Tenorio-Castano J, Feito M, de Lucas R
… +20 more, Sendagorta E, Gómez-Fernández C, Parra A, Vallespin E, Gallego-Zazo N, Cazalla M, Jiménez-Estrada JA, Miranda-Alcaraz L, Mora-Gómez M, Rodríguez-Canó MJ, Vázquez-Amell V, Ramos S, Valle T, Mansilla E, Santiago FG, Galán-Gómez E, Calpena E, Ruíz-Pérez VL, Nevado J, Lapunzina P
We describe three unrelated individuals with congenital generalized hypertrichosis with gingival hyperplasia (CGHGH), each carrying a distinct structural rearrangement (duplication, deletion, inversion) at 17q24.2-q24.3...We describe three unrelated individuals with congenital generalized hypertrichosis with gingival hyperplasia (CGHGH), each carrying a distinct structural rearrangement (duplication, deletion, inversion) at 17q24.2-q24.3 identified by CMA and WGS. Despite differences in the type of rearrangement, all three patients seem to exhibit alterations affecting the genomic architecture of a cluster of genes, particularly involving the ABCA family (notably ABCA5, ABCA6, ABCA9, ABCA10), MAP2K6, and potassium channels (KCNJ16, KCNJ2). These findings suggest that disruption of the local chromatin organization, including topologically associating domains (TADs), may contribute to the pathogenesis of CGHGH. Although previous studies implicated deletions affecting ABCA5 as the likely cause of CGHGH, our findings emphasize a broader spectrum of structural variation capable of producing similar phenotypes. Interestingly, one patient involved a cryptic 1.2 Mb inversion that disrupted the region between ABCA9 and KCNJ2, detectable only by whole genome sequencing, reinforcing the need for advanced molecular diagnostics in patients with syndromic hypertrichosis. In all three individuals, gingival overgrowth co-occurred with typical facial features, coarse hair, and normal cognitive development, adding evidence to the phenotype-genotype correlation. Overall, this study strengthens the hypothesis that disruption of regulatory elements and chromatin architecture at 17q24.2-q24.3, rather than single nucleotide variants alone, can be a primary driver of CGHGH. These findings underscore the need to incorporate genome-wide structural variant analysis in the diagnostic workflow of rare developmental disorders, especially those with heterogeneous or subtle clinical presentations.
The SMARCA4 gene encodes a catalytic subunit of the BRG1/BRM-associated factor complex, which regulates gene expression through chromatin remodeling. Heterozygous missense variants in this gene have been linked to Coffin...The SMARCA4 gene encodes a catalytic subunit of the BRG1/BRM-associated factor complex, which regulates gene expression through chromatin remodeling. Heterozygous missense variants in this gene have been linked to Coffin-Siris syndrome, characterized by intellectual development disorder and various congenital anomalies (distinctive facial features, hypoplastic fifth digits, and malformations of the heart and central nervous system), but it is not typically associated with structural eye anomalies. Truncating variants in SMARCA4 have been associated with rhabdoid tumors predisposition syndrome, a group of rare and aggressive tumors occurring predominantly in infancy. Through pangenomic analyses (whole-exome or whole-genome sequencing), we identified loss-of-function variants in SMARCA4 in three unrelated individuals with microphthalmia and/or coloboma. None of these individuals had a history of rhabdoid tumors; however, a regular oncological follow-up was established following the SMARCA4 variant identification. Systemic features observed in these individuals consisted of developmental delay and brain anomalies. However, their clinical presentation does not align with classic features of Coffin-Siris syndrome. Although eye development anomalies have occasionally been reported in individuals with a pathogenic variant in SMARCA4, no clear association has been established to date. The description of these three new individuals provides further evidence supporting the role of SMARCA4 in eye development and its likely involvement in structural eye malformations.
Distal arthrogryposis constitutes a highly heterogeneous group of disorders with a critical need for clear classification. Phenotypes have traditionally been characterized using the classification system proposed by Bams...Distal arthrogryposis constitutes a highly heterogeneous group of disorders with a critical need for clear classification. Phenotypes have traditionally been characterized using the classification system proposed by Bamshad or Hall for distal arthrogryposis. Recessive MYH3 inheritance has been described in contractures, pterygia and spondylocarpotarsal fusion syndrome, and, more recently, in distal arthrogryposis without skeletal fusion. We hereby report a nuclear family affected by distal arthrogryposis with biallelic MYH3-related disorder, identifying two novel variants, which in the heterozygous state yield a subclinical phenotype. Beyond refining the molecular diagnosis and guiding genetic counseling, our study emphasizes that the classification of MYH3-related disorders and their inheritance modes is still evolving, underscoring the need to integrate knowledge gained from careful analyses.
