ClinVar Miner

Submissions for variant NM_002435.3(MPI):c.305C>T (p.Ser102Leu)

gnomAD frequency: 0.00003  dbSNP: rs104894494
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV000015420 SCV002799752 likely pathogenic MPI-congenital disorder of glycosylation 2021-07-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000015420 SCV003845108 likely pathogenic MPI-congenital disorder of glycosylation 2023-02-21 criteria provided, single submitter clinical testing Variant summary: MPI c.305C>T (p.Ser102Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251468 control chromosomes (gnomAD). c.305C>T has been reported in the literature in at least compound heterozygous individual affected with Congenital Disorder Of Glycosylation Type 1B (Jaeken_1998). These data do not allow any conclusion about variant significance. When the variant was introduced into the mouse ortholog of the MPI gene and expressed in an mpi-null yeast strain, the variant showed 0.6% residual activity (He_2014), indicating loss of function. One ClinVar submitter has assessed the variant since 2014: the variant was classified as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV000015420 SCV004193273 likely pathogenic MPI-congenital disorder of glycosylation 2024-02-12 criteria provided, single submitter clinical testing
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV000015420 SCV005051867 pathogenic MPI-congenital disorder of glycosylation 2024-02-01 criteria provided, single submitter curation
OMIM RCV000015420 SCV000035683 pathogenic MPI-congenital disorder of glycosylation 1998-06-01 no assertion criteria provided literature only

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