ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.99del (p.Ala34fs) (rs1408113895)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669032 SCV000793730 likely pathogenic I cell disease; Pseudo-Hurler polydystrophy 2017-08-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590274 SCV000699484 likely pathogenic I cell disease 2016-01-05 criteria provided, single submitter clinical testing Variant summary: This c.99delC variant causes a frameshift, which alters the proteins amino acid sequence beginning at position 34 and leads to a premature termination codon 48 amino acid downstream. It is predicted to cause a truncated or absent protein product. Mutation taster predicts this variant to be disease-causing. The variant was not observed in the large and broad cohorts of the ExAC project or ESP. The variant of interest has not, to our knowledge, been reported in affected individuals via publications, clinical laboratories, or databases; nor evaluated for functional impact by in vivo/vitro studies. Truncations downstream of this position have been listed as disease variants by HGMD and ClinVar (e.g. Gln104Term, Gln278Term, etc). Considering all, this variant has been classified as Likely Pathogenic until additional information becomes available.
Invitae RCV000669032 SCV000954383 pathogenic I cell disease; Pseudo-Hurler polydystrophy 2018-09-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ala34Profs*49) in the GNPTAB gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with Mucolipidosis type II (PMID: 27662472). ClinVar contains an entry for this variant (Variation ID: 496456). Loss-of-function variants in GNPTAB are known to be pathogenic (PMID: 19617216, 25107912). For these reasons, this variant has been classified as Pathogenic.

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