ClinVar Miner

Submissions for variant NM_020751.3(COG6):c.651_654del (p.Leu217fs)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002640805 SCV003529687 pathogenic Inborn genetic diseases 2021-10-05 criteria provided, single submitter clinical testing The c.651_654delACTT (p.L217Ffs*20) alteration, located in exon 7 (coding exon 7) of the COG6 gene, consists of a deletion of 4 nucleotides from position 651 to 654, causing a translational frameshift with a predicted alternate stop codon after 20 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic.
Invitae RCV003777577 SCV004568619 pathogenic COG6-ongenital disorder of glycosylation; Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome 2023-04-01 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: 2203823). This variant has not been reported in the literature in individuals affected with COG6-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu217Phefs*20) in the COG6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COG6 are known to be pathogenic (PMID: 26260076).

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