ClinVar Miner

Submissions for variant NM_152490.5(B3GALNT2):c.979G>A (p.Asp327Asn)

gnomAD frequency: 0.00004  dbSNP: rs753340395
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001854841 SCV002248425 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2023-12-28 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 327 of the B3GALNT2 protein (p.Asp327Asn). This variant is present in population databases (rs753340395, gnomAD 0.004%). This missense change has been observed in individual(s) with B3GALNT2-related conditions (PMID: 24084573, 25326637, 29273094, 33290285). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 242531). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on B3GALNT2 protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Revvity Omics, Revvity RCV001854841 SCV003829700 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2021-09-03 criteria provided, single submitter clinical testing
GeneDx RCV004591091 SCV005081272 pathogenic not provided 2024-05-23 criteria provided, single submitter clinical testing Not observed at a 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: 29273094, 25326637, 24084573, 29302074, 31209396, 33290285)

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