ClinVar Miner

Submissions for variant NM_000528.4(MAN2B1):c.2402G>A (p.Gly801Asp)

dbSNP: rs864621994
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000206924 SCV000795754 uncertain significance Deficiency of alpha-mannosidase 2017-11-22 criteria provided, single submitter clinical testing
GeneDx RCV003318559 SCV004022940 likely pathogenic not provided 2023-01-25 criteria provided, single submitter clinical testing Not observed at 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: 19958498, 15712269)
Labcorp Genetics (formerly Invitae), Labcorp RCV000206924 SCV004297891 likely pathogenic Deficiency of alpha-mannosidase 2024-10-24 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 801 of the MAN2B1 protein (p.Gly801Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with alpha-mannosidosis (PMID: 15712269). 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: 208285). 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) has been performed 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 MAN2B1 protein function. Experimental studies have shown that this missense change affects MAN2B1 function (PMID: 15712269). 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.
ClinVar Staff, National Center for Biotechnology Information (NCBI) RCV000206924 SCV000243995 uncertain significance Deficiency of alpha-mannosidase 2012-06-07 no assertion criteria provided literature only

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