ClinVar Miner

Submissions for variant NM_000528.4(MAN2B1):c.1822G>A (p.Glu608Lys) (rs145062583)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519702 SCV000620699 uncertain significance not specified 2017-09-21 criteria provided, single submitter clinical testing The E608K variant in the MAN2B1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 51/6614 alleles (0.77%) from individuals of Finnish background including one homozygous control individual, and 74/65,758 alleles (0.11%) from individuals of non-Finnish European background, in the ExAC dataset (Lek et al., 2016). The E608K variant 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 across species, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret E608K as a variant of uncertain significance.
Invitae RCV000969160 SCV001116656 likely benign Deficiency of alpha-mannosidase 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000969160 SCV001284405 uncertain significance Deficiency of alpha-mannosidase 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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