ClinVar Miner

Submissions for variant NM_002435.3(MPI):c.488-1G>C

gnomAD frequency: 0.00001  dbSNP: rs759579169
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000412150 SCV000487168 likely pathogenic MPI-CDG 2016-10-17 criteria provided, single submitter clinical testing
Invitae RCV000412150 SCV001581386 pathogenic MPI-CDG 2021-07-22 criteria provided, single submitter clinical testing This sequence change affects an acceptor 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 (rs759579169, ExAC 0.001%). Disruption of this splice site has been observed in individual(s) with MPI-congenital disorder of glycosylation (PMID: 10980531). This variant is also known as IVS4-1G>C. ClinVar contains an entry for this variant (Variation ID: 371556). 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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