ClinVar Miner

Submissions for variant NM_181507.2(HPS5):c.285-10A>G

gnomAD frequency: 0.00006  dbSNP: rs200449378
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000496404 SCV001264729 uncertain significance Hermansky-Pudlak syndrome 5 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
GeneDx RCV001731720 SCV001981927 likely pathogenic not provided 2022-03-03 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect, with reduced levels of mRNA and protein compared to controls and mislocalization of lysosomal markers (Stephen et al., 2017); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 28640947, 28296950, 29090612)
Labcorp Genetics (formerly Invitae), Labcorp RCV001731720 SCV002293787 uncertain significance not provided 2022-07-06 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the HPS5 gene. It does not directly change the encoded amino acid sequence of the HPS5 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of 3 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs200449378, gnomAD 0.04%). This variant has been observed in individual(s) with Hermansky-Pudlak syndrome (PMID: 28296950). ClinVar contains an entry for this variant (Variation ID: 431165). Studies have shown that this variant results in the activation of a cryptic splice site in intron 4 (PMID: 28296950). 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.
OMIM RCV000496404 SCV000586806 pathogenic Hermansky-Pudlak syndrome 5 2017-08-02 no assertion criteria provided literature only

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