Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Illumina Laboratory Services, |
RCV000823785 | SCV000479876 | uncertain significance | Hyperphosphatasia with intellectual disability syndrome 2 | 2018-01-12 | criteria provided, single submitter | clinical testing | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. |
| Gene |
RCV000422600 | SCV000536558 | uncertain significance | not provided | 2018-10-24 | criteria provided, single submitter | clinical testing | A variant of uncertain significance has been identified in the PIGO gene. The A426D variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A426D variant is observed in 13/10,240 (0.1%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A426D variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant. |
| Invitae | RCV000823785 | SCV000964655 | likely benign | Hyperphosphatasia with intellectual disability syndrome 2 | 2024-01-22 | criteria provided, single submitter | clinical testing | |
| New York Genome Center | RCV000823785 | SCV002025731 | uncertain significance | Hyperphosphatasia with intellectual disability syndrome 2 | 2020-04-29 | criteria provided, single submitter | clinical testing |