The recurrent deep intronic pseudoexon-inducing variant COL6A1 c.930+189C>T results in a consistently severe phenotype of COL6-related dystrophy: Towards clinical trial readiness for splice-modulating therapy.

Collagen VI-related dystrophies (COL6-RDs) manifest with a spectrum of clinical phenotypes, ranging from Ullrich congenital muscular dystrophy (UCMD), presenting with prominent congenital symptoms and characterised by progressive muscle weakness, joint contractures and respiratory insufficiency, to Bethlem muscular dystrophy, with milder symptoms typically recognised later and at times resembling a limb girdle muscular dystrophy, and intermediate phenotypes falling between UCMD and Bethlem muscular dystrophy. Despite clinical and immunohistochemical features highly suggestive of COL6-RD, some patients had remained without an identified causative variant in COL6A1, COL6A2 or COL6A3. With combined muscle RNA-sequencing and whole-genome sequencing we uncovered a recurrent, de novo deep intronic variant in intron 11 of COL6A1 (c.930+189C>T) that leads to a dominantly acting in-frame pseudoexon insertion. We subsequently identified and have characterised an international cohort of forty-four patients with this COL6A1 intron 11 causative variant, one of the most common recurrent causative variants in the collagen VI genes. Patients manifest a consistently severe phenotype characterised by a paucity of early symptoms followed by an accelerated progression to a severe form of UCMD, except for one patient with somatic mosaicism for this COL6A1 intron 11 variant who manifests a milder phenotype consistent with Bethlem muscular dystrophy. Characterisation of this individual provides a robust validation for the development of our pseudoexon skipping therapy. We have previously shown that splice-modulating antisense oligomers applied in vitro effectively decreased the abundance of the mutant pseudoexon-containing COL6A1 transcripts to levels comparable to the in vivo scenario of the somatic mosaicism shown here, indicating that this therapeutic approach carries significant translational promise for ameliorating the severe form of UCMD caused by this common recurrent COL6A1 causative variant to a Bethlem muscular dystrophy phenotype.

Towards Uncovering the Role of Incomplete Penetrance in Maculopathies through Sequencing of 105 Disease-Associated Genes.

Inherited macular dystrophies (iMDs) are a group of genetic disorders, which affect the central region of the retina. To investigate the genetic basis of iMDs, we used single-molecule Molecular Inversion Probes to sequence 105 maculopathy-associated genes in 1352 patients diagnosed with iMDs. Within this cohort, 39.8% of patients were considered genetically explained by 460 different variants in 49 distinct genes of which 73 were novel variants, with some affecting splicing. The top five most frequent causative genes were ABCA4 (37.2%), PRPH2 (6.7%), CDHR1 (6.1%), PROM1 (4.3%) and RP1L1 (3.1%). Interestingly, variants with incomplete penetrance were revealed in almost one-third of patients considered solved (28.1%), and therefore, a proportion of patients may not be explained solely by the variants reported. This includes eight previously reported variants with incomplete penetrance in addition to CDHR1:c.783G>A and CNGB3:c.1208G>A. Notably, segregation analysis was not routinely performed for variant phasing-a limitation, which may also impact the overall diagnostic yield. The relatively high proportion of probands without any putative causal variant (60.2%) highlights the need to explore variants with incomplete penetrance, the potential modifiers of disease and the genetic overlap between iMDs and age-related macular degeneration. Our results provide valuable insights into the genetic landscape of iMDs and warrant future exploration to determine the involvement of other maculopathy genes.

The First Registered Type 0 Spinal Muscular Atrophy Patient in Latvia: Call for Change in Prenatal Diagnostic Procedures.

This case report presents the first registered patient in Latvia with type 0 spinal muscular atrophy (SMA). During the first-trimester ultrasonography of the unborn patient, an increased thickness of the nuchal fold was detected. The mother reported decreased foetal movements during the pregnancy. After the boy was born, his general condition was extremely severe. The clinical signs indicated a suspected neuromuscular disorder. A precise diagnosis, type 0 SMA, was determined 7 days after birth through a newborn pilot-screening for SMA, which was conducted for all newborns whose parents consented to participate. The condition of the infant deteriorated. He had severe respiratory distress followed by multiple events leading to his death. Currently, there are only a few published case reports detailing an increased nuchal translucency (NT) measurement in association with a diagnosis of SMA in the foetus. However, an increased NT measurement is a clinically relevant sign as it can be related to genetic syndromes, foetal malformations, disruptions, and dysplasias. Since there is no cure for infants with type 0 SMA at present, it is crucial to be able to detect this disease prenatally in order to provide the best possible care for the patient and parents. This includes the provision of palliative care for the patient, among other measures. This case report highlights the prenatal signs and symptoms in relation to type 0 SMA.

