ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.3127G>A (p.Gly1043Arg)

gnomAD frequency: 0.00002  dbSNP: rs776060270
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001196561 SCV001367169 uncertain significance Fanconi anemia complementation group P 2020-02-10 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2.
Invitae RCV001876275 SCV002114368 uncertain significance Fanconi anemia 2021-06-13 criteria provided, single submitter clinical testing This sequence change replaces glycine with arginine at codon 1043 of the SLX4 protein (p.Gly1043Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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 arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SLX4-related conditions. ClinVar contains an entry for this variant (Variation ID: 930702). This variant is present in population databases (rs776060270, ExAC 0.01%).
Fulgent Genetics, Fulgent Genetics RCV001196561 SCV002815673 uncertain significance Fanconi anemia complementation group P 2022-02-08 criteria provided, single submitter clinical testing

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