Identification of novel pathogenic variants in the PHYH gene and extending the phenotypic range in Refsum disease

Using Molecular Diagnostics for Inherited Retinal Dystrophies: The 6 "I"s That Are Necessary to Diagnose 2 Eyes Genetically.

Utility of genetic work-up for 46, XY patients with severe hypospadias

Response to: Letter to editor—Utility of genetic work-up for 46, XY patients with severe hypospadias

This study aims to assess clinical and genetic characteristics as well as the prevalence of inherited retinal dystrophies (IRD) and their subphenotypes in the Finnish founder population. A retrospective analysis of clinical and genetic data from Northern Finnish patients diagnosed with IRD between 1996 and 2023 at Oulu University Hospital, Finland, was conducted. The cohort comprised 582 patients with IRD, categorised into 16 different subphenotypes. Pathogenic or likely pathogenic variants explaining IRD were identified in 36% (n=210/582) of all patients and 80% (n=210/261) of genetically tested patients with IRD. Diagnostic yields varied between different IRD subphenotypes. The genetic aetiology was most commonly confirmed in X-linked retinoschisis, severe early childhood-onset retinal dystrophy, congenital stationary night blindness and choroideremia. The lowest rates of causative variant identification were observed in cone or cone-rod dystrophy and macular dystrophy. In total, 70 pathogenic or likely pathogenic variants were identified across 39 different genes; variants in the FZD4 and RPGR genes were the most prevalent. Over half of the variants were enriched in the Finnish population. The estimated total prevalence of IRDs in Northern Finland was 69.8/100 000 (1:1432). The prevalence of the most common subphenotypes was as follows: retinitis pigmentosa, 25.3/100 000; X-linked retinoschisis, 10.7/100 000; Usher syndrome, 8.9/100 000; choroideremia, 7/100 000 and cone or cone-rod dystrophy, 6/100 000. The Northern Finnish population exhibits an enrichment of population-specific IRD-associated variants, resulting in a high overall prevalence of IRDs and an increased prevalence of selected retinal subphenotypes, such as retinoschisis, choroideremia and Usher syndrome types 3 and 1.

