ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.265C>T (p.Arg89Trp)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002760974 SCV003013763 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-06-02 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 89 of the POMGNT1 protein (p.Arg89Trp). This variant is present in population databases (rs143033200, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 RCV002731525 SCV003598803 uncertain significance Inborn genetic diseases 2021-12-16 criteria provided, single submitter clinical testing The c.265C>T (p.R89W) alteration is located in exon 4 (coding exon 3) of the POMGNT1 gene. This alteration results from a C to T substitution at nucleotide position 265, causing the arginine (R) at amino acid position 89 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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