ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.1223G>A (p.Arg408Gln)

gnomAD frequency: 0.00009  dbSNP: rs377135500
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001222228 SCV001394321 uncertain significance Fanconi anemia 2023-11-13 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 408 of the SLX4 protein (p.Arg408Gln). This variant is present in population databases (rs377135500, gnomAD 0.02%). 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: 950506). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glutamine 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.
Genetic Services Laboratory, University of Chicago RCV001819919 SCV002070162 uncertain significance not specified 2020-02-26 criteria provided, single submitter clinical testing DNA sequence analysis of the SLX4 gene demonstrated a sequence change, c.1223G>A, in exon 6 that results in an amino acid change, p.Arg408Gln. This sequence change does not appear to have been previously described in patients with SLX4-related disorders and has been described in the gnomAD database with a low frequency of 0.015% in the European sub-population (dbSNP rs377135500). The p.Arg408Gln change affects a poorly conserved amino acid residue located in a domain of the SLX4 protein that is not known to be functional. The p.Arg408Gln substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to the lack of functional studies, the clinical significance of the p.Arg408Gln change remains unknown at this time.
Fulgent Genetics, Fulgent Genetics RCV002491698 SCV002797680 uncertain significance Fanconi anemia complementation group P 2022-03-02 criteria provided, single submitter clinical testing

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