Total submissions: 3
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clinical Biochemistry Laboratory, |
RCV000186477 | SCV000239837 | pathogenic | Primary hyperoxaluria type 3 | 2023-10-27 | criteria provided, single submitter | clinical testing | ACMG: PS5 PM1 PM2 PM3 PP3. Raised urinary hydroxyoxoglutarate and dihydroxyglutarate |
Counsyl | RCV000186477 | SCV000800579 | uncertain significance | Primary hyperoxaluria type 3 | 2017-08-17 | criteria provided, single submitter | clinical testing | |
Invitae | RCV002513971 | SCV002962264 | likely pathogenic | not provided | 2023-04-04 | criteria provided, single submitter | clinical testing | 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 HOGA1 protein function. ClinVar contains an entry for this variant (Variation ID: 204270). This missense change has been observed in individual(s) with autosomal recessive hyperoxaluria (PMID: 26342005). This variant is present in population databases (rs150702945, gnomAD 0.0009%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 113 of the HOGA1 protein (p.Glu113Lys). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. |