ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.2545_2549GAAAA[1] (p.Lys850fs) (rs281864996)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Division,Centre for DNA Fingerprinting and Diagnostics RCV000449538 SCV000537770 likely pathogenic I cell disease; Pseudo-Hurler polydystrophy 2016-01-01 criteria provided, single submitter research
Counsyl RCV000449538 SCV000794572 likely pathogenic I cell disease; Pseudo-Hurler polydystrophy 2017-10-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780319 SCV000917486 likely pathogenic Mucolipidosis 2018-07-02 criteria provided, single submitter clinical testing Variant summary: GNPTAB c.2550_2554delGAAAA (p.Lys850AsnfsX10) 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 (eg. c.2693delA, p.Lys898fsX13; c.3091C>T, p.Arg1031X; c.3410T>A, p.Leu1137X). The variant allele was found at a frequency of 3.3e-05 in 121398 control chromosomes (ExAC). The variant, c.2550_2554delGAAAA, has been reported in the literature in one individual affected with Mucolipidosis type 2 (Tappino_2009). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
GeneReviews RCV000032320 SCV000055964 pathologic I cell disease 2012-05-10 no assertion criteria provided curation Converted during submission to Pathogenic.

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