Structural analysis of variants was performed using Pymol (The Pymol Molecular Graphics System, Version 2.5, Schrödinger, LLC). All Figures were generated using Pymol. Four in silico prediction algorithms were consulted: Sorting Intolerant from Tolerant, Metadome, MutationTaster, and Polymorphism Phenotyping v2.26 (link)–29 (link) All variants were manually analyzed using Alamut Visual v2.15 (Sophia Genetics). Variants were classified according to the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines.30 (link) Episign results were used to support classification according to criterium Pathogenic Strong 3 (PS3), and Pathogenic Moderate 1 (PM1) was applied for variants in the CxxC domain.
van Jaarsveld R.H., Reilly J., Cornips M.C., Hadders M.A., Agolini E., Ahimaz P., Anyane-Yeboa K., Audebert Bellanger S., van Binsbergen E., van den Boogaard M.J., Brischoux-Boucher E., Caylor R.C., Ciolfi A., van Essen T.A., Fontana P., Hopman S., Iascone M., Javier M.M., Kamsteeg E.J., Kerkhof J., Kido J., Kim H.G., Kleefstra T., Lonardo F., Lai A., Lev D., Levy M.A., Lewis M.E., Lichty A., Mannens M.M., Matsumoto N., Maya I., McConkey H., Megarbane A., Michaud V., Miele E., Niceta M., Novelli A., Onesimo R., Pfundt R., Popp B., Prijoles E., Relator R., Redon S., Rots D., Rouault K., Saida K., Schieving J., Tartaglia M., Tenconi R., Uguen K., Verbeek N., Walsh C.A., Yosovich K., Yuskaitis C.J., Zampino G., Sadikovic B., Alders M, & Oegema R. (2022). Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature. Genetics in medicine : official journal of the American College of Medical Genetics.
Other organizations :
University Medical Center Utrecht, Western University, Oncode Institute, Utrecht University, Bambino Gesù Children's Hospital, Columbia University, Centre Hospitalier Régional Universitaire de Brest, Université de franche-comté, Greenwood Genetic Center, Istituti di Ricovero e Cura a Carattere Scientifico, University Medical Center Groningen, University of Groningen, Ospedale Papa Giovanni XXIII, British Columbia Children's Hospital, University of British Columbia, Radboud University Nijmegen, Radboud University Medical Center, London Health Sciences Centre, Kumamoto University, Hamad bin Khalifa University, Boston Children's Hospital, Harvard University, Wolfson Medical Center, Amsterdam University Medical Centers, University of Amsterdam, Yokohama City University, Rabin Medical Center, Rafael Advanced Defense Systems (Israel), Tel Aviv University, Lebanese American University, Fondation Jérôme-Lejeune, Agostino Gemelli University Polyclinic, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Leipzig University, Inserm, Université de Bretagne Occidentale, University of Padua, Howard Hughes Medical Institute, Università Cattolica del Sacro Cuore
Four in silico prediction algorithms: Sorting Intolerant from Tolerant, Metadome, MutationTaster, and Polymorphism Phenotyping v2
Manual analysis using Alamut Visual v2.15
Variant classification according to the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines
Episign results used to support classification
dependent variables
Variant classification (pathogenic, benign, etc.)
control variables
Variants in the CxxC domain (Pathogenic Moderate 1 (PM1) applied)
positive controls
Not specified
negative controls
Not specified
Annotations
Based on most similar protocols
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As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
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