Total submissions: 2
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| 3billion | RCV002250853 | SCV002520997 | likely pathogenic | Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3 | 2022-05-22 | criteria provided, single submitter | clinical testing | Different pathogenic amino acid change has been reported with supporting evidence at the same codon (ClinVar ID: HGMD-PMID:18575922). In silico prediction tools and conservation analysis predicted that this variant was probably damaging to the protein structure/function (REVEL: 0.863>=0.6, 3CNET: 0.994>=0.75). (PP3_P). A missense variant is a common mechanism associated with Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3, and the rate of benign missense variants is relatively low. It is absent from the gnomAD v2.1.1 dataset. Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. |
| Invitae | RCV003094071 | SCV003441595 | pathogenic | not provided | 2022-08-16 | criteria provided, single submitter | clinical testing | For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Phe478 amino acid residue in TWNK. Other variant(s) that disrupt this residue have been observed in individuals with TWNK-related conditions (PMID: 18575922), which suggests that this may be a clinically significant amino acid residue. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TWNK protein function. ClinVar contains an entry for this variant (Variation ID: 1687171). This missense change has been observed in individuals with autosomal dominant progressive external ophthalmoplegia (PMID: 24014582, 25989649; Invitae; Berardo et. al. 2011. Neurología Argentina. doi:10.1016/j.neuarg.2012.01.003). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 478 of the TWNK protein (p.Phe478Cys). |