ClinVar Miner

Submissions for variant NM_000489.6(ATRX):c.5222G>A (p.Arg1741Lys)

gnomAD frequency: 0.00001  dbSNP: rs1448764008
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001555452 SCV001776878 likely pathogenic not provided 2020-04-30 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002032607 SCV002123072 uncertain significance Alpha thalassemia-X-linked intellectual disability syndrome 2021-08-27 criteria provided, single submitter clinical testing This sequence change replaces arginine with lysine at codon 1741 of the ATRX protein (p.Arg1741Lys). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and lysine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with ATRX-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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.
GenomeConnect, ClinGen RCV001824995 SCV002074867 not provided ATRX-related disorder no assertion provided phenotyping only Variant interpreted as Likely pathogenic and reported on 05-04-2020 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
GenomeConnect, ClinGen RCV002032607 SCV002818404 not provided Alpha thalassemia-X-linked intellectual disability syndrome no assertion provided phenotyping only Variant classified as Likely pathogenic and reported on 05-04-2020 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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