scholarly journals Prevalence of ABCA4 Deep-Intronic Variants and Related Phenotype in An Unsolved “One-Hit” Cohort with Stargardt Disease

2019 ◽  
Vol 20 (20) ◽  
pp. 5053 ◽  
Author(s):  
Nassisi ◽  
Mohand-Saïd ◽  
Andrieu ◽  
Antonio ◽  
Condroyer ◽  
...  
Keyword(s):  
In Silico ◽  
Cohort Analysis ◽  
Pathogenic Variant ◽  
Stargardt Disease ◽  
Phenotypic Analysis ◽  
Variable Effect ◽  
Mild Phenotype ◽  
Related Phenotype ◽  
Novel Variants ◽  
Intronic Variants

We investigated the prevalence of reported deep-intronic variants in a French cohort of 70 patients with Stargardt disease harboring a monoallelic pathogenic variant on the exonic regions of ABCA4. Direct Sanger sequencing of selected intronic regions of ABCA4 was conducted. Complete phenotypic analysis and correlation with the genotype was performed in case a known intronic pathogenic variant was identified. All other variants found on the analyzed sequences were queried for minor allele frequency and possible pathogenicity by in silico predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G>A in intron 36 (6 subjects), c.4539+2064C>T in intron 30 (4 subjects) and c.4253+43G>A in intron 28 (4 subjects). Even though the phenotype depends on the compound effect of the biallelic variants, a genotype-phenotype correlation suggests that the c.5196+1137G>A was mostly associated with a mild phenotype and the c.4539+2064C>T with a more severe one. A variable effect was instead associated with the variant c.4253+43G>A. In addition, two novel variants, c.768+508A>G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted in silico. Our study calls for a larger cohort analysis including targeted locus sequencing and 3D protein modeling to better understand phenotype-genotype correlations associated with deep-intronic changes and patients’ selection for clinical trials.

scholarly journals Detailed genetic characteristics of an international large cohort of patients with Stargardt disease: ProgStar study report 8

2018 ◽  
Vol 103 (3) ◽  
pp. 390-397 ◽  
Author(s):  
Kaoru Fujinami ◽  
Rupert W Strauss ◽  
John (Pei-Wen) Chiang ◽  
Isabelle S Audo ◽  
Paul S Bernstein ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Stargardt Disease ◽  
Genetic Characteristics ◽  
Mild Phenotype ◽  
Missense Variants ◽  
Pathogenic Variants ◽  
Significant Difference ◽  
Novel Variants ◽  
The Usa ◽  
Subsequent Comparison

Background/aimsTo describe the genetic characteristics of the cohort enrolled in the international multicentre progression of Stargardt disease 1 (STGD1) studies (ProgStar) and to determine geographic differences based on the allele frequency.Methods345 participants with a clinical diagnosis of STGD1 and harbouring at least one disease-causing ABCA4 variant were enrolled from 9 centres in the USA and Europe. All variants were reviewed and in silico analysis was performed including allele frequency in public databases and pathogenicity predictions. Participants with multiple likely pathogenic variants were classified into four national subgroups (USA, UK, France, Germany), with subsequent comparison analysis of the allele frequency for each prevalent allele.Results211 likely pathogenic variants were identified in the total cohort, including missense (63%), splice site alteration (18%), stop (9%) and others. 50 variants were novel. Exclusively missense variants were detected in 139 (50%) of 279 patients with multiple pathogenic variants. The three most prevalent variants of these patients with multiple pathogenic variants were p.G1961E (15%), p.G863A (7%) and c.5461-10 T>C (5%). Subgroup analysis revealed a statistically significant difference between the four recruiting nations in the allele frequency of nine variants.ConclusionsThere is a large spectrum of ABCA4 sequence variants, including 50 novel variants, in a well-characterised cohort thereby further adding to the unique allelic heterogeneity in STGD1. Approximately half of the cohort harbours missense variants only, indicating a relatively mild phenotype of the ProgStar cohort. There are significant differences in allele frequencies between nations, although the three most prevalent variants are shared as frequent variants.

scholarly journals Autosomal recessive chondrodysplasia with severe short stature caused by a biallelic COL10A1 variant

