Congenital vertebral malformations (CVMs), affecting approximately 0.5-1 per 1000 live births, occur either in an isolated form or as part of syndromic disorders. Despite the identification of numerous causative genes for CVMs, the molecular etiology of most cases remains unknown. In this study, we applied a three-tiered diagnostic approach (chromosomal microarray analysis, followed by custom gene panel analysis, and exome/genome sequencing) in a cohort of 34 patients with CVMs. We achieved a 12% diagnostic success rate, identifying a deletion upstream of SOX9 and pathogenic or likely pathogenic variants in FLNB and KMT2D. Most pathogenic variants were detected by exome or genome sequencing, while earlier-tier analyses yielded limited results. We also identified two candidate genes, NSD2 and TBXT, that may contribute to the phenotype observed in our patients, but warrant future functional validation. Our work expands the molecular spectrum of CVMs and highlights the utility of comprehensive genomic testing for improving diagnosis and understanding of vertebral development disorders.

Spondylocarpotarsal synostosis syndrome (SCTS) is a rare genetic disorder characterized by vertebral fusion, short stature, and skeletal anomalies. SCTS is primarily associated with mutations in filamin B. However, in this report, we present a unique case of SCTS in a 28-year-old male who complained of neck and shoulder pain persisting for 1 year. His clinical presentation included radioulnar synostosis, cervical spine anomalies (scoliosis and agenesis of the posterior arch of C1), and a history of polydactyly. Genetic analysis revealed mutations in GMNN and DLL1. To the best of our knowledge, this is the first report on the association of SCTS with these genes.

Skeletal dysplasia is an ensemble of hereditary conditions that impact bone and cartilage formation, leading to aberrant skeletal growth and proportions. Such illnesses can affect the limbs, spine, and skull, and they can produce a wide range of symptoms, from minor to severe. Filamin A and B are functionally analogous proteins, exhibiting structural resemblance and playing crucial role in the formation of cellular cytoskeleton. Objective of the research was to employ experimental and computational approaches to investigate the contribution of Filamins in skeletal dysplasias. Whole exome sequencing lead to the identification of two mutations involved in a spectrum of skeletal dysplasias with predominant spine and articular association. Here we report two families from Pakistan with distinct mutations in FLNA protein (R196W) causing otopalatodigital syndrome-1 or metaepishyseal dysplasia with short stature, prominent facial dysmorphism including hypertelorism, frontal bossing, down-slanting parpebral fissures and depressed nasal bridge. While novel, homozygous, nonsense FLNB mutation (p.C1081*) is causing Spondylocarpotarsal synostosis syndrome (SCT), an exceptionally rare skeletal disorder marked by disproportionate short stature, spinal deformities, and other associated features like dental enamel hypoplasia, joint laxity, and conductive hearing loss. In silico structural and functional analysis of mutant filamins provide compelling proof for their role in the progression of skeletal dysplasias. Screened variants have not only affected the protein's three-dimensional structure dramatically but also resulted in loss of functional domains, leading to aberrant interactions with binding proteins and progression of disease. The FLNB-related disorders can be divided into two groups of conditions caused by loss of function or gain of function of filamin-B. Biallelic loss-of-function pathogenic variants in FLNB cause spondylocarpotarsal synostosis syndrome (FLNB-SCT). Monoallelic gain-of-function pathogenic variants in FLNB cause a spectrum of phenotypic severity ranging from apparently isolated clubfoot to Larsen syndrome (FLNB-LS), atelosteogenesis type 3 (FLNB-AO3), and atelosteogenesis type 1 (FLNB-AO1), which is perinatal lethal. For the purposes of this GeneReview, the previously described entities Piepkorn dysplasia and boomerang dysplasia are subsumed under the FLNB-AO1 spectrum. FLNB-SCT is characterized by postnatal disproportionate short stature; scoliosis and lordosis due to vertebral fusions; carpal and tarsal synostosis; and, variably, clubfeet, hearing loss, and dental enamel hypoplasia. FLNB-LS is characterized by combinations of congenital dislocations of the hip, knee, and elbow; clubfeet (equinovarus or equinovalgus foot deformities); scoliosis and cervical kyphosis (which can be associated with a cervical myelopathy); short, broad, spatulate distal phalanges; distinctive craniofacial features (prominent forehead, depressed nasal bridge, malar flattening, and widely spaced eyes); vertebral anomalies; and supernumerary carpal and tarsal ossification centers. Individuals with FLNB-LS may also present with midline cleft palate and hearing loss. FLNB-AO1 and FLNB-AO3 are characterized by severe short-limbed dwarfism; dislocated hips, knees, and elbows; and clubfeet. FLNB-AO1 is lethal in the perinatal period. At its most severe, the spectrum of phenotypes assigned FLNB-AO1 can present with perinatal-lethal micromelic dwarfism characterized by flipper-like limbs (polysyndactyly with complete syndactyly of all fingers and toes, hypoplastic or absent first digits, and duplicated intermediate and distal phalanges); macrobrachycephaly; prominent forehead; hypertelorism; and proptosis. Occasional features include cleft palate, omphalocele, and cardiac and genitourinary anomalies. In individuals with FLNB-AO3, survival beyond the neonatal period is possible with intensive and invasive respiratory support. The diagnosis of FLNB-SCT is established in a proband by identification of biallelic loss-of-function pathogenic variants in FLNB by molecular genetic testing. The diagnosis of other FLNB-related disorders (LS, AO1, AO3) is established in a proband by identification of a heterozygous gain-of-function pathogenic variant in FLNB by molecular genetic testing. Treatment of manifestations: Cervical spine instability in asymptomatic infants can be successfully managed with posterior arthrodesis. Function can be stabilized (if not improved) in infants with myelopathic signs by a combination of anterior decompression and circumferential arthrodesis. Hip dislocation in individuals with FLNB-LS usually requires operative reduction. Scoliosis and clubfeet are managed in a routine manner. Anesthetic agents that allow more rapid induction and recovery are preferred in those with laryngotracheomalacia. When possible, cleft palate and hearing loss are best managed by multidisciplinary teams. Surveillance: Annual orthopedic evaluation for progressive scoliosis; feeding and growth assessment for those with cleft palate by a multidisciplinary team; annual audiologic and dental evaluations. Pregnancy management: Delivery of an affected infant has the potential to be complicated by extended breech presentation due to dislocation of the hips and knees. FLNB-SCT is inherited in an autosomal recessive manner. If both parents are known to be heterozygous for an FLNB pathogenic variant, each sib of an affected individual has at conception a 25% chance of inheriting biallelic pathogenic variants and being affected, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the familial FLNB pathogenic variants. Heterozygous sibs of a proband with FLNB-SCT can exhibit mild reductions in stature but no other medically significant phenotypic manifestations. Once the FLNB pathogenic variant(s) have been identified in an affected family member, heterozygote testing for at-risk relatives and prenatal/preimplantation genetic testing are possible. FLNB-LS, FLNB-AO1, FLNB-AO3, and FLNB-related apparently isolated clubfoot are inherited in an autosomal dominant manner. Comparatively mild (e.g., FLNB-LS) and severe (e.g., FLNB-AO3) forms of the autosomal dominant FLNB-related disorders can occur in the same family. Some individuals diagnosed with an autosomal dominant FLNB-related disorder have the disorder as the result of a pathogenic variant inherited from a heterozygous or mosaic parent. Some individuals have the disorder as the result of a de novo pathogenic variant (the vast majority of lethal FLNB conditions are the result of de novo pathogenic variants). Each child of a proband who is heterozygous for an FLNB pathogenic variant has a 50% chance of inheriting the pathogenic variant. Each child of a proband with somatic mosaicism for an FLNB pathogenic variant has up to a 50% chance of inheriting the pathogenic variant. Offspring who inherit an FLNB pathogenic variant from a proband with somatic mosaicism may be more severely affected than the proband. Once the FLNB pathogenic variant has been identified in an affected family member, prenatal/preimplantation genetic testing are possible.

