Intronic Mutation Research Articles

Structural and functional analysis of retinal vasculature in HANAC syndrome with a novel intronic COL4A1 mutation.

Mutations of the COL4A1 gene, a major structural protein of vessels, may cause hereditary angiopathy with nephropathy, aneurysms and muscle cramps (HANAC) syndrome. The vascular structure and function of patients with HANAC is poorly known. Here, we report a family with HANAC syndrome associated to a previously unreported mutation in COL4A1. The structure and function of retinal vessels were detailed by adaptive optics ophthalmoscopy (AOO) and optical coherence tomography (OCT) angiography. Clinical data from six affected individuals (43 to 72years old) from a single family comprising two generations were collected. Imaging charts including conventional fundus imaging, OCT-angiography and AOO in static and dynamic (flicker) mode were reviewed. DNA sequencing was done in the proband. DNA sequencing of the proband revealed a heterozygous deletion of COL4A1 (NM_001845) at position 1120 in the intron 20 resulting in the loss of splicing donor site for exon 20 (c.1120+2_1120+8del heterozygote). Four patients had arterial hypertension, and three had kidney dysfunction, one of which under dialysis. By fundus examination, five had typical retinal arteriolar tortuosity with arteriolar loops. Wall-to-lumen ratio of arteries was within normal limits, that is, lower than expected for hypertensive patients. Several foci of arteriolar irregularities were noted in the two oldest patients. In three affected subjects, evaluation of the neurovascular coupling showed a higher flicker-induced vasodilation than a control population (6% to 11%; n<5%). Structural and dynamic analysis of retinal vessels in a HANAC family bearing a previously unreported intronic COL4 mutation was done. In addition to arteriolar tortuosity, we found reduced wall-to-lumen ratio, arteriolar irregularity and increased vasodilatory response to flicker light. These abnormalities were more marked in the oldest subjects. This abnormal flicker response affected also non-tortuous arteries, suggesting that microvascular dysfunction extends beyond tortuosity. Such explorations may help to better vascular dysfunction related to HANAC and hence better understand the mechanisms of end-organ damage.

Generation of CRB1 RP Patient-Derived iPSCs and a CRISPR/Cas9-Mediated Homology-Directed Repair Strategy for the CRB1 c.2480G>T Mutation.

Mutations in the Crumbs-homologue-1 (CRB1) gene lead to a spectrum of severe inherited retinal diseases, including retinitis pigmentosa (RP). The establishment of a genotype-phenotype correlation in CRB1 patients has been difficult due to the substantial variability and phenotypic overlap between CRB1-associated diseases. This phenotypic modulation may be due to several factors, including genetic modifiers, deep intronic mutations, isoform diversity, and copy number variations. Induced pluripotent stem cell (iPSC)-derived patient retinal organoids are novel tools that can provide sensitive, quantitative, and scalable phenotypic assays. CRB1 RP patient iPSC-derived retinal organoids have shown reproducible phenotypes compared to healthy retinal organoids. However, having genetically defined iPSC isogenic controls that take into account potential phenotypic modulation is crucial. In this study, we generated iPSC from an early-onset CRB1 patient and developed a correction strategy for the c.2480G>T, p.(Gly827Val) CRB1 mutation using CRISPR/Cas9-mediated homology-directed repair.

Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs.

In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G&gt;T, g.60146A&gt;T, and g.61455G&gt;A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G&gt;T, exonic g.4564T&gt;C, exonic g.6378G&gt;A, exonic g.6386C&gt;T, intronic g.8643G&gt;A, and intronic g.8857A&gt;G. Association analysis revealed that g.42101G&gt;T, g.60146A&gt;T, g.61455G&gt;A, g.4374G&gt;T, g.4564T&gt;C, g.6378G&gt;A, g.6386C&gt;T, g.8643G&gt;A, and g.8857A&gt;G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding.

