ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.5072A>G (p.Asn1691Ser)

gnomAD frequency: 0.00006  dbSNP: rs551385115
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000695082 SCV000823561 uncertain significance Fanconi anemia 2022-10-13 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1691 of the SLX4 protein (p.Asn1691Ser). This variant is present in population databases (rs551385115, gnomAD 0.2%). This missense change has been observed in individual(s) with breast cancer (PMID: 22401137). ClinVar contains an entry for this variant (Variation ID: 573413). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 RCV001816714 SCV002064686 uncertain significance not specified 2020-09-08 criteria provided, single submitter clinical testing DNA sequence analysis of the SLX4 gene demonstrated a sequence change, c.5072A>G, in exon 14 that results in an amino acid change, p.Asn1691Ser. This sequence change has been described in the gnomAD database with a frequency of 0.16% in the East Asian sub-population (dbSNP rs551385115). The p.Asn1691Ser change has been reported in the heterozygous state in a family with breast cancer (PMID: 22401137). This sequence 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.Asn1691Ser substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Asn1691Ser change remains unknown at this time.
Fulgent Genetics, Fulgent Genetics RCV002485684 SCV002786501 uncertain significance Fanconi anemia complementation group P 2022-02-08 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV002485684 SCV003823920 uncertain significance Fanconi anemia complementation group P 2019-11-26 criteria provided, single submitter clinical testing

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