ClinVar Miner

Submissions for variant NM_032806.6(POMGNT2):c.161C>T (p.Pro54Leu)

gnomAD frequency: 0.00006  dbSNP: rs748576103
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000813778 SCV000954150 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 54 of the POMGNT2 protein (p.Pro54Leu). This variant is present in population databases (rs748576103, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with POMGNT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 657212). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POMGNT2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV001796246 SCV002032416 uncertain significance not provided 2021-06-07 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 27535533)
Revvity Omics, Revvity RCV001796246 SCV003811785 uncertain significance not provided 2023-12-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV004958141 SCV005481221 uncertain significance Inborn genetic diseases 2024-11-26 criteria provided, single submitter clinical testing The c.161C>T (p.P54L) alteration is located in exon 2 (coding exon 1) of the POMGNT2 gene. This alteration results from a C to T substitution at nucleotide position 161, causing the proline (P) at amino acid position 54 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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