Identification of a novel WAS mutation and the non-splicing effect of a second-site mutation in a Chinese pedigree with Wiskott–Aldrich syndrome

BackgroundWiskott–Aldrich syndrome (WAS) is a rare X-linked immunodeficiency disorder caused by abnormal expression of the WAS protein (WASp) due to mutations in the WAS gene, and is generally characterized by microthrombocytopenia, eczema, recurrent infections, and high susceptibility to autoimmune complications and hematological malignancies.ResultsHerein, we identified a novel WAS mutation (c.158 T > C) using next-generation sequencing in a Chinese pedigree with WAS. The expression of WASp in the patients and their families was detected by flow cytometry and western blot analysis. To explore the exon-splicing effect of intron mutations and the correlation between the genotype and clinical phenotype, four groups of wild-type (WT), exon mutant, intron mutant, and combined mutant recombinant plasmids were transfected into COS-7 cells in vitro. The proband showed dramatically decreased WASp expression, while the female carriers showed a slightly lower level of WASp. The expression of products in the mutant and WT recombinant plasmids was detected by real-time fluorescence quantitative polymerase chain reaction (PCR), which showed a significant reduction in the combined mutant group than in the WT, exon mutant, and intron mutant groups. The length of the expression products in the four groups showed no differences, each containing 360 base pairs. Sequence analysis confirmed that the c.158 T > C mutation appeared in the exon mutant and combined mutant groups, whereas the intron variant c.273 + 14C > T caused no other sequence changes.ConclusionThis study confirmed that the intron mutation did not affect the splicing of exons and excluded the influence of the double mutations at the transcription level on the severe clinical manifestations in the cousin. This in vitro study provided new insights into the pathogenesis of intronic mutations in WAS.

Molecular mechanisms underlying the defects of two novel mutations in the HSD17B3 gene found in the Tunisian population

17β-hydroxysteroid dehydrogenase type 3 (17β-HSD3) converts Δ4-androstene-3,17-dione (androstenedione) to testosterone. It is expressed almost exclusively in the testes and is essential for appropriate male sexual development. More than 70 mutations in the HSD17B3 gene that cause 17β-HSD3 deficiency and result in 46,XY Disorders of Sex Development (46,XY DSD) have been reported. This study describes three novel Tunisian cases with mutations in HSD17B3. The first patient is homozygous for the previously reported mutation p.C206X. The inheritance of this mutation seemed to be independent of consanguineous marriage, which can be explained by its high frequency in the Tunisian population. The second patient has a novel splice site mutation in intron 6 at position c.490 -6 T > C. A splicing assay revealed a complete omission of exon 7 in the resulting HSD17B3 mRNA transcript. Skipping of exon 7 in HSD17B3 is predicted to cause a frame shift in exon 8 that affects the catalytic site and results in a truncation in exon 9, leading to an inactive enzyme. The third patient is homozygous for the novel missense mutation p.K202M, representing the first mutation identified in the catalytic tetrad of 17β-HSD3. Site-directed mutagenesis and enzyme activity measurements revealed a completely abolished 17β-HSD3 activity of the p.K202M mutant, despite unaffected protein expression, compared to the wild-type enzyme. Furthermore, the present study emphasizes the importance of genetic counselling, detabooization of 46,XY DSD, and a sensitization of the Tunisian population for the risks of consanguineous marriage.

Alternative splicing in CEP290 mutant cats results in a milder phenotype than LCACEP290 patients.

The rdAc cat has an intronic mutation in the centrosomal 290 kDa (CEP290) gene resulting in a frameshift and a premature stop codon (c.6960 + 9T > G, p.Ile2321AlafsTer3) predicted to truncate the protein by 157 amino acids. CEP290 mutations in human patients cause a range or phenotypes including syndromic conditions and severe childhood loss of vision while the rdAc cat has a milder phenotype. We sought to further characterize the effect of rdAc mutation on CEP290 expression. TaqMan quantitative real-time polymerase chain reaction assays were used to compare wildtype and truncated transcript levels. Relative protein abundance was analyzed by Western blot. Immunohistochemistry (IHC) was performed to detect CEP290 protein. CEP290 mutant cats show low-level (17.4% of wildtype cats) use of the wildtype splice site and usage of the mutant splice site. Western analysis shows retina from cats homozygous for the mutation has CEP290 protein that likely comprises a combination of both wildtype and truncated protein. IHC detects CEP290 in affected and control retina labeling the region of the interconnecting cilium. The comparably milder phenotype of CEP290 mutant cats is likely due to the retained production of some full-length CEP290 protein with possible functional contributions from presence of truncated protein.

