ClinVar Miner

Submissions for variant NM_001099922.3(ALG13):c.3278C>T (p.Ser1093Phe)

gnomAD frequency: 0.00001  dbSNP: rs1465704791
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000602129 SCV000718828 likely benign not specified 2017-07-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001305780 SCV001495127 uncertain significance Developmental and epileptic encephalopathy, 36 2022-08-01 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 1093 of the ALG13 protein (p.Ser1093Phe). This variant is present in population databases (no rsID available, gnomAD 0.004%). This missense change has been observed in individuals with clinical features of early onset epileptic encephalopathy (Invitae). ClinVar contains an entry for this variant (Variation ID: 509152). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002325153 SCV002611081 uncertain significance Inborn genetic diseases 2019-03-22 criteria provided, single submitter clinical testing The p.S1093F variant (also known as c.3278C>T), located in coding exon 27 of the ALG13 gene, results from a C to T substitution at nucleotide position 3278. The serine at codon 1093 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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