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Background An accurate genetic diagnosis of Becker muscular dystrophy (BMD) can be sometimes challenging due to deep intronic DMD variants. Here, we report on the genetic diagnosis of a BMD patient with a novel deep‐intronic splice‐altering variant in DMD. Methods The index case was a 3.8‐year‐old boy who was suspected of having a diagnosis of BMD based on his clinical, muscle imaging, and pathological features. Routine genomic detection approaches did not detect any disease‐causing variants in him. Muscle‐derived DMD mRNA studies, followed by genomic Sanger sequencing and in silico bioinformatic analyses, were performed in the patient. Results DMD mRNA studies detected a cryptic exon‐containing transcript and normally spliced DMD transcript in the patient. The cryptic exon‐containing transcript encoded a frameshift and premature termination codon (NP_003997.1:p.[=,Asp2740Valfs*52]). Further genomic Sanger sequencing and bioinformatic analysis identified a novel deep‐intronic splice‐altering variant in DMD (c.8217 + 23338A > G). The novel variant strengthened a cryptic donor splice site and activated a cryptic acceptor splice site in the deep‐intronic region of DMD intron 55, resulting in the activation of a new dystrophin cryptic exon found in the patient. Conclusion Our case report expands the genetic spectrum of BMD and highlights the essential role of deep‐intronic cryptic exon‐activating variants in genetically unsolved BMD patients. Our study successfully identified a novel deep‐intronic splice‐altering variant in DMD via the combined application of dystrophin mRNA analysis, genomic Sanger sequencing, and in silico bioinformatic analyses. The novel deep‐intronic variant (c.8217 + 23338A > G) resulted in the activation of a new dystrophin cryptic exon, which confirmed the genetic diagnosis of dystrophinopathy in our patient.

Background Usher syndrome is a condition characterized by partial or total hearing loss and progressive pigmentary retinopathy. Usher syndrome type 1F is caused by biallelic loss‐of‐function variants in Protocadherin 15 (PCDH15), which encodes the PCDH15 protein that plays an important role in the morphogenesis and cohesion of stereocilium bundles and retinal photoreceptor cell maintenance and function. Methods We report a child with bilateral nonsyndromic sensorineural hearing loss who received an inconclusive diagnosis based on clinical gene panel testing, which identified a paternal heterozygous nonsense variant (NM_033056.4: c.733C>T, p.R245*) in PCDH15. This variant has been described as a founder variant in the Ashkenazi Jewish population. Results A novel deep‐intronic variant (NM_033056.4: c.705+3767_705+3768del) inherited from the patient's mother was identified by trio‐based whole‐genome sequencing (WGS). A minigene splicing assay revealed that c.705+3767_705+3768del results in aberrant retention of 50 or 68 bp of intron 7. Conclusion Our genetic test results provided precise genetic counseling and prenatal diagnosis for this family, and our findings highlight the power of WGS for detecting deep‐intronic variants in patients with undiagnosed rare diseases. Additionally, this case expands the variant spectrum of the PCDH15 gene and our results support the extremely low carrier frequency of c.733C>T in the Chinese population. We reported a child with profound bilateral non‐syndromic sensorineural hearing and compound heterozygosity for a common nonsense and novel deep intronic variant that was identified by WGS. The results of genetic testing provided precise genetic counseling and prenatal diagnosis for this family and was contributed to diagnose other USH1F patients in the future. Our findings highlight the power of WGS for detecting deep‐intronic variants in patients with undiagnosed rare diseases. Additionally, this case expands the variant spectrum of the PCDH15 gene, and our results support the extremely low carrier frequency of c.733C>T in the Chinese population.

