ClinVar Miner

Submissions for variant NM_032383.5(HPS3):c.338T>G (p.Val113Gly)

gnomAD frequency: 0.00008  dbSNP: rs763529688
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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 RCV001148660 SCV001309566 uncertain significance Hermansky-Pudlak syndrome 3 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV002557186 SCV003490622 uncertain significance not provided 2022-04-12 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 113 of the HPS3 protein (p.Val113Gly). This variant is present in population databases (rs763529688, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with HPS3-related conditions. ClinVar contains an entry for this variant (Variation ID: 902240). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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 RCV003346338 SCV004061412 uncertain significance Inborn genetic diseases 2023-08-08 criteria provided, single submitter clinical testing The c.338T>G (p.V113G) alteration is located in exon 2 (coding exon 2) of the HPS3 gene. This alteration results from a T to G substitution at nucleotide position 338, causing the valine (V) at amino acid position 113 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV001148660 SCV004235528 uncertain significance Hermansky-Pudlak syndrome 3 2023-11-01 criteria provided, single submitter clinical testing

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