ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.778C>T (p.Arg260Trp)

gnomAD frequency: 0.00008  dbSNP: rs564590745
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001574021 SCV003474315 uncertain significance not provided 2022-08-19 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 260 of the HPS1 protein (p.Arg260Trp). This variant is present in population databases (rs564590745, gnomAD 0.05%). 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: 1206398). 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 tryptophan 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.
Fulgent Genetics, Fulgent Genetics RCV005038266 SCV005665140 uncertain significance Hermansky-Pudlak syndrome 1 2024-01-29 criteria provided, single submitter clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001574021 SCV001800711 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001574021 SCV001970426 likely benign not provided no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004754774 SCV005354144 uncertain significance HPS1-related disorder 2024-07-30 no assertion criteria provided clinical testing The HPS1 c.778C>T variant is predicted to result in the amino acid substitution p.Arg260Trp. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.046% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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