ClinVar Miner

Submissions for variant NM_000202.8(IDS):c.419-1G>A

dbSNP: rs1557339927
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000632182 SCV000753287 pathogenic Mucopolysaccharidosis, MPS-II 2021-08-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000632182 SCV001623170 likely pathogenic Mucopolysaccharidosis, MPS-II 2021-05-17 criteria provided, single submitter clinical testing Variant summary: IDS c.419-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' acceptor site. Four predict the variant creates an adjacent alternative canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 181712 control chromosomes. To our knowledge, no occurrence of c.419-1G>A in individuals affected with Mucopolysaccharidosis Type II (Hunter Syndrome) and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic based on the identification of another splice variant, c.419-1G>C that has been reported in a patient with Mucopolysaccharidosis Type II (Hunter Syndrome). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Genome-Nilou Lab RCV000632182 SCV002014480 pathogenic Mucopolysaccharidosis, MPS-II 2021-09-05 criteria provided, single submitter clinical testing

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