ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.3410T>A (p.Leu1137Ter) (rs142065232)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672006 SCV000797058 likely pathogenic I cell disease; Pseudo-Hurler polydystrophy 2018-01-10 criteria provided, single submitter clinical testing
GeneReviews RCV000032337 SCV000055982 pathologic I cell disease 2012-05-10 no assertion criteria provided curation Converted during submission to Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000032337 SCV000699481 pathogenic I cell disease 2016-07-08 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.3410T>A (p.Leu1137X) 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. Truncations downstream of this position have been classified as pathogenic by reputable sources (e.g.c.3565C>T/p.Arg1189Ter, c.3613C>T/p.Arg1205Ter). One in silico tool predicts a damaging outcome for this variant. This variant has been reported in at least two ML II patients and was found in 2/120516 control chromosomes at a frequency of 0.0000166, which does not exceed the estimated maximal expected allele frequency of a pathogenic GNPTAB variant (0.0022361). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

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