Giedre Grigelioniene

Pathogenic variants in the noncoding gene RNU4‐2 cause ReNU syndrome, a common neurodevelopmental disorder. Although the core phenotype is well described, longitudinal symptom progression and family perspectives remain insufficiently characterized. We identified 11 individuals with RNU4‐2 pathogenic variants through reanalysis of clinical whole genome sequencing (WGS) data from a previously undiagnosed cohort. Using deep phenotyping, including retrospective medical record review and parental insights, we delineated a recognizable age‐dependent clinical trajectory. Infancy was characterized by feeding difficulties, hypotonia, decelerating head growth, and visual abnormalities; early childhood by gait disturbances, autistic behavior, and seizure onset; and later childhood by persistent severe speech impairment with emerging orthopedic complications. Notably, feeding problems and seizures improved over time in several individuals. Core features included developmental delay, intellectual disability, speech abnormalities, hypotonia, autism, postnatal growth retardation, visual and brain abnormalities, and similar facial features. Parents emphasized strong social connectedness and affection and often described infancy as the most challenging stage due to feeding difficulties and failure to thrive. This study refines the natural history of ReNU syndrome and provides guidance for clinical management and counselling. It also highlights the value of routine WGS reanalysis as novel disease genes are identified.

Background: Genetic skeletal disorders (GSDs) comprise a heterogeneous group of rare, predominantly monogenic conditions that are increasingly diagnosed through high-throughput sequencing. While gene discovery has progressed rapidly, interpretation of pathogenic and uncertain variants remains a major bottleneck, in part because their functional consequences are determined at the protein structure level. However, a systematic assessment of structural knowledge across GSD-associated genes is currently lacking. Here, we present a comprehensive protein structure-centric analysis of 674 protein-coding genes implicated in GSDs. Methods: We integrated experimental structures, AlphaFold2 (AF2) models, multimeric states, protein–protein interactions, and ClinVar variant annotations. Results: We quantify experimental structural availability and sequence coverage, revealing that 37% of GSD proteins lack any experimental structure and that, among proteins with structures, sequence coverage is often incomplete. We show that AF2 models provide high-confidence structural information for a substantial subset of proteins lacking experimental data, but that model reliability strongly correlates with existing structural coverage. Analysis of multimeric assemblies and co-occurring partners demonstrates that many GSD proteins function as obligate multimers, highlighting the importance of interface-level interpretation of variants. Finally, mapping clinically annotated missense variants onto representative protein structures illustrates how structural context can inform the interpretation of pathogenic and uncertain variants, particularly at interaction interfaces. Conclusions: Together, this work provides a structure-aware reference framework for GSD genes, highlighting systematic gaps in current protein knowledge and demonstrating how integration of structural data can guide genomic variant interpretation. Our observations support a broader principle of structural equivalence , whereby distinct variants converge on shared structural perturbations that explain clustering patterns and enable mechanistic interpretation of nearby variants of uncertain significance.

Short stature may be caused by a multitude of conditions, including genetic and non-genetic causes. Over the last decade, advances in genetic sequencing technologies have revolutionized our understanding of the underlying physiology of growth and greatly increased our ability to identify genetic etiologies of short stature. The current guideline provides a general overview of the approach to the evaluation of a child with short stature, followed by recommendations identifying factors in the medical and family history, physical examination, radiographic, and laboratory work up which increase the likelihood of identifying a genetic etiology. An algorithm is proposed for the genetic workup of individuals with short stature based on their clinical presentation. The benefits and risks of genetic testing are discussed as well.

Approximately 200 genetic skeletal disorders can present prenatally, detectable through ultrasound abnormalities during pregnancy. Severe forms are typically identified during the first or second trimester, whereas milder phenotypes are recognized later, in the third trimester. Diagnosing skeletal dysplasia prenatally is challenging due to the large number of disorders and the overlapping clinical findings that can be detected by ultrasound. This study, conducted at Karolinska University Hospital between 2015 and 2022, examines the genetic and radiographic findings in 32 fetuses (14 female and 18 male, from unrelated families) with skeletal abnormalities detected on prenatal ultrasound and confirmed by radiographs at birth or after pregnancy termination. Fetal DNA samples from all 32 fetuses underwent singleton genome sequencing using an in silico skeletal dysplasia gene panel. As a second step, for six fetuses with molecularly unsolved diagnoses, trio genome sequencing analysis involving the fetus and both parents was performed. The diagnostic yield of genome sequencing was 72%, with pathogenic or likely pathogenic variants identified in 23 of the 32 fetuses. Additionally, four variants of uncertain significance, strongly suspected to be causative based on clinical and radiographic features, as well as structural protein analyses, were identified in four fetuses with autosomal recessive conditions. The diagnoses of five fetuses remain molecularly unsolved. In conclusion, by combining detailed phenotypic data with singleton genome sequencing we were able to reach a genetic diagnosis in 72% of 32 fetal genetic skeletal disorder cases investigated at the Karolinska University Hospital.

