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      Clinical and neuropathological phenotype associated with the novel V189I mutation in the prion protein gene

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          Abstract

          Prion diseases are neurodegenerative disorders which are caused by an accumulation of the abnormal, misfolded prion protein known as scrapie prion protein (PrP Sc). These disorders are unique as they occur as sporadic, genetic and acquired forms. Sporadic Creutzfeldt-Jakob Disease (CJD) is the most common human prion disease, accounting for approximately 85–90% of cases, whereas autosomal dominant genetic forms, due to mutations in the prion protein gene ( PRNP), account for 10–15% of cases. Genetic forms show a striking variability in their clinical and neuropathological picture and can sometimes mimic other neurodegenerative diseases.

          We report a novel PRNP mutation (V189I) in four CJD patients from three unrelated pedigrees. In three patients, the clinical features were typical for CJD and the diagnosis was pathologically confirmed, while the fourth patient presented with a complex phenotype including rapidly progressive dementia, behavioral abnormalities, ataxia and extrapyramidal features, and the diagnosis was probable CJD by current criteria, on the basis of PrP Sc detection in CSF by Real Time Quaking-Induced Conversion assay. In all the three patients with autopsy findings, the neuropathological analysis revealed diffuse synaptic type deposition of proteinase K-resistant prion protein (PrP res), and type 1 PrP res was identified in the brain by western blot analysis. So, the histopathological and biochemical profile associated with the V189I mutation was indistinguishable from the MM1/MV1 subtype of sporadic CJD.

          Our findings support a pathogenic role for the V189I PRNP variant, confirm the heterogeneity of the clinical phenotypes associated to PRNP mutations and highlight the importance of PrP Sc detection assays as diagnostic tools to unveil prion diseases presenting with atypical phenotypes.

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          The online version of this article (10.1186/s40478-018-0656-4) contains supplementary material, which is available to authorized users.

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          Prediction of protein stability changes for single-site mutations using support vector machines.

          Accurate prediction of protein stability changes resulting from single amino acid mutations is important for understanding protein structures and designing new proteins. We use support vector machines to predict protein stability changes for single amino acid mutations leveraging both sequence and structural information. We evaluate our approach using cross-validation methods on a large dataset of single amino acid mutations. When only the sign of the stability changes is considered, the predictive method achieves 84% accuracy-a significant improvement over previously published results. Moreover, the experimental results show that the prediction accuracy obtained using sequence alone is close to the accuracy obtained using tertiary structure information. Because our method can accurately predict protein stability changes using primary sequence information only, it is applicable to many situations where the tertiary structure is unknown, overcoming a major limitation of previous methods which require tertiary information. The web server for predictions of protein stability changes upon mutations (MUpro), software, and datasets are available at http://www.igb.uci.edu/servers/servers.html. 2005 Wiley-Liss, Inc.
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            Quantifying prion disease penetrance using large population control cohorts.

            More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.
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              Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity.

              We find that the degree of impairment of protein function by missense variants is predictable by comparative sequence analysis alone. The applicable range of impairment is not confined to binary predictions that distinguish normal from deleterious variants, but extends continuously from mild to severe effects. The accuracy of predictions is strongly dependent on sequence variation and is highest when diverse orthologs are available. High predictive accuracy is achieved by quantification of the physicochemical characteristics in each position of the protein, based on observed evolutionary variation. The strong relationship between physicochemical characteristics of a missense variant and impairment of protein function extends to human disease. By using four diverse proteins for which sufficient comparative sequence data are available, we show that grades of disease, or likelihood of developing cancer, correlate strongly with physicochemical constraint violation by causative amino acid variants.
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                Author and article information

                Contributors
                giuseppe.difede@istituto-besta.it
                Journal
                Acta Neuropathol Commun
                Acta Neuropathol Commun
                Acta Neuropathologica Communications
                BioMed Central (London )
                2051-5960
                3 January 2019
                3 January 2019
                2019
                : 7
                : 1
                Affiliations
                [1 ]ISNI 0000 0001 0707 5492, GRID grid.417894.7, Neurology V – Neuropathology Unit, , Fondazione IRCCS Istituto Neurologico Carlo Besta, ; Via Celoria 11, 20133 Milan, Italy
                [2 ]Centro Regionale Malattie da Prioni (DOMP), ASL ‘Città di Torino’, Turin, Italy
                [3 ]ISNI 0000 0001 0707 5492, GRID grid.417894.7, Neuroradiology Unit, , Fondazione IRCCS Istituto Neurologico Carlo Besta, ; Milan, Italy
                [4 ]ISNI 0000 0004 1784 7240, GRID grid.420421.1, Neurology Unit, Multimedica, ; Castellanza, Italy
                [5 ]ISNI 0000 0004 1760 0715, GRID grid.414962.c, Neurology Unit, , AO Ospedale Civile di Legnano, ; Legnano, Italy
                [6 ]Neurology Unit, Foundation IRCCS Centro s. Raffaele del Monte Tabor, Milan, Italy
                [7 ]Neurology Unit - ASST Cremona, Cremona, Italy
                [8 ]Neurology Unit, ASL Biella, Biella, Italy
                [9 ]ISNI 0000 0004 1756 8807, GRID grid.417728.f, Neurology Unit, , Humanitas Clinical Institute Rozzano, ; Milan, Italy
                [10 ]ISNI 0000 0004 1762 9868, GRID grid.5970.b, Laboratory of Prion Biology, Department of Neuroscience, , Scuola Internazionale Superiore di Studi Avanzati (SISSA), ; Trieste, Italy
                [11 ]Neurology Unit, Osp. Maggiore della Carità, Novara, Italy
                [12 ]Neurology Unit, ASL Novara, Ospedale di Borgomanero, Borgomanero, Italy
                [13 ]ISNI 0000 0000 9120 6856, GRID grid.416651.1, Department of Neuroscience, , Istituto Superiore di Sanità, ; Rome, Italy
                [14 ]ISNI 0000 0001 0707 5492, GRID grid.417894.7, Scientific Directorate, , Fondazione IRCCS Istituto Neurologico Carlo Besta, ; Milan, Italy
                Author information
                http://orcid.org/0000-0003-3537-6713
                Article
                656
                10.1186/s40478-018-0656-4
                6317215
                30606247
                cb36b2c1-fe1f-4bf3-9691-cdd9ae0557e9
                © The Author(s). 2019

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 30 October 2018
                : 21 December 2018
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100003196, Ministero della Salute;
                Award ID: -
                Award ID: -
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100013278, EU Joint Programme – Neurodegenerative Disease Research;
                Award ID: -
                Categories
                Research
                Custom metadata
                © The Author(s) 2019

                creutzfeldt-jakob disease,prnp,prion,v189i,cjd,prp,dementia,mutation
                creutzfeldt-jakob disease, prnp, prion, v189i, cjd, prp, dementia, mutation

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