ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.2693dup (p.Tyr899fs)

dbSNP: rs281864999
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001175514 SCV001339119 pathogenic Mucolipidosis 2020-03-30 criteria provided, single submitter clinical testing Variant summary: GNPTAB c.2693dupA (p.Tyr899ValfsX21) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 250934 control chromosomes. c.2693dupA has been reported in the literature in individuals affected with Mucolipidosis and subsequently cited by others (example, Cathey_2010, Wang_2018, Velho_2019 and Yu_2019). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV001230245 SCV001402719 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2022-10-12 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 39057). For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with mucolipidosis II (PMID: 19617216). This variant is present in population databases (rs281864999, gnomAD 0.0008%). This sequence change creates a premature translational stop signal (p.Tyr899Valfs*21) in the GNPTAB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNPTAB are known to be pathogenic (PMID: 19617216, 25107912).
GeneReviews RCV000032322 SCV000055967 not provided Mucolipidosis type II no assertion provided literature only

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