ClinVar Miner

Submissions for variant NM_001543.5(NDST1):c.883G>A (p.Val295Met)

gnomAD frequency: 0.00001  dbSNP: rs747017483
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489709 SCV000577582 uncertain significance not provided 2016-12-02 criteria provided, single submitter clinical testing The V295M variant in the NDST1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The V295M variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position that is conserved across species. However, the V295M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret V295M as a variant of uncertain significance.
Baylor Genetics RCV001328850 SCV001520071 uncertain significance Intellectual disability, autosomal recessive 46 2019-07-31 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV000489709 SCV002133538 uncertain significance not provided 2024-10-14 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 295 of the NDST1 protein (p.Val295Met). This variant is present in population databases (rs747017483, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NDST1-related conditions. ClinVar contains an entry for this variant (Variation ID: 426984). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt NDST1 protein function with a negative 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.
Revvity Omics, Revvity RCV001328850 SCV003813511 uncertain significance Intellectual disability, autosomal recessive 46 2021-12-15 criteria provided, single submitter clinical testing

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