ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.1925del (p.Gly642fs)

dbSNP: rs2136083690
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001380350 SCV001578354 pathogenic not provided 2021-05-07 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant results in an extension of the HPS1 protein. Other variant(s) that result in a similarly extended protein product (p.Tyr645Thrfs*80) have been determined to be pathogenic (PMID: 30387913, 19665357). This suggests that these extensions are likely to be causative of disease. This variant has not been reported in the literature in individuals with HPS1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a frameshift in the HPS1 gene (p.Gly642Glufs*83). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 59 amino acid(s) of the HPS1 protein and extend the protein by 23 additional amino acid residues.
GeneDx RCV001380350 SCV001789335 likely pathogenic not provided 2022-08-17 criteria provided, single submitter clinical testing Frameshift variant in the C-terminus predicted to result in protein extension, as the last 59 amino acids are lost and replaced with 83 aberrant amino acids; Not observed in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Baylor Genetics RCV003469647 SCV004199920 likely pathogenic Hermansky-Pudlak syndrome 1 2023-10-21 criteria provided, single submitter clinical testing

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