ClinVar Miner

Submissions for variant NM_024105.4(ALG12):c.1239G>C (p.Arg413Ser)

gnomAD frequency: 0.00019  dbSNP: rs142027212
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001931484 SCV002207260 uncertain significance ALG12-congenital disorder of glycosylation 2022-07-25 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 413 of the ALG12 protein (p.Arg413Ser). This variant is present in population databases (rs142027212, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with ALG12-related conditions. ClinVar contains an entry for this variant (Variation ID: 1430380). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003387537 SCV004099102 uncertain significance not provided 2023-09-05 criteria provided, single submitter clinical testing PM2, BP4
Ambry Genetics RCV004041947 SCV004889354 uncertain significance Inborn genetic diseases 2023-12-28 criteria provided, single submitter clinical testing The c.1239G>C (p.R413S) alteration is located in exon 10 (coding exon 9) of the ALG12 gene. This alteration results from a G to C substitution at nucleotide position 1239, causing the arginine (R) at amino acid position 413 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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