Novel biallelic mutations in TMEM126B cause splicing defects and lead to Leigh-like syndrome with severe complex I deficiency

Leigh syndrome (LS)/Leigh-like syndrome (LLS) is one of the most common mitochondrial disease subtypes, caused by mutations in either the nuclear or mitochondrial genomes. Here, we identified a novel intronic mutation (c.82-2 A > G) and a novel exonic insertion mutation (c.290dupT) in TMEM126B from a Chinese patient with clinical manifestations of LLS. In silico predictions, minigene splicing assays and patients’ RNA analyses determined that the c.82-2 A > G mutation resulted in complete exon 2 skipping, and the c.290dupT mutation provoked partial and complete exon 3 skipping, leading to translational frameshifts and premature termination. Functional analysis revealed the impaired mitochondrial function in patient-derived lymphocytes due to severe complex I content and assembly defect. Altogether, this is the first report of LLS in a patient carrying mutations in TMEM126B. Our data uncovers the functional effect and the molecular mechanism of the pathogenic variants c.82-2 A > G and c.290dupT, which expands the gene mutation spectrum of LLS and clinical spectrum caused by TMEM126B mutations, and thus help to clinical diagnosis of TMEM126B mutation‐related mitochondrial diseases.

Novel Mutation of Hydroxymethylbilane Synthase in a Case of Acute Intermittent Porphyria Presenting with Posterior Reversible Encephalopathy Syndrome.

Acute intermittent porphyria (AIP) is an autosomal, dominant, hereditary metabolic disease caused by an inherited deficiency of hydroxymethylbilane synthase (HMBS), a crucial enzyme in the heme biosynthetic pathway. It can affect the central, peripheral, and autonomic nervous systems. We report a 23-year Chinese woman who presented with severe abdominal pain, convulsions, constipation, tachycardia, quadriparesis, and hyponatremia, accompanied by posterior reversible encephalopathy syndrome (PRES). The clinical diagnosis of AIP was made after positive urine Watson-Schwartz test for porphobilinogen (PBG). Genetic testing is important for AIP patients in confirming the diagnosis. We identified a new insertion mutation in intron 14 [c.1005dupC (p.I336Hfs*23)] of the HMBS in her genomic DNA. Timely and accurate treatment of AIP may improve disease prognosis. Key Words: Acute intermittent porphyria, Mutation, Posterior reversible encephalopathy syndrome.

Structural and functional exploration of the retinal vasculature in HANAC syndrome associated with a novel intronic COL4A1 mutation

AbstractPurpose: Mutations of the COL4A1 gene may cause hereditary angiopathy with nephropathy, aneurysms and muscle cramps (HANAC) syndrome. The vascular structure and function of patients with HANAC is poorly known. Here, we report a family with HANAC syndrome associated to a previously unreported mutation in COL4A1. The structure and function of retinal vessels were detailed by adaptive optics ophthalmoscopy (AOO) and optical coherence tomography (OCT) angiography.Methods: Clinical data from six affected individuals from a single family over two generations were collected. Imaging charts including conventional fundus imaging, OCT‐angiography and AOO in static and dynamic (flicker) mode were reviewed. DNA sequencing was done in the proband.Results: DNA sequencing of the proband revealed a heterozygous deletion of COL4A1 (NM_001845) at position 1120 in the intron 20 resulting in the loss of splicing donor site for exon 20 (c.1120 + 2_1120 + 8del heterozygote). Four had arterial hypertension, and three had kidney dysfunction, one of which under dialysis. Examination of retinal vessels showed that all patients had retinal arteriolar tortuosity which peaked in precapillary arterioles but spared capillaries and veins. Wall‐to‐lumen ratio of arteries was within normal limits, that is, lower than expected for hypertensive patients. Several foci of arteriolar irregularities were noted I the oldest patients. In three affected subjects, evaluation of the neurovascular coupling showed a high flicker‐induced vasodilation (from 6% to 10.8%; n &lt; 5%).Conclusions: Structural and dynamic analysis of retinal vessels in a HANAC family bearing a novel intronic COL4 mutation showed reduced parietal thickness, arteriolar irregularity and increased dilatory response to flicker light. This affected as well non tortuous arteries, suggesting that HANAC causes diffuse microvascular dysfunction. Our findings may help to better understand end‐organ damage related to HANAC.