Müllerian anomalies are a collection of heterogeneous anatomical disorders of the female genital tract that present with complex clinical features of which severe subtypes like congenital aplasia of the vagina and uterus...Müllerian anomalies are a collection of heterogeneous anatomical disorders of the female genital tract that present with complex clinical features of which severe subtypes like congenital aplasia of the vagina and uterus, may present with primary amenorrhea and dyspareunia, while mild cases like septate uterus, are often asymptomatic. Regardless of the types, the Müllerian anomalies impose both psychological and physical burdens on patients. Currently, the etiology of Müllerian anomalies remains largely unclear, which hinders early diagnosis and intervention. Although the advent of next-generation sequencing technologies has promoted a more comprehensive depiction of genetic features of Müllerian anomalies, there is still a lack of experimental validation for the functions of these genes, where some novel preclinical models having been applied in cancer fields may provide potentially available strategies. Thus, in this review, we aim to summarize the genetic defects and novel validation techniques associated with Müllerian anomalies. Elucidating the genetic mechanisms involving Müllerian anomalies can pave the way for the development of early diagnostic strategies and preventional measures in the future.
STEAP3 (Six-transmembrane epithelial antigen of the prostate 3), a metalloreductase, plays a key role in various cell processes, including iron homeostasis, inflammation, and cancer promotion. Over a decade ago, research...STEAP3 (Six-transmembrane epithelial antigen of the prostate 3), a metalloreductase, plays a key role in various cell processes, including iron homeostasis, inflammation, and cancer promotion. Over a decade ago, researchers reported a single, heterozygous nonsense variant in STEAP3 linked to transfusion-dependent severe hypochromic anemia. However, a later large population study on STEAP3 found no phenotypic red cell changes in heterozygous individuals. While the genotype and phenotype of STEAP3 are tentatively established for hypochromic microcytic anemia with autosomal dominant inheritance (MIM: 615234), we describe an autosomal recessive form of STEAP3-related neonatal familial hemophagocytic lymphohistiocytosis (HLH). We expanded the phenotype to include cytopenia and neonatal HLH. Our report on two affected male siblings highlights the expanded phenotype, clarifies the phenotypic spectrum of STEAP3, and broadens its genetic inheritance, ultimately providing a clinical and molecular workup for neonatal patients with unexplained HLH.
A Japanese boy carried a paternally inherited single-nucleotide deletion in PTF1A exon 1 (c.775delC) and a maternally inherited nucleotide substitution in the distal enhancer region (g.23508356T>G). Both variants were hi...A Japanese boy carried a paternally inherited single-nucleotide deletion in PTF1A exon 1 (c.775delC) and a maternally inherited nucleotide substitution in the distal enhancer region (g.23508356T>G). Both variants were hitherto unreported. The patient exhibited transient anemia in addition to typical clinical features of pancreatic hypoplasia, but no neurodevelopmental abnormalities. These results highlight the clinical importance and broad mutation spectrum of PTF1A variants as a cause of pancreatic hypoplasia. In addition, our data imply that phenotypes of PTF1A abnormalities are variable and include etiology-unknown transient anemia.
