ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.1906dup (p.Arg636fs)

dbSNP: rs747789493
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000174596 SCV000225918 pathogenic not provided 2014-05-20 criteria provided, single submitter clinical testing
Counsyl RCV000669334 SCV000794078 likely pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2017-09-08 criteria provided, single submitter clinical testing
GeneDx RCV000174596 SCV001169045 pathogenic not provided 2019-01-24 criteria provided, single submitter clinical testing The c.1906dupA variant in the GNPTAB gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. However, it is reported as pathogenic or likely pathogenic in ClinVar by different clinical laboratories, but additional evidence is not available (ClinVar SCV000225918.3, SCV000794078.1; Landrum et al., 2016). The c.1906dupA variant causes a frameshift starting with codon Arginine 636, changes this amino acid to a Lysine residue, and creates a premature Stop codon at position 19 of the new reading frame, denoted p.Arg636LysfsX19. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1906dupA variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.1906dupA as a pathogenic variant.
Invitae RCV000669334 SCV001588692 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2022-10-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg636Lysfs*19) 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 (rs747789493, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with mucolipidosis (PMID: 30882951). ClinVar contains an entry for this variant (Variation ID: 194265). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity Omics RCV000174596 SCV003828636 likely pathogenic not provided 2022-06-21 criteria provided, single submitter clinical testing

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