Astrocyte activation and protein aggregation in the retina of Alzheimer's disease patients

AbstractAlzheimer's disease (AD), a primary cause of dementia in the aging population, is characterized by intracellular and extracellular aggregates of misfolded proteins, as amyloid‐beta plaques and tau tangles, together with neurodegeneration and glial activation in the brain. It is commonly thought that the lack of early diagnostic criteria is among the main causes of pharmacological therapy and clinical trials failure; therefore, the actual challenge is to define new biomarkers and non‐invasive technologies to measure neuropathological changes in vivo at pre‐symptomatic stages. Recent evidences obtained from human samples and mouse models indicate the possibility to detect protein aggregates and other pathological features in the retina, paving the road for non‐invasive rapid detection of AD biomarkers. Here, we report the presence of amyloid beta plaques, tau tangles, neurodegeneration and detrimental astrocyte and microglia activation according to a disease associated microglia phenotype (DAM). Thus, we propose the human retina as a useful site for the detection of cellular and molecular changes associated with Alzheimer's disease.We also developed novel 2D and 3D in vitro models of AD related retinal tauopathy, obtaining derived retinal cultures from iPSC harbouring an intronic tau mutation. We report here that mutated tau induces not only tau hyperphosphorylation, but also impaired retinogenesis and altered astrocytic development.

Restoring Dystrophin Expression by Skipping Exons 6 and 8 in Neonatal Dystrophic Dogs.

Duchenne muscular dystrophy (DMD) is caused by the mutations in the DMD gene resulting in no dystrophin production. Skipping DMD exons using phosphorodiamidate morpholino oligomers (PMOs) is an emerging treatment strategy that can restore the reading frame of the mutated gene and produce truncated but functional dystrophin protein. To date, four PMOs, including eteplirsen, casimersen, viltolarsen, and golodirsen, have been conditionally approved by the FDA for the treatment of DMD. Since degeneration of muscle fibers and irreversible fibrosis occur from childhood, the earlier treatment is preferred. The canine X-linked muscular dystrophy in Japan (CXMDj), a dog model of DMD, produces no dystrophin and exhibits a severe phenotype similar to human patients from early childhood. As such, CXMDj, which harborsa splice site mutation in intron 6, is a useful model for examining the long-term effects of early PMO treatment. In this chapter, we describe the systemic delivery of a cocktail of four PMOs that can successfully induce multiple exon skipping (exons 6-9) in neonataldystrophic dogs. We also describe the procedures to evaluate the efficacy and toxicity, including clinical grading of dystrophic dogs, ELISA-based quantification of PMOs, histology, RT-PCR, and western blotting.

Familial Hemophagocytic Lymphohistiocytosis secondary to UNC13D mutation: a report of two cases

BackgroundHemophagocytic lymphohistiocytosis (HLH) is a life-threatening disease characterized by some clinical signs (e.g., non-remitting fever, hepatosplenomegaly) and laboratory findings (e.g., cytopenia, increased ferritin level, hypofibrinogenemia, lipid disorders, coagulopathy, and multiple organ failure). Depending on the etiology, HLH is divided into familial (i.e., primary) and acquired (i.e., secondary) forms. Familial HLH (FHL), an autosomal recessive condition, is classified into five subtypes based on underlying genetic defects. The PRF1, STX11, UNC13D, HPLH1, and STXBP2 are the most well-known genes of this type which are related to granule-mediated cytotoxic T and Natural killer (NK) cells. The treatment is based on the HLH-2004 protocol.Case presentationThe current report presents two cases of HLH with presentations different from each other and previously reported cases. Case 1 was a 15-month-old boy with fever, skin rash, splenomegaly, and bicytopenia, raised triglyceride levels, AST (aspartate transaminase), and ALT (alanine aminotransferase), normal ferritin, and abundant hemophagocytic cell in bone marrow aspiration. He was diagnosed with HLH and received HLH protocol as treatment. The patient had a homozygous intronic mutation; NM_199242: c.2448-13G > A in UNC13D. The associated disease was Familial Hemophagocytic Lymphohistiocytosis 3 (FHL3). Case 2, a 37-day-old female presented with fever, a history of neonatal cholestasis, and huge hepatosplenomegaly. Her whole-exome sequencing report manifested that the patient had the same mutation as case 1. Unfortunately, both patients passed away.ConclusionThe sequencing of the entire UNC13D gene (coding and non-coding regions) is an applicable and valuable diagnostic procedure for the detection of deep intronic splicing variants and large inversions in patients with atypical manifestations of HLH (such as normal ferritin or triglyceride and cholesterol).

