ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1462C>G (p.Arg488Gly)

dbSNP: rs727504103
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000153762 SCV000203336 uncertain significance not provided 2013-12-17 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001850105 SCV002109881 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-07-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 488 of the POMGNT1 protein (p.Arg488Gly). This variant is present in population databases (rs727504103, gnomAD 0.0009%). 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: 167527). 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 expected to disrupt POMGNT1 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 RCV000153762 SCV002762524 uncertain significance not provided 2022-06-07 criteria provided, single submitter clinical testing Reported in an individual with total retinal detachment, peripheral retinal avascularity, and neovascularization of the right eye who harbored a second pathogenic POMGNT1 variant, however, segregation information was not provided (Khan et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24282183, 25390965)
Fulgent Genetics, Fulgent Genetics RCV002492577 SCV002784458 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3; Retinitis pigmentosa 76 2022-03-29 criteria provided, single submitter clinical testing

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