ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.4700C>T (p.Ser1567Phe)

gnomAD frequency: 0.00001  dbSNP: rs755754734
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002208781 SCV002495966 uncertain significance Fanconi anemia complementation group P 2021-07-15 criteria provided, single submitter clinical testing SLX4 NM_032444.2 exon 13 p.Ser1567Phe (c.4700C>T):This variant has been reported in the literature in at least 2 individuals, 1 with suspected telomeropathy and 1 with suspected hereditary breast and/or ovarian cancer (Bonache 2018 PMID:30306255, Arias Salgado 2019 PMID:30995915). This variant is not present in large control databases. Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Labcorp Genetics (formerly Invitae), Labcorp RCV003635981 SCV004550694 uncertain significance Fanconi anemia 2023-03-10 criteria provided, single submitter clinical testing This variant is present in population databases (rs755754734, gnomAD 0.003%). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1675132). This missense change has been observed in individual(s) with clinical features of SLX4-related conditions (PMID: 30306255, 30995915). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 1567 of the SLX4 protein (p.Ser1567Phe).

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