ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.2437G>A (p.Glu813Lys)

gnomAD frequency: 0.00011  dbSNP: rs770020510
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001121831 SCV001280484 uncertain significance Fanconi anemia complementation group P 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 RCV001243534 SCV001416702 uncertain significance Fanconi anemia 2022-10-03 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 813 of the SLX4 protein (p.Glu813Lys). This variant is present in population databases (rs770020510, gnomAD 0.02%). This missense change has been observed in individual(s) with congenital heart disease (PMID: 32368696). ClinVar contains an entry for this variant (Variation ID: 888493). 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.
Genetic Services Laboratory, University of Chicago RCV001819833 SCV002068444 uncertain significance not specified 2018-02-19 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001121831 SCV002793083 uncertain significance Fanconi anemia complementation group P 2022-05-17 criteria provided, single submitter clinical testing
GeneDx RCV003442208 SCV004167750 uncertain significance not provided 2023-04-17 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified as a de novo variant in individuals with congenital heart disease (Edwards et al., 2020; Sevim Bayrak et al., 2020); This variant is associated with the following publications: (PMID: 32368696, 31941532)

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