Total submissions: 3
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Invitae | RCV001242145 | SCV001415213 | likely pathogenic | Alkaptonuria | 2022-06-02 | criteria provided, single submitter | clinical testing | Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 53 of the HGD protein (p.Arg53Trp). This variant is present in population databases (rs759435977, gnomAD 0.003%). This missense change has been observed in individual(s) with HGD-related conditions (PMID: 11001939, 16085442, 19862842; Invitae). ClinVar contains an entry for this variant (Variation ID: 967274). 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 HGD protein function. This variant disrupts the p.Arg53 amino acid residue in HGD. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 25681086, 25804398). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. |
Genomics England Pilot Project, |
RCV001242145 | SCV001760101 | likely pathogenic | Alkaptonuria | no assertion criteria provided | clinical testing | ||
Department Of Human Genetics, |
RCV001242145 | SCV004101014 | pathogenic | Alkaptonuria | no assertion criteria provided | research | The variant was originally described in AKU patient in PMID:11001939. It has been submitted to the HGD gene mutation database (http://hgddatabase.cvtisr.sk/, DB-ID: AKU_00011). |