Copy number variations (CNVs) affecting the imprinted regions in 11p15.5 (imprinting centre 1 and 2/IC1, IC2) account for more than 2% of the molecular disturbances in Beckwith-Wiedemann and Silver-Russell syndrome (BWS,...Copy number variations (CNVs) affecting the imprinted regions in 11p15.5 (imprinting centre 1 and 2/IC1, IC2) account for more than 2% of the molecular disturbances in Beckwith-Wiedemann and Silver-Russell syndrome (BWS, SRS) and are associated with a recurrence probability of up to 50%. However, their clinical impact can be challenging to estimate, as it depends on the type of imbalance, the parental origin of the affected allele, its size and genomic content. As a result, a genotype-phenotype correlation of 11p15.5 alterations is still missing, at least for CNVs affecting only parts of the IC1 or IC2. By comprehensively summarising all published CNVs within 11p15.5 and the available clinical data of their carriers, we aim to further delineate a correlation of these disturbances with BWS and SRS features. In fact, consistent correlations could be delineated only for duplications including either both the telomeric and centromeric regions or complete gains of one of them. In contrast, CNVs encompassing only parts of these regions lead to heterogeneous phenotypes. In summary, our literature review provides support for pathogenicity assessment of CNVs in 11p15.5 as basis for genetic counselling. However, this dataset underlines the need for further research to enlighten the molecular complexity of this region and to better understand the regulation of genomic imprinting mechanisms in 11p15.5.
This schematic illustrates the genetic, molecular, and clinical consequences of ESAM loss-of-function variants identified in two unrelated Turkish families. Family 1 harbors a splice-site variant (c.451 + 5G>C) predicted...This schematic illustrates the genetic, molecular, and clinical consequences of ESAM loss-of-function variants identified in two unrelated Turkish families. Family 1 harbors a splice-site variant (c.451 + 5G>C) predicted to cause aberrant splicing between exons 3 and 4, leading to defective mRNA processing and loss of functional ESAM protein. Family 2 carries a nonsense variant (c.605 T>G; p.Leu202Ter) that introduces a premature stop codon within the second immunoglobulin-like domain, resulting in a truncated protein and expected nonsense-mediated mRNA decay (NMD). Both variants abolish ESAM's membrane anchoring and disrupt endothelial junctional cohesion. Clinically, affected individuals present with a distinct neurovascular phenotype characterized by intrauterine or perinatal intracranial hemorrhage, ventriculomegaly, microcephaly, spastic quadriparesis, and congenital cataracts. The lower panel summarizes the pathophysiological cascade: (1) hemorrhagic stroke resulting from vascular fragility, (2) blood-brain barrier (BBB) disruption due to tight junction dysfunction and increased transcytosis, and (3) impaired vascular network formation caused by defective endothelial tubulogenesis. Collectively, these findings establish ESAM deficiency as a congenital tight-junctionopathy linking molecular endothelial defects to severe neurodevelopmental impairment.
This study aimed to characterize the spectrum of germline pathogenic and likely pathogenic variants in cancer susceptibility genes among Uruguayan patients with breast, ovarian, or prostate cancer (BC, OvC, PCa) who self...This study aimed to characterize the spectrum of germline pathogenic and likely pathogenic variants in cancer susceptibility genes among Uruguayan patients with breast, ovarian, or prostate cancer (BC, OvC, PCa) who self-funded multigene panel testing. We analyzed 119 unrelated adults (93 bc, 12 OvC, 14 PCa) who underwent clinical germline testing using commercially available next-generation sequencing panels (comprising both a 26 gene hereditary breast/ovarian subset and a comprehensive 85/90 gene panel). Variant classification followed international guidelines. Detection rates were calculated with 95% exact binomial confidence intervals. OvC and PCa cases were analyzed separately due to small sample sizes (n < 15). PGVs were found in 16/119 patients (13.4%): 10.8% in BC (10/93), 25% in OvC (3/12), and 21.4% in PCa (3/14). BRCA1/2 variants accounted for 25% of positive cases, while 61.5% involved non-BRCA genes (ATM, RAD51C, MUTYH). No recurrent founder mutations were detected, although MUTYH c.452A>G was observed in multiple unrelated individuals. Variants of uncertain significance were identified in 57% of BC patients (53/93), mostly missense variants in DNA repair genes. The mean age at diagnosis among PGV carriers was 50 years (range 32-66). The germline mutational spectrum in Uruguayan cancer patients is diverse. Most PGVs were found in genes other than BRCA1/2, supporting the use of MGPT for cancer risk assessment. Genetic testing should be considered for all cancer patients in Uruguay, regardless of ancestry or tumor type. Further research is needed to better understand the role of less-characterized genes in BC, OvC, and PCa predisposition.