We report a case of a fetus with short-rib thoracic dysplasia (SRTD) with polydactyly that also presented with atypical severe acro-mesomelic ossification defects. Genetic analysis using massively parallel sequencing of a skeletal dysplasia panel revealed compound heterozygous variants in DYNC2H1. This clinical report highlights the challenges associated with diagnosing the diverse phenotypes in the SRTD group and emphasizes the importance of genetic surveillance with a targeted gene panel for accurate diagnosis.

In the first-ever Undiagnosed Hackathon, nearly 100 experts from 28 countries combined advanced phenotyping and genomic techniques for 48 hours, ultimately providing diagnoses to 40% of the previously undiagnosed families. This inspiring model demonstrates the power of multidisciplinary collaboration and patient partnership in precision diagnostics.

Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2–64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants’ impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.

FOXC1 is a ubiquitously expressed forkhead transcription factor that plays a critical role during early development. Germline pathogenic variants in FOXC1 are associated with anterior segment dysgenesis and Axenfeld-Rieger syndrome (ARS, #602482), an autosomal dominant condition with ophthalmologic anterior segment abnormalities, high risk for glaucoma and extraocular findings including distinctive facial features, as well as dental, skeletal, audiologic, and cardiac anomalies. De Hauwere syndrome is an ultrarare condition previously associated with 6p microdeletions and characterized by anterior segment dysgenesis, joint instability, short stature, hydrocephalus, and skeletal abnormalities. Here, we report clinical findings of two unrelated adult females with FOXC1 haploinsufficiency who have ARS and skeletal abnormalities. Final molecular diagnoses of both patients were achieved using genome sequencing. Patient 1 had a complex rearrangement involving a 4.9 kB deletion including FOXC1 coding region (Hg19; chr6:1,609,721-1,614,709), as well as a 7 MB inversion (Hg19; chr6:1,614,710-8,676,899) and a second deletion of 7.1 kb (Hg19; chr6:8,676,900-8,684,071). Patient 2 had a heterozygous single nucleotide deletion, resulting in a frameshift and a premature stop codon in FOXC1 (NM_001453.3): c.467del, p.(Pro156Argfs*25). Both individuals had moderate short stature, skeletal abnormalities, anterior segment dysgenesis, glaucoma, joint laxity, pes planovalgus, dental anomalies, hydrocephalus, distinctive facial features, and normal intelligence. Skeletal surveys revealed dolichospondyly, epiphyseal hypoplasia of femoral and humeral heads, dolichocephaly with frontal bossin gand gracile long bones. We conclude that haploinsufficiency of FOXC1 causes ARS and a broad spectrum of symptoms with variable expressivity that at its most severe end also includes a phenotype overlapping with De Hauwere syndrome.

Seckel syndrome is an ultrarare autosomal recessive genetically heterogenous condition characterized by intrauterine and postnatal growth restriction, proportionate severe short stature, severe microcephaly, intellectual disability, and distinctive facial features including a prominent nose. Up to now, 40 patients with molecularly confirmed Seckel syndrome have been reported with biallelic variants in nine genes: ATR, CENPJ, CEP63, CEP152, DNA2, NIN, NSMCE2, RBBP8, and TRAIP. Homozygosity for nonsense variant (c.129G>A, p.43*) in CEP63 was described in three cousins with microcephaly, short stature, mild to moderate intellectual disability and diagnoses of Seckel syndrome. Here, we report a second family with three siblings who are compound heterozygous for loss-of-function variants in CEP63, c.1125T>G, p.(Tyr375*) and c.595del, p.(Glu199Asnfs*11). All siblings present with microcephaly, prominent nose, and intellectual disability but only one has severe short stature. Two siblings have aggressive behavior, a feature previously not reported in Seckel syndrome. This report adds two novel truncating variants in CEP63 and extends the clinical knowledge on CEP63-related conditions.