ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1438C>T (p.Arg480Trp)

gnomAD frequency: 0.00001  dbSNP: rs1011150724
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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) RCV000731690 SCV000859537 uncertain significance not provided 2018-02-08 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV001262482 SCV001440378 uncertain significance Retinitis pigmentosa 76 2020-08-07 criteria provided, single submitter clinical testing Criteria applied: PM2,PP3
Labcorp Genetics (formerly Invitae), Labcorp RCV001868965 SCV002172496 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2024-02-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 480 of the POMGNT1 protein (p.Arg480Trp). This variant is present in population databases (no rsID available, gnomAD 0.003%). 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: 595996). 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 with a positive predictive value of 80%. 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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