ClinVar Miner

Submissions for variant NM_002435.3(MPI):c.487+2del

gnomAD frequency: 0.00002  dbSNP: rs1057516550
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410117 SCV000485858 likely pathogenic MPI-congenital disorder of glycosylation 2016-02-22 criteria provided, single submitter clinical testing
Invitae RCV000410117 SCV001223738 likely pathogenic MPI-congenital disorder of glycosylation 2023-12-09 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 4 of the MPI 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 MPI are known to be pathogenic (PMID: 19862844). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with MPI-related conditions. ClinVar contains an entry for this variant (Variation ID: 370515). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV003221965 SCV003917410 pathogenic not provided 2023-04-01 criteria provided, single submitter clinical testing MPI: PVS1, PM2
PreventionGenetics, part of Exact Sciences RCV003401386 SCV004103507 uncertain significance MPI-related disorder 2023-01-24 criteria provided, single submitter clinical testing The MPI c.487+2delT variant is predicted to result in a deletion affecting a canonical splice site. To our knowledge, this variant has not been reported in the literature.This variant is reported in 0.0023% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/15-75185144-GT-G). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Baylor Genetics RCV000410117 SCV004195526 likely pathogenic MPI-congenital disorder of glycosylation 2023-07-12 criteria provided, single submitter clinical testing
Natera, Inc. RCV000410117 SCV002089782 likely pathogenic MPI-congenital disorder of glycosylation 2017-06-24 no assertion criteria provided clinical testing

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