ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.5027C>T (p.Thr1676Ile)

dbSNP: rs377544881
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001094325 SCV000396819 uncertain significance Fanconi anemia complementation group P 2018-01-13 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.
Invitae RCV000370293 SCV000626444 uncertain significance Fanconi anemia 2023-03-16 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. 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. ClinVar contains an entry for this variant (Variation ID: 319146). This variant has not been reported in the literature in individuals affected with SLX4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1676 of the SLX4 protein (p.Thr1676Ile).
Ambry Genetics RCV003165861 SCV003892185 uncertain significance Inborn genetic diseases 2023-02-07 criteria provided, single submitter clinical testing The c.5027C>T (p.T1676I) alteration is located in exon 14 (coding exon 13) of the SLX4 gene. This alteration results from a C to T substitution at nucleotide position 5027, causing the threonine (T) at amino acid position 1676 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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