ClinVar Miner

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

gnomAD frequency: 0.00001  dbSNP: rs142065232
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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 RCV000032337 SCV000699481 pathogenic Mucolipidosis type II 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.
Invitae RCV001044478 SCV001208277 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2023-08-11 criteria provided, single submitter clinical testing This premature translational stop signal has been observed in individual(s) with mucolipidosis II (PMID: 19617216). This sequence change creates a premature translational stop signal (p.Leu1137*) 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). This variant is present in population databases (rs142065232, gnomAD 0.02%). ClinVar contains an entry for this variant (Variation ID: 39071). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV003137550 SCV003828647 likely pathogenic not provided 2022-03-30 criteria provided, single submitter clinical testing
GeneReviews RCV000032337 SCV000055982 not provided Mucolipidosis type II no assertion provided literature only
Counsyl RCV000983987 SCV000797058 likely pathogenic Pseudo-Hurler polydystrophy 2018-01-10 no assertion criteria provided clinical testing

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