ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.3091C>T (p.Arg1031Ter) (rs281865009)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667295 SCV000791725 pathogenic I cell disease; Pseudo-Hurler polydystrophy 2017-05-22 criteria provided, single submitter clinical testing
GeneReviews RCV000032330 SCV000055975 pathologic I cell disease 2012-05-10 no assertion criteria provided curation Converted during submission to Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000780316 SCV000917483 pathogenic Mucolipidosis 2017-09-08 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.3091C>T (p.Arg1031X) 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 our laboratory (e.g. c.3410T>A (p.Leu1137X) and c.3503_3504delTC (p.Leu1168fsX5)). This variant was found in 1/246136 control chromosomes at a frequency of 0.0000041, which does not exceed the estimated maximal expected allele frequency of a pathogenic GNPTAB variant (0.0022361). Multiple publications have cited the variant in compound heterozygote ML2 individuals. A reputable database, GeneReviews, classifies the variant as "pathogenic." Taken together, this variant is classified as pathogenic.

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