ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.485C>T (p.Thr162Met)

gnomAD frequency: 0.00003  dbSNP: rs140876043
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000538861 SCV000626443 uncertain significance Fanconi anemia 2023-10-09 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 162 of the SLX4 protein (p.Thr162Met). This variant is present in population databases (rs140876043, gnomAD 0.01%). 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: 456330). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests 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.
Fulgent Genetics, Fulgent Genetics RCV000764067 SCV000895021 uncertain significance Fanconi anemia complementation group P 2022-03-12 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003387874 SCV004099668 uncertain significance not specified 2023-09-08 criteria provided, single submitter clinical testing Variant summary: BTBD12 c.485C>T (p.Thr162Met) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 251496 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.485C>T in individuals affected with Fanconi Anemia and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Both submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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