ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1759_1763del (p.Phe587fs)

dbSNP: rs1302430730
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001939655 SCV002236331 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2023-12-14 criteria provided, single submitter clinical testing This sequence change results in a frameshift in the POMGNT1 gene (p.Phe587Hisfs*98). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 74 amino acid(s) of the POMGNT1 protein and extend the protein by 23 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1455052). This variant disrupts a region of the POMGNT1 protein in which other variant(s) (p.Arg605His) have been determined to be pathogenic (PMID: 12849864, 21361872; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003464304 SCV004205967 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 2023-08-17 criteria provided, single submitter clinical testing

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