The mechanisms by which the autosomal dominant disorder tuberous sclerosis complex (TSC) results in liver fibrosis remain poorly understood. KDM6A, a histone demethylase, has been implicated in the pathogenesis of fibros...The mechanisms by which the autosomal dominant disorder tuberous sclerosis complex (TSC) results in liver fibrosis remain poorly understood. KDM6A, a histone demethylase, has been implicated in the pathogenesis of fibrosis in multiple tissues. This study aimed to elucidate the molecular mechanism by which KDM6A contributed to TSC-associated fibrosis. We observed fibrogenesis, epithelial-mesenchymal transition (EMT) induction and upregulation of Kdm6a in vivo and in vitro upon Tsc1 or Tsc2 deficiency. Knockdown of Kdm6a attenuated both fibrosis and EMT phenotypes. Mechanistically, Kdm6a depletion reduced phosphorylation of ERK1/2 and downregulated Snai1 expression. Activation of the MAPK/ERK pathway with PMA restored EMT-related protein expression, confirming the functional involvement of this signaling axis. Furthermore, Tsc1 or Tsc2 deficiency promoted Kdm6a expression via the mTORC1 pathway, while Kdm6a knockdown conversely suppressed mTORC1 activity by reducing mTOR protein expression, suggesting a positive feedback loop between Kdm6a expression and mTORC1. These findings indicate that Kdm6a promotes fibrosis in TSC through the activation of the MAPK/ERK/SNAI1 signaling pathway. Moreover, the combination of mTORC1 and KDM6A inhibitors results in marked regression of fibrosis and liver lesions in TSC models, unveiling a potential treatment for TSC patients with inadequate response to mTORC1 inhibitors.
Osteogenesis imperfecta (OI) is a heterogeneous group of genetic diseases characterized by bone fragility and low bone mass. We report the identification of two unrelated families with OI of Bashkir origin-one with homoz...Osteogenesis imperfecta (OI) is a heterogeneous group of genetic diseases characterized by bone fragility and low bone mass. We report the identification of two unrelated families with OI of Bashkir origin-one with homozygous, the other with compound heterozygous probably pathogenic variants of the P3H1 gene, as well as one case of heterozygous carriage in a patient with clinical manifestations that do not correspond in severity to type VIII OI. Thus, an ethnospecific previously undescribed population aspect of the prevalence of recessive pathogenic variants p.Glu351Ter, p.Gly650Arg, 1720 + 4G>A in the P3H1 gene associated with various clinical phenotypes has been identified.
Facchini A, Concas MP, Zampieri S
… +12 more, Scala I, Graziano C, Innoceta AM, Trivisano M, De Dominicis A, Trimarchi G, Garavelli L, Baldassarri M, De Maggio I, Mari F, Greco D, Gasparini P
White-Sutton syndrome (WHSUS) is a rare neurodevelopmental disorder due to pathogenic variants in the POGZ gene. Its phenotype includes developmental delay, behavioral dysfunctions, hypotonia, and dysmorphic features. Th...White-Sutton syndrome (WHSUS) is a rare neurodevelopmental disorder due to pathogenic variants in the POGZ gene. Its phenotype includes developmental delay, behavioral dysfunctions, hypotonia, and dysmorphic features. The condition is still poorly known: comprehensive clinical descriptions and exhaustive genotype-phenotype correlations are lacking, limiting diagnostic and therapeutic advancements. Here, we report molecular, clinical, and instrumental data from the first and largest Italian cohort (19 patients). Our results highlight the importance of an extensive approach at the time of diagnosis-including early nutritional support for preventing obesity-related complications and instrumental screening for congenital malformations. Preliminary data suggest that splicing variants could be associated with more severe phenotypes. This study provides valuable new insights into WHSUS and represents a significant step towards its comprehension.
Acephalic spermatozoa syndrome (ASS) is a severe form of male infertility, but its genetic etiology remains largely unclear. In this study, we identified a novel homozygous frameshift variant in NME5 (c.163delA, p.Ser55V...Acephalic spermatozoa syndrome (ASS) is a severe form of male infertility, but its genetic etiology remains largely unclear. In this study, we identified a novel homozygous frameshift variant in NME5 (c.163delA, p.Ser55Valfs*16) in an infertile man with ASS. Subsequent functional analyses revealed complete loss of NME5 protein. Moreover, ultrastructural analysis of sperm revealed abnormalities in the head-tail coupling apparatus (HTCA) and mitochondrial sheath, as well as defects in the radial spokes and microtubules. Immunofluorescence analysis further confirmed the near absence of the HTCA marker SPATA6 in the patient's sperm. In addition, NME5 expression was assessed across spermatogenic stages in both humans and mice, with predominant expression from round to elongated spermatids. Notably, the patient harboring the NME5 variant achieved a favorable clinical outcome after intracytoplasmic sperm injection. Overall, our findings revealed for the first time that NME5 is a causative gene for human ASS, further expanding the gene mutational spectrum associated with human male infertility and ultimately offering potential new avenues for diagnostic and therapeutic strategies in clinical practice.
