ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.1940+2T>C

gnomAD frequency: 0.00001  dbSNP: rs972096803
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001888087 SCV002126745 pathogenic not provided 2023-05-17 criteria provided, single submitter clinical testing Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the HPS1 protein in which other variant(s) (p.Gln686*) have been determined to be pathogenic (PMID: 26575419). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 1355628). This variant has not been reported in the literature in individuals affected with HPS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 19 of the HPS1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.
PreventionGenetics, part of Exact Sciences RCV003426221 SCV004118550 likely pathogenic HPS1-related disorder 2023-04-11 criteria provided, single submitter clinical testing The HPS1 c.1940+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or in a large population database (, indicating this variant is rare. Variants that disrupt the consensus splice donor site in HPS1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Baylor Genetics RCV003470960 SCV004199959 likely pathogenic Hermansky-Pudlak syndrome 1 2023-02-11 criteria provided, single submitter clinical testing

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