Purpose Using exome sequencing, the underlying variants in many persons with autosomal recessive diseases remain undetected. We explored autosomal recessive Stargardt disease (STGD1) as a model to identify the missing heritability. Methods Sequencing of ABCA4 was performed in 8 STGD1 cases with one variant and p.Asn1868Ile in trans , 25 cases with one variant, and 3 cases with no ABCA4 variant. The effect of intronic variants was analyzed using in vitro splice assays in HEK293T cells and patient-derived fibroblasts. Antisense oligonucleotides were used to correct splice defects. Results In 24 of the probands (67%), one known and five novel deep-intronic variants were found. The five novel variants resulted in messenger RNA pseudoexon inclusions, due to strengthening of cryptic splice sites or by disrupting a splicing silencer motif. Variant c.769-784C>T showed partial insertion of a pseudoexon and was found in cis with c.5603A>T (p.Asn1868Ile), so its causal role could not be fully established. Variant c.4253+43G>A resulted in partial skipping of exon 28. Remarkably, antisense oligonucleotides targeting the aberrant splice processes resulted in (partial) correction of all splicing defects. Conclusion Our data demonstrate the importance of assessing noncoding variants in genetic diseases, and show the great potential of splice modulation therapy for deep-intronic variants.

Purpose Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4 -associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. Methods Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. Results In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Conclusion Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.

Background The c.1199 + 502 A > T variant of the phenylalanine hydroxylase ( PAH ) gene, which is the most frequently reported deep intronic variant involved in phenylketonuria (PKU), is mainly observed in patients with classical or mild PKU. Prior to this study, no mouse models of PKU featuring deep intronic variants of PAH had been reported. Methods To phenotypically simulate the pathogenicity of this variant, we used CRISPR/Cas9 genome editing technology and homologous recombination to generate homozygous PKU model mice with a partially humanized Pah gene incorporating human PAH exons 11–12 carrying c.1199 + 502 A > T or wild-type (c.1199 + 502WT) control sequences. Results Humanized homozygous Pah c.1199 + 502 A > T mice exhibited a classical PKU phenotype, including a higher serum phenylalanine concentration, yellowing of the fur, and other traits. The homozygous mutant group had poorer spatial learning and spatial memory compared with the wild-type group. Conclusion This construction of the first humanized mice carrying a deep intronic variant of PAH provides a new animal model for the pathogenesis and treatment of PKU, and may serve as a reference for future research on the pathogenicity of deep intronic variation.

Biallelic gene defects in MFSD8 are not only a cause of the late-infantile form of neuronal ceroid lipofuscinosis, but also of rare isolated retinal degeneration. We report clinical and genetic data of seven patients compound heterozygous or homozygous for variants in MFSD8, issued from a French cohort with inherited retinal degeneration, and two additional patients retrieved from a Swiss cohort. Next-generation sequencing of large panels combined with whole-genome sequencing allowed for the identification of twelve variants from which seven were novel. Among them were one deep intronic variant c.998+1669A>G, one large deletion encompassing exon 9 and 10, and a silent change c.750A>G. Transcript analysis performed on patients’ lymphoblastoid cell lines revealed the creation of a donor splice site by c.998+1669A>G, resulting in a 140 bp pseudoexon insertion in intron 10. Variant c.750A>G produced exon 8 skipping. In silico and in cellulo studies of these variants allowed us to assign the pathogenic effect, and showed that the combination of at least one severe variant with a moderate one leads to isolated retinal dystrophy, whereas the combination in trans of two severe variants is responsible for early onset severe retinal dystrophy in the context of late-infantile neuronal ceroid lipofuscinosis.

Usher syndrome is an autosomal recessive disorder characterized by congenital hearing loss combined with retinitis pigmentosa, and in some cases, vestibular areflexia. Three clinical subtypes are distinguished, and MYO7A and USH2A represent the two major causal genes involved in Usher type I, the most severe form, and type II, the most frequent form, respectively. Massively parallel sequencing was performed on a cohort of patients in the context of a molecular diagnosis to confirm clinical suspicion of Usher syndrome. We report here 231 pathogenic MYO7A and USH2A genotypes identified in 73 Usher type I and 158 Usher type II patients. Furthermore, we present the ACMG classification of the variants, which comprise all types. Among them, 68 have not been previously reported in the literature, including 12 missense and 16 splice variants. We also report a new deep intronic variant in USH2A. Despite the important number of molecular studies published on these two genes, we show that during the course of routine genetic diagnosis, undescribed variants continue to be identified at a high rate. This is particularly pertinent in the current era, where therapeutic strategies based on DNA or RNA technologies are being developed.