2017 ◽  
Vol 55 (6) ◽  
pp. 403-407 ◽  
Author(s):  
Noor ul Ain ◽  
Outi Makitie ◽  
Sadaf Naz
Keyword(s):  
Short Stature ◽  
Skeletal Dysplasia ◽  
In Silico ◽  
Autosomal Recessive ◽  
Limb Deformity ◽  
Mild Phenotype ◽  
Whole Exome ◽  
New Type ◽  
Severe Short Stature ◽  
Amino Acid Conservation

BackgroundHeterozygous mutations in COL10A1 underlie metaphyseal chondrodysplasia, Schmid type (MCDS), an autosomal dominant skeletal dysplasia.ObjectiveTo identify the causative variant in a large consanguineous Pakistani family with severe skeletal dysplasia and marked lower limb deformity.MethodsWhole exome sequencing was completed followed by Sanger sequencing to verify segregation of the identified variants. In silico variant pathogenicity predictions and amino acid conservation analyses were performed.ResultsA homozygous c.133 C>T (p.Pro45Ser) variant was identified in COL10A1 in all six severely affected individuals (adult heights 119–130 cm, mean ~−6.33 SD). The individuals heterozygous for the variant had mild phenotype of short stature (adult heights 140–162 cm, mean ~−2.15 SD) but no apparent skeletal deformities. The variant was predicted to be pathogenic by in silico prediction tools and was absent from public databases and hundred control chromosomes. Pro45 is conserved in orthologues and is located in the non-collagenous 2 domain of COL10A1, variants of which have never been associated with skeletal dysplasia.ConclusionsThis first report of individuals with a homozygous variant in COL10A1 defines a new type of autosomal recessive skeletal dysplasia. The observations in COL10A1 variant carriers suggest a phenotypic overlap between the mildest forms of MCDS and idiopathic short stature.

scholarly journals ABCA4 Gene Screening in a Chinese Cohort With Stargardt Disease: Identification of 37 Novel Variants

2019 ◽  
Vol 10 ◽  
Author(s):  
Fang-Yuan Hu ◽  
Jian-kang Li ◽  
Feng-Juan Gao ◽  
Yu-He Qi ◽  
Ping Xu ◽  
...  
Keyword(s):  
Stargardt Disease ◽  
Gene Screening ◽  
Disease Identification ◽  
Abca4 Gene ◽  
Novel Variants ◽  
Chinese Cohort

EYSmutation update: In silico assessment of 271 reported and 26 novel variants in patients with retinitis pigmentosa

2017 ◽  
Vol 39 (2) ◽  
pp. 177-186 ◽  
Author(s):  
Muriël Messchaert ◽  
Lonneke Haer-Wigman ◽  
Muhammad I. Khan ◽  
Frans P. M. Cremers ◽  
Rob W. J. Collin
Keyword(s):  
Retinitis Pigmentosa ◽  
In Silico ◽  
Novel Variants

scholarly journals In silico prioritization and further functional characterization of SPINK1 intronic variants

2017 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Bin Zou ◽  
Hao Wu ◽  
Arnaud Boulling ◽  
David N. Cooper ◽  
Zhao-Shen Li ◽  
...  
Keyword(s):  
In Silico ◽  
Functional Characterization ◽  
Intronic Variants

scholarly journals Meta analysis of variant predictions in congenital adrenal hyperplasia caused by mutations in CYP21A2.

2021 ◽  
Author(s):  
Mayara Jorgens Prado ◽  
Rodrigo Ligabue-Braun ◽  
Arnaldo Zaha ◽  
Maria Lucia Rosa Rossetti ◽  
Amit V Pandey
Keyword(s):  
Congenital Adrenal Hyperplasia ◽  
In Silico ◽  
Meta Analysis ◽  
Genetic Disorders ◽  
In Silico Prediction ◽  
Adrenal Hyperplasia ◽  
Single Nucleotide Variants ◽  
Mild Phenotype ◽  
The Impact