Mother and Daughter with Short Stature, Microcephaly, Mild Dysmorphic Features, and Learning Disabilities Due to Ververi-Brady Syndrome Associated with a New Variant of the QRICH1 Gene.

BACKGROUND Ververi-Brady syndrome (VEBRAS) is an autosomal dominant condition associated with short stature, microcephaly, mild dysmorphic features, and learning disabilities. It was first described in 2018, and only 38 cases have been reported since then. All patients have mutation in the Glutamine-rich protein 1 (QRICH1) gene, yet clinical presentation has a broad spectrum and continues to expand. This report is of a mother and daughter pair with VEBRAS, associated with a new variant of the QRICH1 gene, NM_017730.3: c.337C>T; p.(Gln113*), and few previously undescribed phenotypic features. CASE REPORT We present 2 new cases, a mother and daughter, with novel heterozygous nonsense variant NM_017730.3: c.337C>T; p.(Gln113*). The daughter was referred to a geneticist at the age of 17 years because of seizures, dysmorphic features, and magnetic resonance imaging suggestive of leukodystrophy. In addition to already described clinical features, she had diffuse infantile hemangiomatosis and occipital balding. She was accompanied by her mother, who shared similar phenotypic features, raising suspicion for a similar genetic condition. Unlike the daughter, the mother never had any significant health problems or concerns and described herself as perfectly healthy. Genetic testing was performed in both individuals, and a novel pathogenic QRICH1 variant was discovered. CONCLUSIONS Considering the novelty of VEBRAS, every new clinical case contributes to the enlargement of the VEBRAS cohort, expanding the phenotypical and mutational spectrum, with potential improvement in the further care and observation of probands and their offspring. This report has highlighted the importance of clinical genetics in the identification of familial genetic disorders with complex phenotypes.

Clinical and genetic characterization of Netherton syndrome due to SPINK5 founder variant in Latvian population.

OBJECTIVE: Netherton syndrome (NS) (OMIM:256500) is a very rare autosomal recessive multisystem disorder mostly affecting ectodermal derivatives (skin and hair) and immune system. It is caused by biallelic loss-of-function variants in the SPINK5 gene, encoding the protease inhibitor lymphoepithelial Kazal-type-related inhibitor (LEKTI). MATERIAL, METHODS AND RESULTS: Here, we describe NS clinical and genetic features of homogenous patient group: 9 individuals from 7 families with similar ethnic background and who have the same SPINK5 variant (NM_006846.4: c.1048C > T, p.(Arg350*)) in homozygous or compound heterozygous states, suggesting that it is a common founder variant in Latvian population. Indeed, we were able to show that the variant is common in general Latvian population, and it shares the same haplotype among the NS individual. It is estimated that the variant arose >1000 years ago. Clinically, all nine patients exhibited typical NS skin changes (scaly erythroderma, ichthyosis linearis circumflexa, itchy skin), except for one patient who has a different skin manifestation-epidermodysplasia. Additionally, we show that developmental delay, previously underrecognized in NS, is a common feature among these patients. CONCLUSIONS: This study shows that the phenotype of NS individuals with the same genotype is highly homogeneous.

Overview of Neuromuscular Disorder Molecular Diagnostic Experience for the Population of Latvia.

