ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.1408+1G>T

dbSNP: rs1060499680
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS RCV000449512 SCV000537764 likely pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2016-01-01 criteria provided, single submitter research
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001420190 SCV001622391 pathogenic Mucolipidosis type II 2021-04-20 criteria provided, single submitter clinical testing A homozygous 3’ splice site variation in intron 11 of the GNPTAB gene that affects the invariant AG acceptor splice site upstream of exon 12 was detected. The observed variant c.1408+1G>T has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant is damaging by MutationTaster, DANN and FATHMM. In summary, the variant meets our criteria to be classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000449512 SCV004580225 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2023-11-06 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 11 of the GNPTAB gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GNPTAB are known to be pathogenic (PMID: 19617216, 25107912). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with GNPTAB-related conditions (PMID: 32651481). ClinVar contains an entry for this variant (Variation ID: 397559). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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