Contractures, pterygia, and spondylocarpotarsal fusion syndrome (CPSFS) comprises a group of extremely rare genetic disorders characterized by congenital craniofacial and musculoskeletal abnormalities. With fewer than 500 cases reported globally, this scarcity contributes to limited clinical recognition, frequent diagnostic delays or errors, and missed opportunities for timely intervention. We present this case to enhance awareness of CPSFS and report a novel pathogenic variant in MYH3 (previously undocumented in the literature) that broadens the known mutational spectrum of MYH3 and enriches the phenotypic profile of CPSFS. A female neonate was born at 29 weeks, prenatal ultrasound and magnetic resonance imaging revealed scoliosis and vertebral fusion. The postnatal examination showed microstomia, low-set ears, a short neck with webbing, and flexion contractures at shoulders, elbows, knees, and hands. The whole genome sequencing found novel variants, namely NM_002470.4: c.1914del C; p. Lys639Argfs*18 and NM_002470.4: c.-68 + 4A > T, in the MYH3. CPSFS 1. Immediately after birth, noninvasive ventilatory support was initiated. The surgical team conducted comprehensive evaluations, while concurrent genetic testing was performed. Given the infant's multiple systemic skeletal malformations and inability to sustain spontaneous respiration, surgical intervention was deemed nonviable. Due to severe thoracic deformity and bronchopulmonary dysplasia, the infant required continuous noninvasive ventilation from birth and remained ventilator-dependent. At a corrected gestational age of 36 weeks and 4 days, life-sustaining therapy was withdrawn following thorough counseling and parental deliberation. The infant died shortly thereafter. Prenatal ultrasound and fetal magnetic resonance imaging can reliably detect characteristic manifestations including scoliosis, joint developmental abnormalities, and clubfoot. Thus, regular prenatal surveillance plays a critical role in early disease identification. For suspected cases, genetic counseling and diagnostic testing enable informed parental decision-making regarding management of affected offspring and future reproductive planning.

Ultrasound diagnosis of fetal skeletal conditions remains challenging. MYH3 is a gene that encodes the embryonic myosin heavy chain; it is important for skeletal and muscular development and is strongly expressed during fetal development. Variants in MYH3 are involved in distal arthrogryposes 2A and 2B3 and in spondyocarpotarsal synostosis syndrome with contractures and pterygia, contractures of proximal and distal joints, variable spine anomalies and vertebral, carpal and tarsal fusions. We describe a case in which prenatal ultrasonography detected abnormal bone density in the fetal spine. The fetus showed abnormal spinal segmentation, characterised by demineralisation and lacunar morphological tracts. x-rays and histological examination confirmed the ultrasonographic findings. We describe a unique ultrasonographic phenotype of fetal spine that has not yet been described in the literature. This is likely associated with two MYH3 variants. Therefore, we believe that abnormal spinal segmentation should be considered a relevant ultrasound finding. Fetal ultrasound, together with radiological investigations, clinical examination of the fetal phenotype and histological investigations are essential in directing molecular genetic testing to identify rare diseases. We review the literature and describe a prenatal case with abnormal bone density in the spine. Whole-exome sequencing (WES) analysis in the fetus was performed to explore variants compatible with ultrasound signs.