Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.
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http://dx.doi.org/10.1016/j.ymgme.2023.107668 | DOI Listing |
Front Genet
December 2024
Genomenon, Ann Arbor, MI, United States.
Accurate variant classification is critical for genetic diagnosis. Variants without clear classification, known as "variants of uncertain significance" (VUS), pose a significant diagnostic challenge. This study examines AlphaMissense performance in variant classification, specifically for VUS.
View Article and Find Full Text PDFGenet Med Open
January 2024
Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Purpose: Arginase 1 (ARG1) deficiency manifests with hyperargininemia and progressive neurological impairment. Recent estimates of birth prevalence using allele frequencies of variants do not sufficiently distinguish benign from pathogenic variants. Additionally, ongoing discussions of reproductive carrier screening for diseases such as ARG1 creates a need for improved understanding of variant classification.
View Article and Find Full Text PDFPurpose: Pulmonary arterial hypertension (PAH) is a rare disease that can be caused by pathogenic variants, most frequently in the bone morphogenetic protein receptor type 2 ( ) gene. We formed a ClinGen variant curation expert panel to devise guidelines for the clinical interpretation of variants identified in PAH patients.
Methods: The general ACMG/AMP variant classification criteria were refined for PAH and adapted to following ClinGen procedures.
J Pediatr Endocrinol Metab
December 2024
Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Women's and Children's Hospital/The Affiliated Women's and Children's Hospital of Chengdu Medical College, Chengdu, Sichuan, China.
Objectives: Mutations in the gene are the most common cause of nephrogenic diabetes insipidus(NDI). In-frame deletions of the gene are a rare variant that results in NDI. We report a novel variant of the p.
View Article and Find Full Text PDFNAR Genom Bioinform
December 2024
Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden.
The ACMG/AMP guidelines include five categories of which variants of uncertain significance (VUSs) have received increasing attention. Recently, Fowler and Rehm claimed that all or most VUSs could be reclassified as pathogenic or benign within few years. To test this claim, we collected validated benign, pathogenic, VUS and conflicting variants from ClinVar and LOVD and investigated differences at gene, protein, structure, and variant levels.
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