq data demonstrated preferential accessibility in osteoblasts over chondrocytes in both human and mouse models, further implicating this region in bone development. The duplicated region was fully contained within a single topologically associating domain (TAD), suggesting that intra‐TAD duplications may disrupt spatial and temporal MSX2 regulation, contributing to the CCD‐like phenotype. Phenotypic variations, such as synpolydactyly in a previously reported patient, likely arise from additional regulatory elements outside the minimal overlapping region. Our findings establish a causal link between MSX2 upstream duplications and CCD‐like phenotypes, emphasizing the role of epigenetic mechanisms and TAD structures in regulating skeletal development. Further studies, including long‐read sequencing and ChIP‐seq, are needed to clarify the precise regulatory pathways involved.
Mamiko Yamada, M. Cleghorn, Prabhakara Krishnamurthy et al.· Human Mutation· 0 citations
ABSTRACT Background Deletions involving the 1q43q44 region are among the most recurrent terminal chromosomal imbalances and are associated with a recognizable neurodevelopmental phenotype. These deletions may occur as isolated events or in the context of more complex rearrangements. Case Presentation We describe presumed monozygotic twin sisters (patients 1 and 2) with a de novo 1q43q44 deletion and an unrelated patient (patient 3) carrying a similar deletion combined with a 21q22.3 duplication derived from a t(1;21)(q43;q22.3)mat. All three patients exhibited features consistent with the distal 1q43q44 deletion syndrome, including microcephaly, corpus callosum abnormalities, developmental delay, intellectual disability, language impairment, hypotonia, micro−/retrognathia, and congenital heart defects. Results Cytogenetics and FISH analyses confirmed distal 1q deletions in all patients. Chromosomal microarray analysis identified a ~9.5 Mb deletion in patient 1 (her twin was not tested) and a ~12.1 Mb deletion in patient 3. Despite differences in deletion size and genomic context, both rearrangements disrupted a largely overlapping interval containing 171 genes, including the dosage‐sensitive neurodevelopmental genes AKT3, HNRNPU, and ZBTB18 as well as other monoallelic expressed genes (GREM2 and NLRP3) and, in patient 3 only, RYR2. Functional enrichment analyses highlighted pathways related to neurodevelopment, epilepsy, and cardiac function. Although the twins showed similar congenital manifestations, patient 1 later developed seizures whose origin could not be assessed. Conclusion These findings further support the role of haploinsufficient genes within the distal 1q43q44 region, particularly AKT3, HNRNPU, and ZBTB18, to the core neurodevelopmental phenotype and highlight the value of high‐resolution genomic analysis for patient characterization.
Ma. Guadalupe Domínguez-Quezada, H. Rivera, L. E. Figuera et al.· Journal of clinical laborato...· 0 citations
Chromosomal microarray analysis (CMA) is a first-tier diagnostic tool for children with neurodevelopmental disorders and congenital anomalies; however, interpretation of variants of uncertain significance (VUS) remains challenging. This study aimed to characterize the copy number variant (CNV) spectrum in pediatric patients with congenital anomalies and/or dysmorphic features, focusing on VUS interpretation through segregation analysis and detailed phenotype–genotype correlation. We retrospectively evaluated 28 pediatric patients with abnormal CMA results referred to two tertiary genetics clinics between 2021 and 2022. Indications included neurodevelopmental delay, intellectual disability, dysmorphism, and/or congenital anomalies. CNVs were classified according to 2020 ACMG/ClinGen standards. Parental segregation analysis was performed for 15 CNVs in 13 families, with particular attention to gene disruption caused by CNV breakpoints. The cohort included 16 males and 12 females, with a mean age of 5.28±4.39 years. Thirty-four CNVs were identified, including 14 deletions and 20 duplications; seven were pathogenic/likely pathogenic and 27 were VUS. Segregation analysis identified five de novo, six maternal, and four paternal variants. A 2q22.2 gain disrupting KYNU at intron 12 was identified in a patient with VACTERL-like features. Three patients had additional karyotypic abnormalities, highlighting the complementary role of CMA. A de novo 4p16.3 duplication disrupting both HTT and ADD1 was also identified. Our findings highlight the importance of detailed phenotyping, breakpoint analysis, and segregation studies in interpreting CNVs, particularly VUS and rare intragenic disruptions. Integrating genomic findings with clinical features and inheritance patterns may improve phenotype–genotype correlation and support the identification of candidate loci.
Silver–Russell syndrome (SRS) is most commonly caused by epigenetic alterations at 11p15.5 or maternal uniparental disomy of chromosome 7 [upd(7)mat], though other molecular mechanisms remain unclear. While microdeletions encompassing MEST have been associated with SRS-like phenotypes, no pathogenic intragenic MEST variants have been reported to date. We describe a 6-month-old male infant with clinical features suggestive of a SRS-like phenotype, including intrauterine and postnatal growth restriction, triangular facies, prominent forehead, and small extremities. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) revealed neither methylation abnormalities at 11p15.5, 7p13, or 7q32 nor copy number variations (CNVs) in these regions. Trio whole-exome sequencing (trio-WES) identified a paternally inherited splice-site variant (c.890 + 1G > A) in MEST. Given the paternal-specific expression of MEST, this variant resides on the functionally active allele. Based on in silico predictions and clinical correlation, this case identifies MEST as a plausible candidate gene for SRS and provides a rationale for further functional studies. Phenotypic variation exists across molecular subtypes, yet definitive genotype–phenotype correlations await larger, systematically ascertained cohorts.
The findings suggest that PPP1R12A-related disorders may exhibit a broader phenotypic variability than previously recognized and it is proposed that HL and inner ear malformations may represent novel features associated with this clinical spectrum.
G. Pianigiani, Lara Emily Rosso, Anna Morgan et al.· Genes· 0 citations