ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.1744-2A>C

gnomAD frequency: 0.00001  dbSNP: rs281865088
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
NIHR Bioresource Rare Diseases, University of Cambridge RCV000851717 SCV000899552 likely pathogenic Hermansky-Pudlak syndrome 2019-02-01 criteria provided, single submitter research
Invitae RCV001058416 SCV001222982 likely pathogenic not provided 2023-09-27 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 17 of the HPS1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in HPS1 are known to be pathogenic (PMID: 12442288, 16185271). This variant is present in population databases (rs281865088, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with Hermansky-Pudlak syndrome (PMID: 29941477). ClinVar contains an entry for this variant (Variation ID: 21097). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus 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.
Fulgent Genetics, Fulgent Genetics RCV002482892 SCV002781757 likely pathogenic Hermansky-Pudlak syndrome 1 2021-10-16 criteria provided, single submitter clinical testing
Baylor Genetics RCV002482892 SCV004199957 pathogenic Hermansky-Pudlak syndrome 1 2023-03-24 criteria provided, single submitter clinical testing

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