ClinVar Miner

Submissions for variant NM_001099922.3(ALG13):c.1747A>G (p.Ile583Val) (rs377397506)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000498678 SCV000590312 uncertain significance not provided 2017-06-07 criteria provided, single submitter clinical testing A variant of unknown significance has been identified in the ALG13 gene. The c.1747 A>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1747 A>G variant is observed in 4/7863 (0.05%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In silico splice prediction models are inconsistent in their predictions as to whether or not c.1747 A>G may reduce the quality of the natural splice acceptor site for intron 15, which may supplant the and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. If c.1747 A>G does not alter splicing, it will result in the I583V missense change. The I583V 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 Isoleucine are tolerated across species and in silico analysis predicts this variant likely does not alter the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000650342 SCV000772185 likely benign Epileptic encephalopathy, early infantile, 36 2019-12-31 criteria provided, single submitter clinical testing

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