Adult Refsum disease (ARD) is a progressive multisystem disorder that is characterized by retinitis pigmentosa, hearing and smell loss, skeletal deformities, and elevated levels of phytanic acid (PA) in tissues. Peripheral neuropathy, cardiac abnormalities, and skin ichthyosis are considered subsequent manifestations, and are often described in patients not treated with PA dietary restriction. Mutations of the gene encoding the phytanoyl-coenzyme A (CoA) hydroxylase enzyme (PHYH) are the major genetic cause of ARD,1 and in a small number of cases a second gene, PEX7, which encodes peroxin 7 receptor protein (PEX7), has been associated with the ARD phenotype.2 We observed two Italian siblings who presented with late-onset progressive ataxia and cognitive decline. They comprised a 56-year-old woman and her 63-year-old brother, born from consanguineous parents, and presented with infantile bilateral cataract and retinitis pigmentosa. Except for the visual defect, both siblings exhibited normal psychomotor development. In adulthood (at age 40 years for the brother and 53 years for the sister), both patients manifested progressive behavioral and cognitive abnormalities associated with ataxic gait. At the latest examination, at ages 57 and 63 years, respectively, they presented with dementia (Mini-Mental State Examination scores of 19/30 and 13/30, respectively), motor apraxia, ophthalmoparesis, mild dysarthria, ataxic gait, mild limb dysmetria, Babinski sign, and decreased lower-limb deep-tendon reflexes. Neither of the patients had hearing loss, anosmia, or short metacarpals/metatarsals, and only the brother presented with dilated cardiomyopathy. Brain MRI revealed mild diffuse atrophy, and muscle biopsy sampling revealed normal morphology. Nerve conduction studies demonstrated a mild motor demyelinating neuropathy in the lower limbs, and somatosensory evoked potentials revealed a prolongation of the central conduction time. Both patients also presented with increased plasma PA levels (387.5 and 188.9 µmol/L), suggesting a diagnosis of ARD. Mutational screening of PHYH was negative, but there was a novel homozygous mutation in PEX7, p.Leu12Pro, caused by a T>C transition at nucleotide 35 (c.35T>C). This missense variation involved a well-conserved residue, and has not been reported as a single-nucleotide polymorphism (SNP) in the Human Gene Mutation Database, National Center for Biotechnology Information database for SNPs (dbSNP132ver) or Exome Variant Server. In silico analyses predicted the mutation as probably damaging: the scores were 0.98 (PolyPhen-2-HumDiv), 0.635 (PolyPhen-2-HumVar), and 0 (Sorting Tolerant From Intolerant). The parents were not available for segregation analysis, and an asymptomatic brother was found to be heterozygous for this mutation. The patients refused a skin biopsy procedure, preventing investigations of plasmalogen synthesis.3 PEX7 mutations are most frequently found in infants affected by rhizomelic chondrodysplasia punctata type 1 (RCDP1), a congenital and rapidly worsening syndrome that is characterized by rhizomelia, chondrodysplasia punctata, cataract, and severe growth and mental retardation.3 The protein encoded by PEX7, Pex7, is essential for peroxisomal delivery of matrix enzymes containing the peroxisomal targeting signal type 2 in the amino acid sequence, including the phytanoyl-CoA hydroxylase and the plasmalogen synthesis apparatus.4 In both RCDP1 and ARD, patients present with elevated PA levels due to either a defect in the peroxisomal import of the metabolic enzymes or a primary loss-of-function of the phytanoyl-CoA hydroxylase enzyme.4 Several PEX7 mutations have so far been described in association with the RCDP1 phenotype. Only eight patients with PEX7 mutations and the Refsum phenotype have been reported, and in all of these cases the presentation was consistent with the ARD phenotype with a mild disease course (Table 1).2,3,5 In the previously reported cases, the most frequent disease manifestations were retinopathy, cataract, anosmia, hearing loss, and neuropathy (Table 1). In the cases described herein, the ocular abnormalities were also the earliest signs, but neither anosmia nor deafness was observed, while in the fifth decade both siblings developed progressive signs of dementia and ataxia. It is known that the clinical severity of this disease is associated with the residual activities and reduced amounts of Pex7.3 In particular, functional and modeling analyses have demonstrated that missense mutations associated with a severe phenotype are located in within the β sheets, probably causing a disruption of the protein structure.3 The p.Leu12Pro mutation, unlike previous missense mutations, is not located on the WD-40 repeat motif in PEX7, and it can be hypothesized that a less adverse effect on protein structure-allowing correct folding and greater residual activity-can account for the mild phenotype in these two patients. Table 1 Clinical, biochemical, and genetic characteristics of the patients with PEX7 gene mutations associated with Refsum disease phenotype, including the cases described in this study and review of the literature

Bardet-Biedl syndrome is a rare condition characterized by obesity, retinitis pigmentosa, polydactyly, development delay, and structural kidney anomalies. This syndrome has an autosomal recessive type of inheritance. For the first time, molecular genetic testing has been provided for a large cohort of Russian patients with Bardet-Biedl syndrome. Genetic testing was provided to 61 unrelated patients using an MPS panel that includes coding regions and intronic areas of all genes (n = 21) currently associated with Bardet-Biedl syndrome. The diagnosis was confirmed for 41% of the patients (n = 25). Disease-causing variants were observed in BBS1, BBS4, BBS7, TTC8, BBS9, BBS10, BBS12, and MKKS genes. In most cases, pathogenic and likely pathogenic variants were localized in BBS1, BBS10, and BBS7 genes; recurrent variants were also observed in these genes. The frequency of pathogenic and likely pathogenic variants in the BBS1 and BBS10 genes among Russian patients matches the research data in other countries. The frequency of pathogenic variants in the BBS7 gene is about 1.5%-2% of patients with Bardet-Biedl syndrome, while in the cohort of Russian patients, the fraction is 24%. In addition, the recurrent pathogenic variant c.1967_1968delinsC was detected in the BBS7 gene. The higher frequency of this variant in the Russian population, as well as the lack of association of this pathogenic variant with Bardet-Biedl syndrome in other populations, suggests that the variant c.1967_1968delinsC in the BBS7 gene is major and has a founder effect in the Russian population. Results provided in this article show the significant role of pathogenic variants in the BBS7 gene for patients with Bardet-Biedl syndrome in the Russian population.

