ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.320G>A (p.Arg107Gln)

gnomAD frequency: 0.00005  dbSNP: rs538482143
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV002486048 SCV002777041 uncertain significance Hermansky-Pudlak syndrome 1 2024-01-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002537821 SCV003294539 uncertain significance not provided 2022-04-08 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 107 of the HPS1 protein (p.Arg107Gln). This variant is present in population databases (rs538482143, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with HPS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 990848). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Ambry Genetics RCV004987016 SCV005597978 likely benign Inborn genetic diseases 2024-10-16 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc. RCV001278957 SCV001466003 uncertain significance Hermansky-Pudlak syndrome 2020-04-11 no assertion criteria provided clinical testing

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