ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.85C>T (p.Arg29Cys)

gnomAD frequency: 0.00078  dbSNP: rs144832924
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000527683 SCV000626456 likely benign Fanconi anemia 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001118601 SCV001276896 uncertain significance Fanconi anemia complementation group P 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV001775845 SCV002009213 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
GeneDx RCV001775845 SCV002013160 uncertain significance not provided 2019-10-24 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genetic Services Laboratory, University of Chicago RCV001821493 SCV002068137 uncertain significance not specified 2021-01-05 criteria provided, single submitter clinical testing 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 relatively high population frequency of 0.49% in the Finnish subpopulation (dbSNP rs144832924). The p.Arg29Cys change affects a poorly conserved amino acid residue located in a domain of the SLX4 protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Arg29Cys substitution. Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Arg29Cys change remains unknown at this time.
Sema4, Sema4 RCV000527683 SCV002529398 likely benign Fanconi anemia 2021-06-13 criteria provided, single submitter curation

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