ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.287G>C (p.Arg96Pro)

gnomAD frequency: 0.00003  dbSNP: rs200227264
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522693 SCV000618897 uncertain significance not provided 2017-06-30 criteria provided, single submitter clinical testing The R96P variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R96P ariant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function.
Labcorp Genetics (formerly Invitae), Labcorp RCV001240358 SCV001413294 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-08-02 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 96 of the POMGNT1 protein (p.Arg96Pro). This variant is present in population databases (rs200227264, gnomAD 0.004%). 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: 450326). 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. 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.
Ambry Genetics RCV002525167 SCV003713801 uncertain significance Inborn genetic diseases 2024-07-17 criteria provided, single submitter clinical testing The c.287G>C (p.R96P) alteration is located in exon 4 (coding exon 3) of the POMGNT1 gene. This alteration results from a G to C substitution at nucleotide position 287, causing the arginine (R) at amino acid position 96 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV000522693 SCV003811768 uncertain significance not provided 2019-01-23 criteria provided, single submitter clinical testing
Natera, Inc. RCV001834691 SCV002090233 uncertain significance Muscle eye brain disease 2019-10-28 no assertion criteria provided clinical testing

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