Context: CYP21A2 deficiency represents 95% of congenital adrenal hyperplasia cases (CAH), a group of genetic disorders that affect steroid biosynthesis. The genetic and functional analysis provides critical tools to elucidate complex CAH cases. One of the most accessible tools to infer the pathogenicity of new variants is in silico prediction. Objective: Analyze the performance of in silico prediction tools to categorize missense single nucleotide variants (SNVs) of the CYP21A2. Methods: SNVs of the CYP21A2 characterized in vitro by functional assays were selected to assess the performance of online single and meta predictors. SNVs were tested separately or in combination with the related phenotype (severe or mild CAH form). In total, 103 SNVs of the CYP21A2 (90 pathogenic and 13 neutral) were used to test the performance of 13 single-predictors and four meta-predictors. Results: SNVs associated with the severe phenotypes were well categorized by all tools, with an accuracy between 0.69 (PredictSNP2) and 0.97 (CADD), and Matthews' correlation coefficient (MCC) between 0.49 (PoredicSNP2) and 0.90 (CADD). However, SNVs related to the mild phenotype had more variation, with the accuracy between 0.47 (S3Ds&GO and MAPP) and 0.88 (CADD), and MCC between 0.18 (MAPP) and 0.71 (CADD). Conclusion: From our analysis, we identified four predictors of CYP21A2 pathogenicity with good performance. These results can be used for future analysis to infer the impact of uncharacterized SNVs' in CYP21A2.

scholarly journals Novel Genetic Variants in Complement-Mediated Thrombotic Microangiopath

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1050-1050 ◽  
Author(s):  
Jennifer Yui ◽  
Roshini S Abraham ◽  
Dong Chen ◽  
Fernando Fervenza ◽  
Ronald S. Go ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Genetic Variants ◽  
In Silico ◽  
Factor H ◽  
Complement Factor ◽  
Complement Pathway ◽  
Microangiopathic Hemolytic Anemia ◽  
Novel Variants ◽  
Alternative Complement ◽  
Unknown Significance

Abstract BACKGROUND: Complement-mediated thrombotic microangiopathies (TMAs) are a subset of TMAs in which the thrombocytopenia, microangiopathic hemolytic anemia, and end organ damage are caused by mutations in genes encoding the alternative complement pathway. Numerous complement genes have been implicated in complement-mediated TMAs including complement factor H (CFH), CD46 (MCP), complement factor I (CFI), complement component 3 (C3), complement factor B (CFB), factor H related 5 (CFHR5), and thrombomodulin (THBD) among others. Genetic analysis typically yields a mutation in 60% of patients whose TMA is presumed to be mediated by complement dysregulation. However, the description of novel disease-associated variants may increase this proportion. METHODS: A retrospective study of patients with TMAs diagnosed between 2000 and 2014 was performed. TMA diagnosis was made based on thrombocytopenia and evidence of microangiopathic hemolytic anemia. Analysis was performed with Alamut¨ software with additional in silico prediction tools (SIFT, MutationTaster, and Polyphen) for classification of gene variants. Variants of unknown significance (VUS) and likely pathogenic variants were further assessed using several mutation databases, including HGMD, ClinVar, and Factor H database RESULTS: Of patients diagnosed with a TMA, genetic analysis was performed in only a 10% of patients. Of the 29 patients with genetic studies performed, mutations were identified in 18 patients (62%). The majority of the mutations had been described previously in the literature, but four novel variants were identified: three missense and one splice-site. The table below summarizes these variants as well as laboratory findings on presentation. These were two variants of CFH, one variant of CFHR5, and one variant of CFI. In silico modeling of these variants revealed two polymorphisms likely to be pathogenic, one polymorphism likely benign given the lack of predicted splicing changes, and one VUS. Table 1. Protein Mutation Classification Age Sex Hemoglobin (g/dL) Platelets (thousands) Creatinine (mg/dL) CFH c.245-10_245-9dup Likely benign 61 F 11.6 51 6.7 CFH c.476G>A, p.Ser159Asn Likely pathogenic 43 F 9.1 101 9.1 CFHR5 c.1412G>A p.Gly471Glu Likely pathogenic 30 F 9.8 129 4.9 CFI c.1190T>A p.Val397Glu Unknown significance 51 M 9.4 125 6.1 DISCUSSION: With therapy available to target the alternative complement pathway, genetic analysis to identify genetic variants capable of causing complement mediated TMAs is an essential part of the evaluation. This genetic data must be interpreted and correlated with functional analysis and clinical phenotype. The reporting of novel variants in clinical databases, with inclusion of relevant clinical findings, is necessary to accurately classify and verify variants as pathologic mutations or benign polymorphisms. The full understanding of this diverse disease requires a more complete understanding of its genetics. While complement pathway-directed therapies are available, their rational use requires thorough interpretation of laboratory data, including genetic analysis. Disclosures Murray: Mayo Clinic: Patents & Royalties: Patent Application Filed.

scholarly journals Generation and characterization of Ccdc28b mutant mice links the Bardet-Biedl associated gene with social behavioral phenotypes

