ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.1581del (p.Cys528fs)

dbSNP: rs36007394
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Total submissions: 5
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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 RCV000031968 SCV000699473 pathogenic Mucolipidosis type II 2016-08-25 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.1581delC (p.Cys528Valfs) variant results in a premature termination codon, predicted to cause a truncated or absent GNPTAB protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 26/121412 (1/4670), which does not exceed the estimated maximal expected allele frequency for a pathogenic GNPTAB variant of 1/447. The variant of interest has been reported in multiple affected individuals as homozygotes and compound hetereozygotes. In addition, GeneReviews cites the variant as "pathogenic." Therefore, the variant of interest has been classified as Pathogenic.
Counsyl RCV000669422 SCV000794172 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2017-09-18 criteria provided, single submitter clinical testing
Invitae RCV000669422 SCV002123116 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2021-08-14 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individual(s) with GNPTAB-related conditions (PMID: 16465621, 19617216, 19659762). This variant is also known as c.1744delC, p.Cys528fs*546. ClinVar contains an entry for this variant (Variation ID: 38414). This variant is present in population databases (rs775700652, ExAC 0.3%). This sequence change creates a premature translational stop signal (p.Cys528Valfs*19) 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 RCV000031968 SCV000054661 pathologic Mucolipidosis type II 2012-05-10 no assertion criteria provided curation Converted during submission to Pathogenic.
Natera, Inc. RCV000031968 SCV001458981 pathogenic Mucolipidosis type II 2020-09-16 no assertion criteria provided clinical testing

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