ClinVar Miner

Submissions for variant NM_005787.6(ALG3):c.349C>T (p.Arg117Ter)

gnomAD frequency: 0.00003  dbSNP: rs753238253
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clinical Genetics and Genomics, Karolinska University Hospital RCV001269547 SCV001449605 pathogenic not provided 2015-12-15 criteria provided, single submitter clinical testing
GeneDx RCV001269547 SCV003798890 uncertain significance not provided 2023-01-31 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge
Neuberg Centre For Genomic Medicine, NCGM RCV004584871 SCV005073903 likely pathogenic ALG3-congenital disorder of glycosylation criteria provided, single submitter clinical testing The stop gained c.349C>T (p.Arg117Ter) variant in the ALG3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is reported with the allele frequency (0.004%) in the gnomAD Exomes. It is submitted to ClinVar as Pathogenic/ Uncertain Significance. However, no details are available for independent assessment. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Loss of function variants have been previously reported to be disease causing. The nucleotide change c.349C>T in ALG3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Further studies are required to prove the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic.

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