ClinVar Miner

Submissions for variant NM_000203.5(IDUA):c.1487C>T (p.Pro496Leu)

gnomAD frequency: 0.00003  dbSNP: rs772416503
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666799 SCV000791155 likely pathogenic Hurler syndrome 2017-05-01 criteria provided, single submitter clinical testing
GeneDx RCV001756126 SCV001986004 uncertain significance not provided 2019-05-09 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 7550232)
Revvity Omics, Revvity RCV001756126 SCV002016666 likely pathogenic not provided 2023-12-14 criteria provided, single submitter clinical testing
Invitae RCV002530697 SCV003522990 pathogenic Mucopolysaccharidosis type 1 2023-12-20 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 496 of the IDUA protein (p.Pro496Leu). This variant is present in population databases (no rsID available, gnomAD 0.007%). This missense change has been observed in individuals with mucopolysaccharidosis type I (PMID: 7550232, 11735025). ClinVar contains an entry for this variant (Variation ID: 551675). 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 IDUA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects IDUA function (PMID: 7550232). This variant disrupts the p.Pro496 amino acid residue in IDUA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11735025, 21394825, 27520059). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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