ClinVar Miner

Submissions for variant NM_006412.4(AGPAT2):c.315G>T (p.Met105Ile) (rs746809573)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000389300 SCV000478817 uncertain significance Congenital generalized lipodystrophy type 1 2018-01-13 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.
GeneDx RCV000418715 SCV000529032 uncertain significance not provided 2016-06-21 criteria provided, single submitter clinical testing The M105I variant in the AGPAT2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The M105I variant was observed on 29/8598 (0.3%) alleles from individuals of East Asian background in the Exome Aggregation Consortium (ExAC) data set, indicating it may be a rare variant in this population. The M105I variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Methionine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret M105I as a variant of uncertain significance.
Invitae RCV000418715 SCV001128938 likely benign not provided 2018-12-31 criteria provided, single submitter clinical testing

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