Muhammad A, Nosrati MSS, Dostmohammadi A
… +9 more, Khorasanian R, Severino M, Doustmohammadi M, Madia F, Srivastava S, Quinlan A, Paladini D, Zara F, Scala M
Deleterious variants in COL4A2, encoding type IV collagen's alpha-2 chain, cause heterogeneous cerebrovascular and developmental brain malformations. While many dominant variants are known, biallelic changes are rarely r...Deleterious variants in COL4A2, encoding type IV collagen's alpha-2 chain, cause heterogeneous cerebrovascular and developmental brain malformations. While many dominant variants are known, biallelic changes are rarely reported. We reported two severe cases: Case #1, an aborted fetus with cerebral calcifications, hemorrhages, periventricular leukomalacia, and cerebellar disruption; and Patient #2, a 2-year-old girl with neurodevelopmental impairment, cortical malformations (frontal schizencephaly, polymicrogyria), and reduced white matter volume. Exome sequencing identified a homozygous missense COL4A2 variant in case #1 and compound heterozygous loss-of-function variants (splicing and truncating) in case #2. All variants were rare and predicted to affect protein stability and function in silico. Our cases reinforce the association between biallelic COL4A2 variants and brain small vessel disease, expanding the recessive COL4A2-related phenotype to include cortical malformations.
Kilicarslan OA, Gangfuß A, Hentschel A
… +13 more, Kölbel H, Muhmann D, Töpf A, Stöhr M, Chen L, Horvath R, Thompson R, Schara-Schmidt U, Kurth I, Lochmüller H, Kraft F, Polavarapu K, Roos A
The cleavage and polyadenylation specific factor 1 (CPSF1) gene encodes a subunit of the cleavage and polyadenylation specificity factor (CPSF), a multi-protein complex essential for mRNA 3' end processing. The role of C...The cleavage and polyadenylation specific factor 1 (CPSF1) gene encodes a subunit of the cleavage and polyadenylation specificity factor (CPSF), a multi-protein complex essential for mRNA 3' end processing. The role of CPSF1 in retinal function and eye development has been demonstrated using zebrafish models and heterozygous variants in CPSF1 have been reported in early-onset high myopia (MIM: 618827). Here, we present a patient with bilateral congenital cataracts and intellectual disability with a novel homozygous missense variant (c.3817G>C; p.Asp1273His) in CPSF1. This amino acid change is predicted to change the protein structure with likely damaging effect. Proteomic results in white blood cells revealed increased CPSF1 protein abundance and dysregulated proteins in pathways linked to cellular signalling processes, protein degradation, and exosome biology. To our knowledge, this is the first report of recessive CPSF1-related disease in humans presenting as a case with congenital cataracts, intellectual disability, and hyperphagia.
Hereditary mucoepithelial dysplasia (HMD) is a rare autosomal dominant disorder characterized by non-scarring alopecia, skin and mucosal lesions, and keratitis. Autosomal dominant SREBF1-related Ichthyosis Follicularis,...Hereditary mucoepithelial dysplasia (HMD) is a rare autosomal dominant disorder characterized by non-scarring alopecia, skin and mucosal lesions, and keratitis. Autosomal dominant SREBF1-related Ichthyosis Follicularis, Atrichia, Photophobia (IFAP) syndrome is another rare, similar disorder. Both are now known to be caused by the same NM_004176.5(SREBF1):c.1579C>T variant, but were previously described as separate disorders. Here, we describe a case series of four novel patients that we diagnosed with SREBF1-related IFAP due to the NM_004176.5(SREBF1):c.1579C>T variant. We also performed a literature review and applied the ClinGen Lumping and Splitting criteria to these two disorders. Three of our four patients had significant gastrointestinal manifestations including gastroesophageal reflux disease and esophageal strictures/webs. To date, no gastrointestinal manifestations have been described in SREBF1-related IFAP. There are, however, multiple reports of these manifestations in cases of HMD. Applying the ClinGen Lumping and Splitting criteria demonstrated that these two previously distinct disorders are actually favored to be "lumped" into one. Taken together, a documented overlap in clinical features, the shared variant, and the gastrointestinal manifestations of our SREBF1-related IFAP patients provide evidence that HMD and SREBF1-related IFAP better represent variable expressivity of the same disorder. We propose using the unifying name of "SREBF1-syndromic epidermal differentiation disorder" (SREBF1-sEDD).
