Total submissions: 2
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Gene |
RCV000489223 | SCV000576832 | likely pathogenic | not provided | 2017-04-18 | criteria provided, single submitter | clinical testing | The c.20delT variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.20delT variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The deletion causes a frameshift starting with codon Valine 7, changes this amino acid to a Glycine residue and creates a premature Stop codon at position 24 of the new reading frame, denoted p.Val7GlyfsX24. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we interpret this variant as likely pathogenic. |
| Labcorp Genetics |
RCV002526017 | SCV003484284 | pathogenic | Glycogen storage disease type X | 2024-06-10 | criteria provided, single submitter | clinical testing | This sequence change creates a premature translational stop signal (p.Val7Glyfs*24) in the PGAM2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PGAM2 are known to be pathogenic (PMID: 8447317, 19273759). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PGAM2-related conditions. ClinVar contains an entry for this variant (Variation ID: 426405). For these reasons, this variant has been classified as Pathogenic. |