ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.358C>G (p.Leu120Val)

gnomAD frequency: 0.00001  dbSNP: rs373016708
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000593833 SCV000708468 uncertain significance not provided 2017-05-08 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000593833 SCV001475412 uncertain significance not provided 2019-11-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001296019 SCV001484973 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-08-10 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 120 of the POMGNT1 protein (p.Leu120Val). This variant is present in population databases (rs373016708, gnomAD 0.002%). 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: 501934). 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 POMGNT1 protein function. This variant disrupts the p.Leu120 amino acid residue in POMGNT1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27391550, 31872526). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.

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