ClinVar Miner

Submissions for variant NM_032383.5(HPS3):c.1189C>T (p.Arg397Trp) (rs121908316)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001070228 SCV001235446 likely pathogenic not provided 2019-10-27 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 397 of the HPS3 protein (p.Arg397Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs121908316, ExAC 0.01%). This variant has been observed to segregate with Hermansky-Pudlak syndrome (HPS) in a family and has also been observed individuals affected with HPS (PMID: 11590544, 27593200). ClinVar contains an entry for this variant (Variation ID: 4613). 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: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
OMIM RCV000004876 SCV000025052 pathogenic Hermansky-Pudlak syndrome 3 2001-11-01 no assertion criteria provided literature only
GeneReviews RCV000004876 SCV000041518 pathologic Hermansky-Pudlak syndrome 3 2012-10-11 no assertion criteria provided curation Converted during submission to Pathogenic.

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