ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.2584C>T (p.Arg862Ter)

gnomAD frequency: 0.00001  dbSNP: rs200715208
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778907 SCV000915315 uncertain significance Fanconi anemia complementation group P 2017-05-15 criteria provided, single submitter clinical testing The SLX4 gene is one of at least 18 genes in which variants are known to cause Fanconi anemia. The SLX4 c.2584C>T (p.Arg862Ter) variant is a stop-gained variant predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The p.Arg862Ter variant is reported at a frequency of 0.00015 in the European (Finnish) population of the Exome Aggregation Consortium, but this is based on one allele so the variant is presumed to be rare. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for Fanconi anemia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV003768435 SCV004678289 pathogenic Fanconi anemia 2023-03-13 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 632059). This variant has not been reported in the literature in individuals affected with SLX4-related conditions. This variant is present in population databases (rs200715208, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Arg862*) in the SLX4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLX4 are known to be pathogenic (PMID: 21240277).

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