Total submissions: 3
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Illumina Laboratory Services, |
RCV001148770 | SCV001309681 | uncertain significance | Hermansky-Pudlak syndrome 3 | 2018-01-13 | 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. |
| Invitae | RCV002032380 | SCV002224505 | uncertain significance | not provided | 2021-09-01 | criteria provided, single submitter | clinical testing | This sequence change replaces glutamic acid with lysine at codon 603 of the HPS3 protein (p.Glu603Lys). The glutamic acid residue is weakly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is present in population databases (rs143804526, ExAC 0.002%). This variant has not been reported in the literature in individuals affected with HPS3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. |
| Ambry Genetics | RCV003163330 | SCV003902511 | uncertain significance | Inborn genetic diseases | 2023-02-23 | criteria provided, single submitter | clinical testing | The c.1807G>A (p.E603K) alteration is located in exon 10 (coding exon 10) of the HPS3 gene. This alteration results from a G to A substitution at nucleotide position 1807, causing the glutamic acid (E) at amino acid position 603 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. |