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      Expanding the β-III Spectrin-Associated Phenotypes toward Non-Progressive Congenital Ataxias with Neurodegeneration

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          Abstract

          (1) Background: A non-progressive congenital ataxia (NPCA) phenotype caused by β-III spectrin ( SPTBN2) mutations has emerged, mimicking spinocerebellar ataxia, autosomal recessive type 14 (SCAR14). The pattern of inheritance, however, resembles that of autosomal dominant classical spinocerebellar ataxia type 5 (SCA5). (2) Methods: In-depth phenotyping of two boys studied by a customized gene panel. Candidate variants were sought by structural modeling and protein expression. An extensive review of the literature was conducted in order to better characterize the SPTBN2-associated NPCA. (3) Results: Patients exhibited an NPCA with hypotonia, developmental delay, cerebellar syndrome, and cognitive deficits. Both probands presented with progressive global cerebellar volume loss in consecutive cerebral magnetic resonance imaging studies, characterized by decreasing midsagittal vermis relative diameter measurements. Cortical hyperintensities were observed on fluid-attenuated inversion recovery (FLAIR) images, suggesting a neurodegenerative process. Each patient carried a novel de novo SPTBN2 substitution: c.193A > G (p.K65E) or c.764A > G (p.D255G). Modeling and protein expression revealed that both mutations might be deleterious. (4) Conclusions: The reported findings contribute to a better understanding of the SPTBN2-associated phenotype. The mutations may preclude proper structural organization of the actin spectrin-based membrane skeleton, which, in turn, is responsible for the underlying disease mechanism.

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          Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

          The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1 In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next generation sequencing. By adopting and leveraging next generation sequencing, clinical laboratories are now performing an ever increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes and epigenetic assays for genetic disorders. By virtue of increased complexity, this paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP and CAP stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories including genotyping, single genes, panels, exomes and genomes. This report recommends the use of specific standard terminology: ‘pathogenic’, ‘likely pathogenic’, ‘uncertain significance’, ‘likely benign’, and ‘benign’ to describe variants identified in Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a CLIA-approved laboratory with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or equivalent.
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            <i>Coot</i> : model-building tools for molecular graphics

            Acta Crystallographica Section D Biological Crystallography, 60(12), 2126-2132
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              Comparative Protein Structure Modeling Using MODELLER.

              Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                02 March 2021
                March 2021
                : 22
                : 5
                : 2505
                Affiliations
                [1 ]Unit of Rare Neurodegenerative Diseases, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain; psancho91@ 123456hotmail.com (P.S.); dandres@ 123456cipf.es (A.A.-B.); mdmartinez@ 123456cipf.es (D.M.-R.); asanchez@ 123456cipf.es (A.S.-M.); vlupo@ 123456cipf.es (V.L.)
                [2 ]Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
                [3 ]Pediatric Neurology Unit, Department of Pediatrics, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain; nerea.gorria.redondo@ 123456navarra.es (N.G.-R.); yoldi.petri@ 123456navarra.es (M.E.Y.-P.)
                [4 ]Clinical Psychology, Department of Psychiatry, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain; katia.llano.ordonez@ 123456navarra.es
                [5 ]Pediatric Neurology Unit, Wolfson Medical Center, Holon, Sackler School of Medicine, Tel-Aviv University, 69978 Tel-Aviv, Israel; luba.blumkin@ 123456gmail.com
                [6 ]Pediatric Imaging Unit, Department of Radiology, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain; pablo.rodriguez.delafuente@ 123456navarra.es
                [7 ]CELLS-ALBA Synchrotron Light Source, 08290 Barcelona, Spain; fgil@ 123456cells.es
                [8 ]Molecular Oncology Laboratory, Hospital Arnau de Vilanova, 46015 Valencia, Spain; malefermu67@ 123456gmail.com
                [9 ]Pediatric Neurology Research Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; belen.perez@ 123456vhir.org
                [10 ]Navarrabiomed-Fundación Miguel Servet, 31008 Pamplona, Spain
                Author notes
                [* ]Correspondence: cespinos@ 123456cipf.es (C.E.); saguilera@ 123456navarra.es (S.A.-A.); Tel.: +34-963-289-680 (C.E.); +34-848-422-563 (S.A.-A.)
                [†]

                P.S. and A.A.-B. contributed equally.

                [‡]

                C.E. and S.A.-A. contributed equally.

                Author information
                https://orcid.org/0000-0003-4435-1809
                Article
                ijms-22-02505
                10.3390/ijms22052505
                7958857
                33801522
                6c2085a3-1098-41da-acc5-bebebb866310
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 29 January 2021
                : 25 February 2021
                Categories
                Article

                Molecular biology
                sptbn2 gene,β-iii spectrin,non-progressive congenital ataxia,neurodegeneration

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