Emicizumab and Females with Hemophilia A: Case Series from ATHN 7

Background: ATHN 7, A Natural History Cohort Study of the Safety, Effectiveness, and Practice of Treatment for People with Hemophilia (NCT03619863), monitors the use of current hemophilia A (HA) and B therapies, including the substitution therapy, emicizumab. Emicizumab is a bispecific monoclonal antibody that bridges activated factor (F)IX and FX, substituting for the function of deficient activated FVIII in people with hemophilia A (PwHA). Emicizumab is approved in the United States for prophylaxis in PwHA ages newborn and older, with or without FVIII inhibitors. The population of females with HA is rare and under-represented in the medical literature. This analysis aims to characterize the females with HA enrolled in ATHN 7 who were receiving emicizumab and present their associated experience on this therapy, including the safety profile of emicizumab in this population. Methods: ATHN 7 is a longitudinal, prospective observational cohort study conducted at 26 American Thrombosis and Hemostasis Network (ATHN)-affiliated sites. Ethics approval was obtained and participants and/or parents/guardians provided consent. Females (assigned sex at birth) with HA receiving care at participating sites were eligible for inclusion. Demographic information was collected at baseline. Clinical information was collected at baseline and at least quarterly through participant interview and medical record review. Descriptive statistics of medical history and demographic data as well as longitudinal data were used to characterize the study population. Adverse events (AEs) were documented. Results: As of December 31, 2021, demographic information was available for three emicizumab-treated females with HA in ATHN 7 (Table 1). One of the three was postmenarchal (11 years of age), while the other two were premenarchal. Two of the participants had baseline factor FVIII activity of less than 1% (classified as severe HA) and no history of FVIII inhibitors, while the third participant had a baseline FVIII activity of 1% (classified as moderate HA) and a history of tolerized low titer FVIII inhibitors. Two participants (one with severe HA, and one with moderate HA with FVIII inhibitors) had a FVIII inversion mutation in intron 22 and the third participant (with severe HA) a FVIII frameshift mutation c.5351delC. All three participants had >50 exposure-days to FVIII at study entry and no target joints present. There were no other reported hemophilia-related concomitant conditions in any of the three participants in this analysis. Participants received emicizumab once every 2 weeks (Table 2). Emicizumab exposure ranged from approximately 81.0 to 94.9 weeks, the longest follow-up in female participants reported to date in the literature. The data represent a total of 5.18 patient-years exposure to emicizumab. Only one participant experienced a treated bleed, which was associated with a dental procedure. This participant also reported one bleed that was not treated (menses). There were no other treated or untreated bleeds reported in these participants. During the study, one participant underwent surgery (pressure equalization tube removal), with no unexpected bleeds associated with the procedure. No AEs were reported for any of the three female participants while being treated with emicizumab. Conclusions: This analysis contributes to filling the data gap existing for females with HA. In the largest multi-center, prospective observational experience of emicizumab-treated PwHA in the US (ATHN 7), two of the three female participants had no bleeds (treated or untreated), while the third participant had one treated bleed associated with a dental procedure and one untreated bleed associated with menses. No AEs were reported. Continued data collection is vital to further understand safety and effectiveness in this rare and under-represented population to optimize care for females with HA. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Case report of a pediatric Chinese cystic fibrosis patient with the c.1521_1523delCTT/c.3874-4522A>G genotype.

This report describes a case of an 11-year-old Chinese boy with cystic fibrosis (CF) bearing the c.1521_1523delCTT/c.3874-4522A>G genotype, an extremely rare CF genotype in the Chinese population. Notably, the deep intron mutation c.3874-4522A>G, which has mainly been reported in patients with phenotypically mild CF, is identified here for the first time in a Chinese patient with severe CF. In the case discussed here, the c.3874-4522A>G mutation was associated with severe pulmonary disease with early symptoms onset, progressive bronchiectasis, recurrent airway infection with both Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus, rapid decline of lung function and poor weight gain. Despite intensive hospital-based pulmonary care and optimized therapy, the child died of cardiopulmonary failure 3 months after discharge.

Polymorphism in ovine ADCY8 gene and its association with residual feed intake in Hu sheep

Feed efficiency makes up a large part of sheep production, which also has a crucial impact on the economic benefits of producers. This study explores the polymorphism of Adenylyl cyclase 8 gene associated with feed efficiency and detects the expression characteristics of ADCY8 in ten tissues of Hu sheep. The polymorphism of ADCY8 was recognized by using PCR amplification and Sanger sequencing, KASPar technology was used for genotyping subsequently, and the relationship between SNP and RFI is also studied. The results indicated that an intronic mutation g.24799148 C > T (rs 423395741) was identified in ADCY8, and association analysis showed that the SNP g.24799148 C > T (rs 423395741) was significantly associated with RFI at 100–120, 100–140, 100–160, and 100–180 days (p < 0.05). The quantitative real-time PCR (qRT-PCR) result showed that ADCY8 was expressed in ten tissues, and the expression of ADCY8 gene in rumen tissue was significantly higher than in the other tested tissues. Therefore, these results indicated that the ADCY8 mutation locus may be used as a candidate molecular marker for evaluating the feed efficiency of Hu sheep.

