ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.800C>T (p.Ala267Val)

gnomAD frequency: 0.00004  dbSNP: rs752160984
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001047560 SCV001211525 uncertain significance Fanconi anemia 2022-08-19 criteria provided, single submitter clinical testing 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 missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 844651). This variant has not been reported in the literature in individuals affected with SLX4-related conditions. This variant is present in population databases (rs752160984, gnomAD 0.01%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 267 of the SLX4 protein (p.Ala267Val).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003490028 SCV004241755 uncertain significance not specified 2023-12-28 criteria provided, single submitter clinical testing Variant summary: BTBD12 c.800C>T (p.Ala267Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 251390 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.800C>T in individuals affected with Fanconi Anemia and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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