ClinVar Miner

Submissions for variant NM_006348.5(COG5):c.81del (p.Glu27fs)

dbSNP: rs777937112
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778808 SCV000915188 uncertain significance COG5-congenital disorder of glycosylation 2018-11-20 criteria provided, single submitter clinical testing The COG5 c.174delA (p.Glu58AspfsTer12) variant results in a frameshift and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The p.Glu58AspfsTer12 variant is reported at a frequency of 0.000015 in the European (non-Finnish) population of the Exome Aggregation Consortium though this is based on one allele in a region of good sequence coverage, so the variant is presumed to be rare. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for congenital disorders of glycosylation. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Labcorp Genetics (formerly Invitae), Labcorp RCV000778808 SCV002206980 pathogenic COG5-congenital disorder of glycosylation 2021-12-02 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 631993). This variant has not been reported in the literature in individuals affected with COG5-related conditions. This variant is present in population databases (rs777937112, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Glu58Aspfs*12) in the COG5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COG5 are known to be pathogenic (PMID: 23228021).

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