Variants in the dentin sialophosphoprotein (DSPP) gene are associated with dentin dysplasia type II (DD-II; OMIM # 125420) and dentinogenesis imperfecta (DI) types II (OMIM # 125490) and III (OMIM # 125500). DSPP encodes a precursor protein cleaved into three dentin matrix proteins: dentin sialoprotein (DSP), dentin phosphoprotein/phosphophoryn (DPP) and dentin glycoprotein (DGP). Exon 5 contains over 200 tandem 9-base pair repeats (DSS domain), complicating sequencing with standard methods.
We studied 112 individuals (42 index cases and 70 relatives) with clinical signs of DI or DD. DNA extracted from saliva was analysed using the GenoDENT next-generation sequencing panel. For inconclusive cases, long-range PCR and Oxford Nanopore Technology (ONT) long-read sequencing were used to overcome limitations in analysing the repetitive DSPP region.
Pathogenic or likely pathogenic DSPP variants were identified in 41 families, including 8 known and 14 novel variants. Most were in exon 5, causing frameshifts resulting in a –1 reading-frame shift with a hydrophobic C-terminal extension and termination at a downstream stop codon. ONT sequencing enabled detection in cases where short-read methods failed. Several variants showed familial segregation and variable expressivity.
This study demonstrates the value of long-read sequencing to resolve complex DSPP regions and expands the variant spectrum. The variability in clinical presentation suggests the influence of modifier factors, warranting further genotype–phenotype studies.
Type II, IX and XI collagenopathies encompass Stickler syndrome and a spectrum of related connective tissue disorders with diverse and overlapping phenotypes. This study evaluated outcomes of commercial gene panels to understand how genetic testing was used in these collagenopathies.
A retrospective review was undertaken of genetic tests including genes COL2A1, COL11A1, COL11A2, COL9A1, COL9A2 and COL9A3 from a clinical diagnostic laboratory. Cases harbouring pathogenic/likely pathogenic (P/LP) variants were categorised by the ordering panel. Indications for testing were classified into ocular, orofacial, auditory, musculoskeletal, cardiovascular or other symptoms/signs.
Between February 2020 and May 2024, 7798 diagnostic panels were ordered containing the six collagen genes of interest, with 214 unique cases reporting at least one P/LP variant. Overall, Stickler syndrome was the main indication for testing in 48% of cases. Family history and ocular signs were the most common indications in Stickler syndrome genetic testing, while musculoskeletal and neurological/developmental signs more frequently prompted testing with other panel types. The diagnostic yield of Stickler syndrome panels was 50%, with a higher rate among cases reporting a family history (OR: 2.6 (95% CI 1.3 to 5.4); p=0.005) or presenting with ocular signs (OR: 2.2 (95% CI 1.1 to 4.5), p=0.03).
Stickler syndrome is the primary indication for half of the genetic tests ordered for type II, IX and XI collagenopathies, yet accurate diagnosis remains challenging due to overlapping collagenopathy phenotypes. Diagnosis and management could be enhanced through comprehensive documentation of multisystem signs, identification of syndrome-specific features and multidisciplinary care approaches.
von Hippel-Lindau (VHL) syndrome-related renal cell carcinoma (RCC) is the most prevalent hereditary RCC and exhibits clinical heterogeneity, complicating patient management. While VHL gene inactivation is the primary driver, the impact of co-occurring germline mutations in other renal cancer predisposition genes on clinical phenotype remains poorly understood. This study aimed to investigate whether such co-mutations define a distinct clinical and molecular subgroup of patients with VHL syndrome.
115 patients with VHL syndrome were enrolled in this study. All patients underwent germline sequencing of a 39-gene panel for hereditary RCC. Pathogenic/likely pathogenic variants of the VHL gene were identified, and patients were stratified into a VHL single-mutation group and a VHL co-mutation group. Clinical characteristics, tumour manifestations, renal lesion growth kinetics and age-related tumour risks were compared.
42.6% of patients harboured germline co-mutations. The co-mutation group exhibited a greater proportion of symptomatic patients (95.9% vs 78.7%, p=0.012) and increased penetrance of RCC (79.6% vs 57.6%, p=0.013) and pancreatic cystic tumours (77.6% vs 48.5%, p=0.002). This group had a lower incidence of positive family history (40.8% vs 69.7%, p=0.002). Co-mutation status is an independent predictor for RCC development (HR 1.798, p=0.016), and their RCC lesions exhibited significantly faster linear (0.376 cm/year vs 0.225 cm/year, p=0.022) and volumetric (3.132 cm3/year vs 1.167 cm3/year, p=0.049) growth metrics.
Germline co-mutations are prevalent in VHL syndrome and define a clinically distinct subset of patients characterised by higher disease penetrance and a more aggressive RCC phenotype. Our findings suggest that co-mutation status is a critical determinant of clinical heterogeneity and a powerful biomarker for risk stratification.
This study aimed to analyse the distribution and genotype-phenotype correlations of pathogenic variants among 11 509 newborns carrying at least one common deafness-associated variant.
A genotype distribution analysis was performed on 11 509 neonates identified as carriers of ≥1 pathogenic variant across four common deafness genes (GJB2, SLC26A4, MT-RNR1 and GJB3) at our centre between January 2022 and December 2024. Hearing outcomes were assessed through a comprehensive evaluation protocol, initial screening (>48 hour after birth, before discharge), re-screening at 42 days and diagnostic evaluation by 3 months. Sanger sequencing identified potential compound heterozygous variants, and genotype-phenotype analysis was performed on infants with hearing loss (HL).