We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype–phenotype correlations. A subset of 26 families from a cohort of 73 families with clinical diagnosis of autosomal recessive IRD (AR-IRD) excluding Usher syndrome was analyzed by whole exome sequencing and autozygosity mapping. Causative pathogenic variants were identified in 50 families (68.4%), 42% of which were novel.The most prevalent pathogenic variants were observed in ABCA4 (14%) and RPE65, CRB1 and CERKL (8% each). 26 variants (8 novel and 18 known) in 19 genes were identified in 26 families (14 missense substitutions, 5 deletions, 4 nonsense pathogenic variants and 3 splice site variants), with further allelic heterogeneity arising from different pathogenic variants in the same gene. The most common phenotype in our cohort is retinitis pigmentosa (23%) and cone rod dystrophy (23%) followed by Leber congenital amaurosis (19.2%). We report the association of new disease phenotypes. This research was carried out in Tunisian patients with IRD in order to delineate the genetic population architecture.

Inherited retinal dystrophies (IRD) include a wide range of genetically and phenotypically heterogeneous diseases that lead to progressive loss of vision. With the development of gene therapy, it has become possible to treat two forms of IRD caused by biallelic mutations in the RPE65 gene: isolated retinitis pigmentosa (IRP) type 20 and Leber's congenital amaurosis (LCA) type 2. These nosologies are included in the list of orphan diseases of the Russian Ministry of Health. The success factor for the use of IRD gene therapy is the early stage of the disease, when the viability of retinal cells is preserved. An interdisciplinary approach to diagnostics makes it possible to timely establish the clinical and genetic variant of IRD and refer the patient to targeted therapy. Therefore, at a joint meeting of the Council of Experts of the North-Western Federal District of the Russian Federation, which included ophthalmologists and medical geneticists, a scheme for managing patients with IRD was accepted, including the stages of clinical and functional ophthalmological examination and molecular genetic testing. In addition, regional centers of expertise for IRD were approved in two federal medical institutions in St. Petersburg, whose task is to optimize the quality of diagnosing patients with IRP and LCA.

Inherited Retinal Dystrophies (IRD) are rare and heterogeneous blindness-causing diseases caused by pathogenic variants in genes involved in retina function. Thus, the diagnosis in patients with IRD is complicated and late, and it can also be confused with other diseases. For this reason, exome sequencing is a tool for accurate diagnosis. In this work, the exome of 17 Mexican patients clinically evaluated with IRD at the Conde de Valenciana Institute was analyzed. The exome sequencing analyses indicated that 88% (15/17) of the patients suffer from IRD: seven have conerod disorders, two suffer Usher syndrome, three suffer retinitis pigmentosa, two suffer Stargardt disease, and one suffer corneal dystrophy. Within the cohort, there are cases with complex alleles, and one case with a homogeneous variant, previously reported as heterogeneous, including a case whose variant causes lipofuscinosis but with an impact on IRD. Therefore, exome sequencing is an effective great tool for diagnosing rare diseases.

Inherited retinal dystrophies (IRD) are a group of predominantly monogenic disorders which have genetically heterogeneous origins and display wide clinical phenotypic heterogeneity. The current study describes the clinical diagnoses, demographics and genetic aetiology of a cohort of Welsh patients to provide insight into the rates of genetic diagnosis of IRD. This will help inform patient prognosis and counselling in future clinical encounters. A comprehensive database of patients attending the tertiary referral clinic from January 2011 to December 2023 was compiled contemporaneously. Demographic data were collated from patients' clinical records. Subjects underwent genetic screening, including targeted gene sequencing, next-generation sequencing-based gene panel or whole exome sequencing, to investigate the causative pathogenic variants. A total of 403 probands (207 men and 196 women) were ascertained. The mean age at which the patients developed visual symptoms related to IRD was 43±18.1 years (range, 1-86 years). Retinitis pigmentosa (187; 46.4%), macular dystrophy (115; 28.5%) and cone rod dystrophy (41; 10.2%) were the most common clinical diagnoses. Among all the subjects, genetic pathogenic variants were identified in 166 (41%) patients. Pathogenic variants were identified in 49 retinal genes, with the most commonly affected genes being ABCA4, USH2A and GUCY2D. The establishment of a molecular genetic diagnosis in this group of patients serves as a basis for genetic counselling and will allow patients to enrol in current and future gene-based clinical trials and benefit from any future novel therapeutic interventions and treatments.