Background and Objectives: Genetic testing has become an integral part of health care, allowing the confirmation of thousands of hereditary diseases, including neuromuscular disorders (NMDs). The reported average prevalence of individual inherited NMDs is 3.7-4.99 per 10,000. This number varies greatly in the selected populations after applying population-wide studies. The aim of this study was to evaluate the effect of genetic analysis as the first-tier test in patients with NMD and to calculate the disease prevalence and allelic frequencies for reoccurring genetic variants. Methods: Patients with NMD from Latvia with molecular tests confirming their diagnosis in 2008-2020 were included in this retrospective study. Results: Diagnosis was confirmed in 153 unique cases of all persons tested. Next-generation sequencing resulted in a detection rate of 37%. Two of the most common childhood-onset NMDs in our population were spinal muscular atrophy and dystrophinopathies, with a birth prevalence of 1.01 per 10,000 newborns and 2.08 per 10,000 (male newborn population), respectively. The calculated point prevalence was 0.079 per 10,000 for facioscapulohumeral muscular dystrophy type 1, 0.078 per 10,000 for limb-girdle muscular dystrophy, 0.073 per 10,000 for nondystrophic congenital myotonia, 0.052 per 10,000 for spinobulbar muscular atrophy, and 0.047 per 10,000 for type 1 myotonic dystrophy. Discussion: DNA diagnostics is a successful approach. The carrier frequencies of the common CAPN3, FKRP, SPG11, and HINT1 gene variants as well as that of the SMN1 gene exon 7 deletion in the population of Latvia are comparable with data from Europe. The carrier frequency of the CLCN1 gene variant c.2680C>T p.(Arg894Ter) is 2.11%, and consequently, congenital myotonia is the most frequent NMD in our population.

Clinical and Genetic Characterisation of Cystic Fibrosis Patients in Latvia: A Twenty-Five-Year Experience.

Cystic fibrosis (CF) is the most common life-limiting genetic disorder in European descent populations. It is caused by pathogenic variants in the CFTR gene, and inheritance is autosomal recessive. This study provides an up-to-date, comprehensive estimation of the distribution of CFTR pathogenic variants in Latvia and their phenotypic characteristics. It also reports the first results of the CF newborn screening programme following its implementation in 2019. We analysed the clinical and molecular data of CF patients treated at the only tertiary hospital in Latvia providing specialised healthcare for the disorder. Between 1997 and 2022, 66 CF patients from 62 families were diagnosed based on symptoms or a molecular confirmation (six patients were diagnosed through the CF newborn screening programme). F508del was identified in 70.5% of all CF chromosomes. Known variants were identified in more than one family: dele2,3, R1006H, L1335P, W57R, R553X, 2143delT and 3849+10kb C>T (legacy names used). Furthermore, two novel variants were identified, namely, c.503C>A p.(Ser168Ter) and c.(743+1_744-1)_(1584+1_1585-1)del p.(?). The available follow-up results indicated that Latvian CF patients demonstrated similar tendencies to CF patients worldwide. The oldest age at diagnosis prior to the implementation of the CF newborn screening programme was 14 years. We provide here, for the first time, a comprehensive description of Latvian CF patients. An improvement in the healthcare of CF patients over time, including access to diagnosis, is evident. Two novel CF-causing variants are reported, and F508del is the most frequently occurring variant in the population, thus suggesting that F508del screening should be followed by the testing of the full CFTR gene.

Two Cases of Leigh Syndrome in One Family: Diagnostic Challenges and Clinical Management Experience in Latvia.

Leigh syndrome is a neurodegenerative disorder with an incidence of 1 : 40,000 live births. The clinical presentation of LS is highly variable with heterogeneity in the disease-associated symptoms of cerebellar, motor, and extrapyramidal dysfunction and common infections. There is no effective treatment for this condition; as such, the prognosis of this condition is very poor with death occurring within the first few years of life. In this study, we report the first LS case in Latvia with SURF1 pathogenic variants in two siblings. The difficulties encountered establishing a diagnosis for the first proband and the effective prenatal diagnosis for the second offspring that led to termination of the pregnancy are discussed.

GJB1 Gene Analysis in Two Extended Families with X-Linked Charcot-Marie-Tooth Disease.

X-linked Charcot-Marie-Tooth (CMT) disease type I (CMTX1) is the second most frequent type of CMT disease caused by pathogenic variants in the GJB1 gene. We described 2 extended cases (families) with CMTX1 with identified pathogenic variants - p.Val139Met and p.Arg215Trp. In both the families, neurological symptoms started earlier in male than in female patients. In some family members, molecular diagnostics was performed prior to neurological investigation due to family cascade screening. There was variable neurological phenotype representing CMT. Conclusions: There is a large clinical heterogeneity in CMTX, even amongst the family members.

The need for widely available genomic testing in rare eye diseases: an ERN-EYE position statement.

