All detected point variants were harmonized according to the canonical KDM6A transcript NM_021140.3 using MutationTaster2 (http://www.mutationtaster.org/). InterVar (http://wintervar.wglab.org/) was used to apply the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for variant interpretation.19 (link) Protein altering variants (PAVs) were analyzed by the Variant Effect Predictor (http://grch37.ensembl.org/Homo_sapiens/Tools/VEP) to obtain minor allele frequencies (MAFs) in controls, exon location, in silico predictions, previous reports, and evolutionary conservation. Alamut® Visual 2.11 (Interactive Biosoftware, France) and UniProtKB (https://www.uniprot.org/uniprot/O15550) were used for exon-skipping analyses and determining affected domains, respectively. PAVs with decreased in vitro demethylation were obtained from the work of Shpargel et al.20 (link) To analyze copy-number variants (CNVs) encompassing KDM6A, the University of California–Santa Cruz (UCSC) Genome Browser (GRCh37) was used.
Faundes V., Goh S., Akilapa R., Bezuidenhout H., Bjornsson H.T., Bradley L., Brady A.F., Brischoux-Boucher E., Brunner H., Bulk S., Canham N., Cody D., Dentici M.L., Digilio M.C., Elmslie F., Fry A.E., Gill H., Hurst J., Johnson D., Julia S., Lachlan K., Lebel R.R., Byler M., Gershon E., Lemire E., Gnazzo M., Lepri F.R., Marchese A., McEntagart M., McGaughran J., Mizuno S., Okamoto N., Rieubland C., Rodgers J., Sasaki E., Scalais E., Scurr I., Suri M., van der Burgt I., Matsumoto N., Miyake N., Benoit V., Lederer D, & Banka S. (2021). Clinical delineation, sex differences, and genotype–phenotype correlation in pathogenic KDM6A variants causing X-linked Kabuki syndrome type 2. Genetics in Medicine, 23(7), 1202-1210.
Corresponding Organization : Manchester University NHS Foundation Trust
Other organizations :
University of Chile, Northwick Park Hospital, Tygerberg Hospital, Stellenbosch University, University of Iceland, Johns Hopkins Medicine, Johns Hopkins University, Children's Health Ireland at Crumlin, Université de franche-comté, Radboud University Nijmegen, Radboud University Medical Center, Centre Hospitalier Universitaire de Liège, Liverpool Women's Hospital, University of Liverpool, Bambino Gesù Children's Hospital, St George's, University of London, University Hospital of Wales, Great Ormond Street Hospital, University College London, Sheffield Children's NHS Foundation Trust, Northern General Hospital, Princess Anne Hospital, SUNY Upstate Medical University, Yale New Haven Health System, Royal University Hospital, University of Saskatchewan, Centre Hospitalier Régional de Namur, Royal Brisbane and Women's Hospital, Aichi Developmental Disability Center, Osaka Women's and Children's Hospital, University Hospital of Bern, University of Bern, University Hospitals Bristol NHS Foundation Trust, Nottingham City Hospital, Yokohama City University, Institute of Pathology and Genetics
Harmonization of detected point variants according to the canonical KDM6A transcript NM_021140.3 using MutationTaster2
Application of the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for variant interpretation using InterVar
Analysis of protein altering variants (PAVs) using Variant Effect Predictor to obtain minor allele frequencies, exon location, in silico predictions, previous reports, and evolutionary conservation
Exon-skipping analyses using Alamut® Visual 2.11
Determining affected domains using UniProtKB
Analysis of copy-number variants (CNVs) encompassing KDM6A using the University of California–Santa Cruz (UCSC) Genome Browser (GRCh37)
dependent variables
Detected point variants
Protein altering variants (PAVs) with decreased in vitro demethylation (obtained from the work of Shpargel et al.)
Copy-number variants (CNVs) encompassing KDM6A
control variables
Canonical KDM6A transcript NM_021140.3
positive controls
Not specified
negative controls
Not specified
Annotations
Based on most similar protocols
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