ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.2715+2T>G

gnomAD frequency: 0.00002  dbSNP: rs281865001
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666563 SCV000790873 likely pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2017-04-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000666563 SCV000893261 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000666563 SCV001398075 pathogenic Mucolipidosis type II; Pseudo-Hurler polydystrophy 2023-08-28 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 13 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 present in population databases (rs281865001, gnomAD 0.0009%). Disruption of this splice site has been observed in individuals with mucolipidosis or suspected mucolipidosis (PMID: 16116615, 21549105, 27662472, 29704188). ClinVar contains an entry for this variant (Variation ID: 39059). 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.
GeneDx RCV001588838 SCV001827129 pathogenic not provided 2019-10-03 criteria provided, single submitter clinical testing Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 19617216, 29704188, 20301728, 25525159)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001804753 SCV002050961 pathogenic Mucolipidosis 2021-12-02 criteria provided, single submitter clinical testing Variant summary: GNPTAB c.2715+2T>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5` splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 251262 control chromosomes (gnomAD). c.2715+2T>G has been reported in the literature in individuals affected with Mucolipidosis III (Cathey_2010, Oussoren_2018). 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. Four ClinVar submitters (evaluation after 2014) cite the variant as pathogenic (n=2) and likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic.
GeneReviews RCV000032324 SCV000055969 not provided Pseudo-Hurler polydystrophy no assertion provided literature only

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.