Among the 11 509 newborns carrying ≥1 pathogenic variant, two high-risk groups were identified: 653 newborns (5.67%) carrying biallelic pathogenic variants in GJB2 and 113 newborns (0.98%) carrying the MT-RNR1 m.1555A>G or m.1494C>T variants. However, only 58 infants were confirmed with HL, and 15.52% of these passed the initial hearing screening. Sanger sequencing reclassified 23.08% of presumed heterozygotes with HL as compound heterozygotes. Acoustic diagnostic results showed that GJB2 c.235del homozygotes exhibited higher HL incidence (50% vs 6.51%) and more severe/profound HL (66.67% vs 7.14%) than GJB2 c.109G>A homozygotes.
Our data demonstrated that while genetic screening readily identifies infants with hereditary deafness susceptibility, newborn hearing screening fails to detect most of these high-risk cases due to the absence or delayed onset of HL. This gap obligates long-term audiological monitoring and highlights genetic testing’s critical role in enabling early surveillance for later-onset HL.
The disruption of neural progenitor proliferation is a key mechanism underlying primary microcephaly, yet how cell cycle arrest leads to progenitor loss remains only partially understood. Cyclin-dependent kinases, CDK4 and CDK6, are central regulators of the G₁/S transition, but their role in cellular stress responses during neurodevelopment remains unclear.
We studied fibroblasts from affected individuals in two families: siblings homozygous for a CDK4 frameshift (p.Glu94Argfs*65) presenting with microcephaly and pontine hypoplasia
and a child homozygous for a CDK6 missense variant (p.Thr154Ile) with microcephaly, brain atrophy, neutropenia and ovarian failure.
Loss-of-function variants in CDK4 and CDK6, core G₁/S regulators, impaired proliferation and induced mitochondrial stress responses and apoptosis. Mutant fibroblasts exhibited significantly reduced DNA synthesis and cell cycle progression, along with increased mitochondrial activity, elevated reactive oxygen species and increased apoptosis. Mitochondrial responses differed by gene: CDK4 deficiency caused mitochondrial hyperpolarisation, while CDK6 deficiency resulted in depolarisation, suggesting differences in mitochondrial apoptotic dynamics. Both variants affected mTOR pathway signalling, linking cell cycle kinase loss to disrupted metabolic regulation.
These findings uncover a previously unrecognised mitochondrial stress response accompanying proliferative failure, offering mechanistic insight into how cell cycle arrest could lead to neural progenitor depletion and brain growth disorders. More broadly, our results connect cyclin-dependent kinase dysfunction with mitochondrial homeostasis in neurodevelopment, highlighting shared pathways with neurodegeneration and cancer.
Potocki-Lupski syndrome (PTLS) is a rare genetic disorder, with an estimated prevalence of 1:25 000. Detection of a duplication at position 17p11.2 comprising the RAI1 gene establishes the diagnosis. Deletion of this same region is responsible for Smith-Magenis syndrome (SMS). Hitherto, the non-specific clinical features included psychomotor and growth retardation and multiple congenital anomalies. Our aim was to further delineate the clinical spectrum of PLTS.
We gathered a series of 56 individuals carrying a 17p11.2 duplication, one of the largest reported to date. We collected detailed phenotypic data and established a phenotypic comparison with individuals already described in the literature.
We corroborated the main clinical signs associated with PTLS and highlighted additional features present in a significant proportion in our series, such as intrauterine growth retardation or low birth weight, musculoskeletal and ophthalmological anomalies, and abnormalities of the skin appendages. In line with previous reports, behavioural disorders were frequently identified (23%). Yet unexpectedly, self-aggressive and hetero-aggressive behaviours, characteristic features of SMS, were found in a small number of individuals. Forty-six individuals harboured the recurrent duplication (85%), five had larger duplications (9%) and three had smaller duplications (6%). We did not identify inherited duplications when parental information was available (n=43).
Our study refined the clinical features of PTLS and their relative frequencies. Our findings therefore contribute to improving management of people with PTLS. These open up new pathophysiological hypotheses involving RAI1 gene dosage of the genesis and control of behaviour, as well as new, more complex regulatory pathways.
The BRCA2 c.7847C>T (p.Ser2616Phe) variant is specific to the Japanese population and has long remained a variant of uncertain significance. Because BRCA1/2 genetic testing serves as a companion diagnostic for poly (ADP-ribose) polymerase inhibitor therapy in Japan, unresolved classification has limited access to targeted treatment.
We conducted a nationwide study using the national Hereditary Breast and Ovarian Cancer registry. Pathogenicity was assessed through quantitative cosegregation analysis, a systematic review of functional and clinical evidence and evaluation of variant frequency in population databases. Evidence was integrated using the ClinGen ENIGMA BRCA1/2 Variant Curation Expert Panel framework.
We identified 44 carriers from 35 distinct Japanese families. Quantitative cosegregation analysis yielded a combined likelihood ratio of approximately 60, satisfying the PP1_Strong criterion. This was supported by robust evidence from multiple functional studies, including Mixed-All-Nominated-in-One-BRCA, homology-directed repair and saturation genome editing assays (PS3) and a reported case of Fanconi anaemia (PM3_Moderate). This variant is rare, with an allele frequency of 6.20x10–7 in gnomAD and 1.06x10–4 in ToMMo 61KJPN (PM2_Supporting). Although the BayesDel noAF score met the benign criterion (BP4), other in silico tools indicated deleterious effects. In total, the accumulated evidence reached 10 points, corresponding to an estimated odds of pathogenicity of 895:1, exceeding the ‘Pathogenic’ threshold.
By integrating newly collected genetic data with functional and clinical evidence, we provide robust support for reclassifying the BRCA2 c.7847C>T (p.Ser2616Phe) variant as ‘Pathogenic’. This reclassification is crucial for ensuring that eligible Japanese patients gain access to appropriate targeted therapies.