ClinVar Miner

Submissions for variant NM_032806.6(POMGNT2):c.758C>T (p.Pro253Leu)

gnomAD frequency: 0.00001  dbSNP: rs374042455
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000656413 SCV000778421 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 2017-04-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000656413 SCV003525437 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 2024-01-19 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 253 of the POMGNT2 protein (p.Pro253Leu). This variant is present in population databases (rs374042455, gnomAD 0.006%). This missense change has been observed in individual(s) with muscular dystrophy-dystroglycanopathy (PMID: 27066570). ClinVar contains an entry for this variant (Variation ID: 545449). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on POMGNT2 protein function. Experimental studies have shown that this missense change affects POMGNT2 function (PMID: 27066570). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000684835 SCV000812295 pathogenic Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8 2018-10-01 no assertion criteria provided literature only

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