ClinVar Miner

Submissions for variant NM_001025603.2(RFX5):c.1673T>C (p.Ile558Thr)

gnomAD frequency: 0.00002  dbSNP: rs966468525
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001040188 SCV001203749 uncertain significance MHC class II deficiency 2022-07-03 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: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine 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: 838606). This variant has not been reported in the literature in individuals affected with RFX5-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.008%). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 558 of the RFX5 protein (p.Ile558Thr).
Ambry Genetics RCV002552492 SCV003526153 uncertain significance Inborn genetic diseases 2022-06-09 criteria provided, single submitter clinical testing The c.1673T>C (p.I558T) alteration is located in exon 11 (coding exon 9) of the RFX5 gene. This alteration results from a T to C substitution at nucleotide position 1673, causing the isoleucine (I) at amino acid position 558 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV001040188 SCV004049742 uncertain significance MHC class II deficiency 2023-04-11 criteria provided, single submitter clinical testing

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