ClinVar Miner

Submissions for variant NM_000046.5(ARSB):c.904G>A (p.Gly302Arg)

dbSNP: rs779378413
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova RCV000677605 SCV000803122 uncertain significance Mucopolysaccharidosis type 6 2018-01-01 criteria provided, single submitter curation Very low frequency in GnomAD(PM2)
Invitae RCV000677605 SCV002237685 pathogenic Mucopolysaccharidosis type 6 2023-11-24 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 302 of the ARSB protein (p.Gly302Arg). This variant is present in population databases (rs779378413, gnomAD 0.003%). This missense change has been observed in individual(s) with mucopolysaccharidosis type VI (PMID: 10206678, 17161971, 31009684). ClinVar contains an entry for this variant (Variation ID: 559822). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ARSB protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000677605 SCV002583244 likely pathogenic Mucopolysaccharidosis type 6 2022-08-08 criteria provided, single submitter clinical testing A homozygous missense variation in exon 5 of the ARSB gene that results in the amino acid substitution of Arginine for Glycine at codon 302 was detected. The observed variant c.904G>A (p.Gly302Arg) has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant are possibly damaging by Mutation Taster ,LRT ,MutPred ,FATHMM-MKL, MVP , EIGEN and SIFT. The reference codon is conserved across species. Therefore, the variant meets our criteria to be classified as pathogenic based on absence from controls and in silico prediction models.
Baylor Genetics RCV000677605 SCV004209948 pathogenic Mucopolysaccharidosis type 6 2023-02-06 criteria provided, single submitter clinical testing

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