Background Bardet–Biedl syndrome (BBS) is a rare nonmotile ciliopathy characterized by retinal dystrophy, polydactyly, obesity, genital anomalies, renal dysfunction, and learning difficulties. The objectives were to describe the retinal, oral, and metabolic characteristics relevant to adults with BBS as well as the prevalence of genetic variants. Methods A cross-sectional study of 30 adults with BBS (15 males, 15 females, mean age 39.8 ± 13.6 years) was recruited from a single centre for rare disorders in Norway. Participants attended a one day hospital visit including medical (blood pressure, body mass index), ophthalmological and oral examinations. Blood samples were collected and genetic analyses were performed. Results Age at diagnosis varied from one year to 30 years. The incidence of overweight/obesity, hypertension, kidney disease, and diabetes mellitus was 82%, 67%, 27%, and 23%, respectively. All had retinitis pigmentosa. Prior to the study, 14 participants (47%) had confirmed extinguished electroretinography. Eleven participants were examined with electroretinography during the study period, and all had extinguished electroretinography. 50% perceived light, 23% saw hand motion, and one participant did not perceive light. Oral anomalies were identified in 77% of the participants, including abnormal palates (58%), crowded teeth (50%), and small teeth (60%). A genetic cause was identified in all participants, most commonly in BBS1 ( n  = 11) and BBS10 ( n  = 9). Other variants were found in BBS5 , BBS7 , BBS9 , and MKKS. In addition to exon-located variants, a novel deep intronic variant causing mis-splicing was identified in BBS7 . Conclusions A multidisciplinary examination is important for proper management of BBS. The genotype and phenotype of this sample were heterogeneous, including kidney failure, genital anomalies and obesity. Genome sequencing increased the likelihood of identifying the genetic cause. In BBS populations, the patients will benefit from testing or reanalysis, preferably with genome sequencing, including searching for deep intronic variants.

Multiple acyl-CoA dehydrogenase deficiency (MADD) is a rare inborn error of metabolism affecting fatty acid and amino acid oxidation with an incidence of 1 in 200,000 live births. MADD has three clinical phenotypes: severe neonatal-onset with or without congenital anomalies, and a milder late-onset form. Clinical diagnosis is supported by urinary organic acid and blood acylcarnitine analysis using tandem mass spectrometry in newborn screening programs. MADD is an autosomal recessive trait caused by biallelic mutations in the ETFA, ETFB, and ETFDH genes encoding the alpha and beta subunits of the electron transfer flavoprotein (ETF) and ETF-coenzyme Q oxidoreductase enzymes. Despite significant advancements in sequencing techniques, many patients remain undiagnosed, impacting their access to clinical care and genetic counseling. In this report, we achieved a definitive molecular diagnosis in a newborn by combining whole-genome sequencing (WGS) with RNA sequencing (RNA-seq). Whole-exome sequencing and next-generation gene panels fail to detect variants, possibly affecting splicing, in deep intronic regions. Here, we report a unique deep intronic mutation in intron 1 of the ETFDH gene, c.35-959A>G, in a patient with early-onset lethal MADD, resulting in pseudo-exon inclusion. The identified variant is the third mutation reported in this region, highlighting ETFDH intron 1 vulnerability. It cannot be excluded that these intronic sequence features may be more common in other genes than is currently believed. This study highlights the importance of incorporating RNA analysis into genome-wide testing to reveal the functional consequences of intronic mutations.