2021 ◽  
Author(s):  
Matías Fabregat ◽  
Sofía Niño ◽  
Sabrina Pose ◽  
Magdalena Cárdenas-Rodríguez ◽  
Corrine Smolen ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Causal Link ◽  
Autism Spectrum ◽  
Phenotypic Characterization ◽  
Murine Models ◽  
Phenotypic Analysis ◽  
Behavioral Phenotypes ◽  
Mild Phenotype ◽  
Bardet Biedl Syndrome

CCDC28B (coiled-coil domain-containing protein 28B) was identified as a modifier in the ciliopathy Bardet-Biedl syndrome (BBS). Our previous work in cells and zebrafish showed that CCDC28B plays a role regulating cilia length in a mechanism that is not completely understood. Here we report the generation of a Ccdc28b mutant mouse using CRISPR/Cas9 (Ccdc28b mut). After confirming the depletion of Ccdc28b ;we performed a phenotypic characterization showing that Ccdc28b mut animals present a mild phenotype: i) do not present clear structural cilia affectation, although we did observe mild defects in cilia density and cilia length in some tissues, ii) reproduce normally, and iii) do not develop retinal degeneration or obesity, two hallmark features of reported BBS murine models. In contrast, Ccdc28b mut mice did show clear social interaction defects as well as stereotypical behaviors suggestive of autism spectrum disorder (ASD). This finding is indeed relevant regarding CCDC28B as a modifier of BBS since behavioral phenotypes have been documented in BBS. Importantly however, our data suggests a possible causal link between CCDC28B and ASD-like phenotypes that exceeds the context of BBS: filtering for rare deleterious variants, we found CCDC28B mutations in eight probands from the Simmons Simplex Collection cohort. Furthermore, a phenotypic analysis showed that CCDC28B mutation carriers present lower BMI and mild communication defects compared to a randomly selected sample of SSC probands. Thus, our results suggest that mutations in CCDC28B lead to mild autism-like features in mice and humans. Overall, this work reports a novel mouse model that will be key to continue evaluating genetic interactions in BBS, deciphering the contribution of CCDC28B to modulate the presentation of BBS phenotypes. In addition, our data underscores a novel link between CCDC28B and ASD-like phenotypes, providing a novel opportunity to further our understanding of the genetic, cellular, and molecular basis of ASD.

Cost‐effective molecular inversion probe‐based ABCA4 sequencing reveals deep‐intronic variants in Stargardt disease

2019 ◽  
Vol 40 (10) ◽  
pp. 1749-1759 ◽  
Author(s):  
Mubeen Khan ◽  
Stéphanie S. Cornelis ◽  
Muhammad Imran Khan ◽  
Duaa Elmelik ◽  
Eline Manders ◽  
...  
Keyword(s):  
Cost Effective ◽  
Stargardt Disease ◽  
Molecular Inversion Probe ◽  
Intronic Variants

scholarly journals A mild phenotype of sensorineural hearing loss and palmoplantar keratoderma caused by a novel GJB2 dominant mutation

2017 ◽  
Vol 37 (4) ◽  
pp. 308-311
Author(s):  
I. Stanghellini ◽  
E. Genovese ◽  
S. Palma ◽  
C. Falcinelli ◽  
L. Presutti ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Sensorineural Hearing Loss ◽  
In Silico ◽  
Sensorineural Hearing ◽  
Palmoplantar Keratoderma ◽  
Dominant Mutation ◽  
Mild Phenotype ◽  
Gene Gjb2

Le mutazioni dominanti del gene GJB2 sono causa di forme di sordità neurosensoriale sindromiche associate a manifestazioni cutanee palmo-plantari. In questo lavoro viene descritta la correlazione genotipo / fenotipo di una nuova mutazione nel gene GJB2 identificata in tre generazioni di una famiglia italiana (probando, madre e nonno) i cui membri presentano ipoacusia neurosensoriale associata a cheratoderma palmo-plantare ad insorgenza nell’età adulta. Una nuova mutazione di GJB2 (c.66G > T, p.Lys22Asn) allo stato eterozigote è stata identificata in tutti membri affetti. La segregazione della mutazione, la sua frequenza nella popolazione generale e predizioni in silico ne attribuiscono un ruolo patogenetico. La mutazione p.Lys22Asn GJB2 determina una forma di sordità dominante associata ad un’espressione variabile di cheratoderma palmo-plantare, rappresentando un modello di penetranza completa con effetto età-dipendente sul fenotipo.

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