BACKGROUND: Rare Eye Diseases (RED) are the leading cause of visual impairment and blindness for children and young adults in Europe. This heterogeneous group of conditions includes over 900 disorders ranging from relatively prevalent disorders such as retinitis pigmentosa to very rare entities such as developmental eye anomalies. A significant number of patients with RED have an underlying genetic etiology. One of the aims of the European Reference Network for Rare Eye Diseases (ERN-EYE) is to facilitate improvement in diagnosis of RED in European member states. MAIN BODY: Technological advances have allowed genetic and genomic testing for RED. The outcome of genetic testing allows better understanding of the condition and allows reproductive and therapeutic options. The increase of the number of clinical trials for RED has provided urgency for genetic testing in RED. A survey of countries participating in ERN-EYE demonstrated that the majority are able to access some forms of genomic testing. However, there is significant variability, particularly regarding testing as part of clinical service. Some countries have a well-delineated rare disease pathway and have a national plan for rare diseases combined or not with a national plan for genomics in medicine. In other countries, there is a well-established organization of genetic centres that offer reimbursed genomic testing of RED and other rare diseases. Clinicians often rely upon research-funded laboratories or private companies. Notably, some member states rely on cross-border testing by way of an academic research project. Consequently, many clinicians are either unable to access testing or are confronted with long turnaround times. Overall, while the cost of sequencing has dropped, the cumulative cost of a genomic testing service for populations remains considerable. Importantly, the majority of countries reported healthcare budgets that limit testing. SHORT CONCLUSION: Despite technological advances, critical gaps in genomic testing remain in Europe, especially in smaller countries where no formal genomic testing pathways exist. Even within larger countries, the existing arrangements are insufficient to meet the demand and to ensure access. ERN-EYE promotes access to genetic testing in RED and emphasizes the clinical need and relevance of genetic testing in RED.

Clinical Phenotyping and Biomarkers in Spinal and Bulbar Muscular Atrophy.

Background: Spinal and bulbar muscular atrophy (SBMA) or Kennedy disease [OMIM: 313200] is a rare X-linked neuromuscular disease. Patients commonly present with muscle cramps, tremors, leg weakness, dysarthria and dysphagia. Methods: We deeply phenotyped and evaluated the possible extent of affected systems in all patients with SBMA in Latvia (n = 5). In addition, neurophysiological studies and blood analyses were used to perform a molecular diagnosis and evaluate biochemical values. We analyzed neurofilament light (NfL) as a possible biomarker. Results: Neurological examination revealed typical SBMA clinical manifestations; all patients had small or large nerve fiber neuropathy. Three of five patients had increased neurofilament light levels. Conclusion: The study confirms the systemic involvement in patients suffering from SBMA. Increased NfL concentration was associated with either peripheral neuropathy or decreased body mass index. The complex phenotype of the disease should be kept in mind, as it could help to diagnose patients with SBMA.

A Giant Arteriovenous Malformation and Fistula in a Newborn with Parkes Weber Syndrome. Case Report.

Parkes Weber syndrome (PWS) is a rare congenital condition characterized by capillary cutaneous malformation, limb hypertrophy and multiple arteriovenous fistulas of the affected extremity. Another feature is a port-wine stain on the affected area. PWS is caused by genetic variations in the RAS p21 protein activator (RASA1) gene which affects the development of the vascular system. We report a case of a female neonate presenting with dyspnoea and cardiovascular insufficiency at the time of birth. The left upper extremity (LUE) and shoulder were enlarged (circumference at the midpoint was 17 cm compared to 11 cm on the right arm), edematous, hyperemic with a port-wine stain. Structural changes of the bones of LUE were discovered on X-ray. Echocardiography revealed right-sided volume overload, a large ductus arteriosus, a possible pathology of the aortic arch and branch arteries. Chest X-rays showed cardiomegaly. Therapy with milrinone and diuretics was started. A multislice CT angiography scan revealed arteriovenous fistula (AVF) between a. subclavia sin. and v. bra-chiocephalica sin, arteriovenous malformations (AVM) and a dilated a.subclavia sin. of 11 mm, as well as dilatation of other arteries of the LUE. Next generation sequencing revealed a pathogenic variation (c.2245C>T, p.Arg749*) in the RASA1 gene in the heterozygous state. Four consecutive embolizations of the AVM and AVF were performed in the first 16 months.