ClinVar Miner

Submissions for variant NM_000202.8(IDS):c.1477C>T (p.Arg493Cys)

gnomAD frequency: 0.00001  dbSNP: rs782190885
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001901601 SCV002172050 likely benign Mucopolysaccharidosis, MPS-II 2023-07-10 criteria provided, single submitter clinical testing
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli RCV001901601 SCV002577692 likely pathogenic Mucopolysaccharidosis, MPS-II 2022-10-04 criteria provided, single submitter clinical testing PM1;PM2_supporting;PM5;PP3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004782821 SCV005395264 uncertain significance not specified 2024-09-20 criteria provided, single submitter clinical testing Variant summary: IDS c.1477C>T (p.Arg493Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 7.4e-06 in 1209710 control chromosomes, including 3 hemizygotes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1477C>T has been reported in the literature in an individual without reported sex or genotype affected with iduronate-2-sulfatase enzyme pseudodeficiency without Mucopolysaccharidosis Type II phenotype by age 3 years (e.g. Burton_2023) and in a hemizygous male affected with intellectual disability and/or global developmental delay (e.g. Spataro_2023). These reports do not provide unequivocal conclusions about association of the variant with Mucopolysaccharidosis Type II (Hunter Syndrome). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 36907694, 36980980). ClinVar contains an entry for this variant (Variation ID: 1404345). Based on the evidence outlined above, the variant was classified as uncertain significance.

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