ClinVar Miner

Submissions for variant NM_000379.4(XDH):c.2362A>T (p.Ile788Phe)

gnomAD frequency: 0.00083  dbSNP: rs141050887
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000805413 SCV000945367 uncertain significance Xanthinuria type II 2022-10-18 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 788 of the XDH protein (p.Ile788Phe). This variant is present in population databases (rs141050887, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with XDH-related conditions. ClinVar contains an entry for this variant (Variation ID: 650290). 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 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.
Illumina Laboratory Services, Illumina RCV001137768 SCV001297745 uncertain significance Hereditary xanthinuria type 1 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.
PreventionGenetics, part of Exact Sciences RCV003413614 SCV004114360 uncertain significance XDH-related condition 2023-05-10 criteria provided, single submitter clinical testing The XDH c.2362A>T variant is predicted to result in the amino acid substitution p.Ile788Phe. This variant has not been reported in the literature in individuals with XDH-related disorders. This variant is reported in 0.13% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-31588936-T-A). 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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