The presence of phytanic acid in tissues and plasma has been considered diagnostic of heredopathia atactica polyneuritiformis (Refsum's disease), but recently slightly raised plasma phytanic acid levels have been reported in other conditions. Forty two normal people were found to have a phytanic acid level of 0-33 mumol/l. Fourteen patients with heredopathia atactica polyneuritiformis had a plasma phytanic acid level before treatment of 992-6400 mumol/l. Five patients with retinitis pigmentosa but not heredopathia atactica polyneuritiformis had plasma levels of 38-192 mumol/l. It was concluded that some patients with retinitis pigmentosa without heredopathia atactica polyneuritiformis but a raised plasma phytanic acid may represent a group of patients with a disease or diseases as yet uncharacterised apart from the retinal condition.

Mutations in the Gene Encoding Peroxisomal Sterol Carrier Protein X (SCPx) Cause Leukencephalopathy with Dystonia and Motor Neuropathy

Retinal dystrophies: A look beyond the eyes

ABSTRACTPurpose: Inherited retinal dystrophies (IRDs) and inherited optic neuropathies (IONs) are rare diseases defined by specific clinical and molecular features. The relative prevalence of these conditions was determined in Southern France.Methods: Patients recruited from a specialized outpatient clinic over a 21-year period underwent extensive clinical investigations and 107 genes were screened by polymerase chain reaction/sequencing.Results: There were 1957 IRD cases (1481 families) distributed in 70% of pigmentary retinopathy cases (56% non-syndromic, 14% syndromic), 20% maculopathies and 7% stationary conditions. Patients with retinitis pigmentosa were the most frequent (47%) followed by Usher syndrome (10.8%). Among non-syndromic pigmentary retinopathy patients, 84% had rod-cone dystrophy, 8% cone-rod dystrophy and 5% Leber congenital amaurosis. Macular dystrophies were encountered in 398 cases (30% had Stargardt disease and 11% had Best disease). There were 184 ION cases (127 families) distributed in 51% with dominant optic neuropathies, 33% with recessive/sporadic forms and 16% with Leber hereditary optic neuropathy. Positive molecular results were obtained in 417/609 families with IRDs (68.5%) and in 27/58 with IONs (46.5%). The sequencing of 5 genes (ABCA4, USH2A, MYO7A, RPGR and PRPH2) provided a positive molecular result in 48% of 417 families with IRDs. Except for autosomal retinitis pigmentosa, in which less than half the families had positive molecular results, about 75% of families with other forms of retinal conditions had a positive molecular diagnosis.Conclusions: Although gene discovery considerably improved molecular diagnosis in many subgroups of IRDs and IONs, retinitis pigmentosa, accounting for almost half of IRDs, remains only partly molecularly defined.

PurposeCyclic nucleotide-gated (CNG) channels are ligand-gated ion channels that transduce light signals into electrical signals in the retinal photoreceptors. Pathogenic variants in CNG channel genes are reported to cause inherited retinal dystrophies (IRDs). The current study used targeted panel sequencing to describe the mutational spectrum of CNG channel genes in familial cases of IRDs from eight consanguineous Pakistani families.MethodsThe current study included consanguineous Pakistani families with at least two affected members. DNA was extracted from whole blood samples by the phenol-chloroform method. Two affected members from each family were initially analyzed using targeted panel sequencing of 344 known IRD genes. The pathogenicity of candidate variants was assessed using the American College of Medical Genetics and Genomics guidelines. Segregation testing was performed by Sanger sequencing.ResultsResults of eight IRD families revealed a total of four reported variants in CNGA3 (c.827A>G, c.955T>C, c.1641C>A, c.1810C>T) and three novel variants, including c.1633A>T, c.800G>T, and c.1153T>C in CNGA1, CNGA3, and CNGB3 genes, respectively, segregating in each respective family. Among disease-causing variants identified in our study cohort, 87.5% were missense. Furthermore, one of the reported missense variants (i.e., c.1641C>A in CNGA3) was segregating in two unrelated families. All identified variants were homozygous and segregated in an autosomal recessive form.ConclusionsCNGA3 was the most frequently mutated gene in our study cohort. Only the c.1641C>A variant of CNGA3 was repeated in two families, showing genetic diversity. The identification of three novel pathogenic variants in CNG channel genes in the present study reaffirms the allelic and genetic heterogeneity of IRDs in the Pakistani population.