ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.4856C>T (p.Pro1619Leu)

gnomAD frequency: 0.00005  dbSNP: rs771200478
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000630945 SCV000751920 uncertain significance Fanconi anemia 2022-10-07 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1619 of the SLX4 protein (p.Pro1619Leu). This variant is present in population databases (rs771200478, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with SLX4-related conditions. ClinVar contains an entry for this variant (Variation ID: 526418). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV002483776 SCV002789750 uncertain significance Fanconi anemia complementation group P 2022-03-19 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003411492 SCV004113336 uncertain significance SLX4-related disorder 2023-06-07 criteria provided, single submitter clinical testing The SLX4 c.4856C>T variant is predicted to result in the amino acid substitution p.Pro1619Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.15% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-3633395-G-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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