Protein truncation mutations in the gene for XPG nuclease cause a very severe clinical phenotype. Two siblings have splicing mutations, which result in in-frame deletions and a less severe phenotype.Protein truncation mutations in the gene for XPG nuclease cause a very severe clinical phenotype. Two siblings have splicing mutations, which result in in-frame deletions and a less severe phenotype.
Retinol dehydrogenases (RDHs) catalyze multiple steps in the visual cycle to regenerate 11-cis-retinal, a critical component in rod phototransduction. The structural homology between RDHs enables functional redundancy; y...Retinol dehydrogenases (RDHs) catalyze multiple steps in the visual cycle to regenerate 11-cis-retinal, a critical component in rod phototransduction. The structural homology between RDHs enables functional redundancy; yet Mendelian disorders are linked to RDHs. Variants in RDH12 and RDH5 cause non-syndromic inherited retinal dystrophy (IRD), whilst variants in RDH11 cause syndromic IRD. RDH11 is a minor isoenzyme catalyzing two reactions: (i) reduction of all-trans-retinal in rod photoreceptors alongside RDH12 and RDH8, and (ii) oxidation of 11-cis-retinol in the retinal pigment epithelium (RPE) alongside RDH5 and RDH10. Prior cases with RDH11 demonstrated a generalized photoreceptor dystrophy, similar to RDH12-retinopathy. We describe a visually asymptomatic 7-year-old boy carrying a homozygous null variant in RDH11 [NM_016026.4:c.216C>A:p.(Cys72*)] with autism, dysmorphic features, oligodontia, microcephaly and a novel IRD. This retinopathy consisted of yellow deposits and hyperpigmentation within the RPE with absent autofluorescence and a normal electroretinogram implying sub-optimal oxidation of 11-cis-retinol. These features are reminiscent of RDH5-retinopathy but milder. We termed this phenotype Retinal pigment Epitheliopathy due to Sub-Optimal Recycling of Vitamin A (RESORVA). We propose that the divergence in retinal phenotypes among RDH11 cases is likely due to variant-specific protein effects on paralogous gene functioning, such as differences in activation of transcriptional adaptation.
Geroderma osteodysplastica (GO) is a rare autosomal recessive connective tissue disorder. It presents with progeroid craniofacial features, lax skin, hypermobile joints, and osteoporosis. GO arises from pathogenic varian...Geroderma osteodysplastica (GO) is a rare autosomal recessive connective tissue disorder. It presents with progeroid craniofacial features, lax skin, hypermobile joints, and osteoporosis. GO arises from pathogenic variants in GORAB that disrupt Golgi apparatus function and extracellular matrix organization. This narrative review synthesizes the current evidence on its clinical presentation, differential diagnosis, molecular basis, and treatment. Management is largely supportive and interdisciplinary, involving orthopedic, dental, and physiotherapeutic care. Therapeutic intervention focuses on preventing bone density loss and decreasing fracture risk with bisphosphonates and vitamin D supplementation. Improved understanding of GO through larger cohort studies and care protocols is needed to improve patient outcomes and guide translational research.
We chronicle the diagnostic journey of a young patient suffering from severe arrhythmias and left ventricular hypertrophy, for which, after about 15 years of inconclusive genetic testing, a definitive diagnosis was made...We chronicle the diagnostic journey of a young patient suffering from severe arrhythmias and left ventricular hypertrophy, for which, after about 15 years of inconclusive genetic testing, a definitive diagnosis was made possible by finding an undescribed homozygous variant in POPDC2, a gene recently associated with CCDs and HCM.