Alport Syndrome Caused by a Novel Intronic Mutation Leading to Partial Aberrant mRNA Splicing: A Case Report

Alport Syndrome Caused by a Novel Intronic Mutation Leading to Partial Aberrant mRNA Splicing: A Case Report

Congenital diaphragmatic eventration with pulmonary dysplasia in Frasier syndrome due to a WT1 mutation of c.1432+5(IVS9)G>A

WT1 disorder is caused by a heterozygous variant in the gene WT1 (Wilms' tumor suppressor gene 1), and is clinically diagnosed as Denys-Drash, Meacham, or Frasier syndrome, on a phenotypic continuum that presents as abnormalities of the urogenital system and gonads. Rarely, manifestations appear in the lung, especially in Frasier syndrome. Here we describe the first noted case of congenital diaphragmatic eventration with pulmonary dysplasia in a child with Frasier syndrome. A c.1432+5G > A mutation in intron 9 of WT1 was found. We also summarize pulmonary diseases associated with WT1 mutations in WT1 disorder.

Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing.

Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373-2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.

Direct sequencing of β-globin gene reveals a rare combination of two exonic and two intronic variants in a β-thalassemia major patient: a case report

BackgroundDue to indels in the β-globin gene, patients with β-thalassemia major exhibit a range of severity, with genotype β0β0 > β0β+ > β+β+, according to the production level of the β-globin chain. More than 300 mutations have been identified in the β-globin gene.Case presentationIn this case study, we report a compound heterozygous condition with a rare concoction of four different variants (CD 3(T > C), CD41/42 (-CTTT), IVS II-16 (G > C), and IVS II-666 (C > T) in a single β-globin gene. A regular transfusion-dependent 4-year-old male patient from India was included in the study. Augmented direct sequencing of the β-globin gene helped reveal the presence of an unusual combination of different variants in a single gene. This patient clinically presented as β-thalassemia major and was genotypically considered as β0β+, although CD41/42(-CTTT) was the only causative/pathogenic mutation in the disease severity.ConclusionAlthough CD41/42-(CTTT) is the only pathogenic variant among the four variants, the clinical complications of such a combination of variants (pathogenic and benign) is not well understood. Intronic mutations may have the ability to modify clinical characteristics. The variants must therefore be reclassified using additional mRNA splicing and expression-based studies. Additionally, these types of combinations may have significance in studying population migration around the world.

Analysis of RPGR gene mutations in 41 Chinese families affected by X-linked inherited retinal dystrophy.

Background: This study analyzed the phenotypes and genotypes of 41 Chinese families with inherited retinal dystrophy (IRD) and RPGR gene mutations. Methods: This retrospective analysis evaluated a cohort of 41 patients who were subjected to a specific Hereditary Eye Disease Enrichment Panel (HEDEP) analysis. All (likely) pathogenic variants were determined by Sanger sequencing, and co-segregation analyses were performed on the available family members. All cases were subjected to Sanger sequencing for RPGR open reading frame 15 (ORF15) mutations. Results: A total of 41 probands from different families with a clinical diagnosis of retinitis pigmentosa (RP; 34 cases) and cone-rod dystrophy (CORD; 7 cases) were included in this cohort. According to clinical information, 2, 18, and 21 cases were first assigned as autosomal dominant (AD), sporadic, and X-linked (XL) inheritance, respectively. Several cases of affected females who presented with a male phenotype have been described, posing challenges at diagnosis related to the apparent family history of AD. Mutations were located in RPGR exons or introns 1–14 and in ORF15 of 12 of 41 (29.3%) and 29 of 41 (70.7%) subjects, respectively. Thirty-four (likely) pathogenic mutations were identified. Frameshifts were the most frequently observed variants, followed by nonsense, splice, and missense mutations. Herein, a detailed description of four RP patients carrying RPGR intronic mutations is reported, and in vitro splice assays were performed to confirm the pathogenicity of these intronic mutations. Conclusion: Our findings provide useful insights for the genetic and clinical counseling of patients with XL IRD, which will be useful for ongoing and future gene therapy trials.