ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.3293A>G (p.Gln1098Arg) (rs1060501590)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000581017 SCV000682115 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-10 criteria provided, single submitter clinical testing
GeneDx RCV000482771 SCV000573400 uncertain significance not provided 2017-02-14 criteria provided, single submitter clinical testing This variant is denoted ATM c.3293A>G at the cDNA level, p.Gln1098Arg (Q1098R) at the protein level, and results in the change of a Glutamine to an Arginine (CAG>CGG). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. ATM Gln1098Arg was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Glutamine and Arginine differ in some properties, this is considered a semi-conservative amino acid substitution. ATM Gln1098Arg occurs at a position that is conserved in mammals and is located in the region of interaction with beta-adaptin (Tavitigian 2009). In silico analyses predict that this variant is unlikely to alter protein structure or function. Based on currently available evidence, it is unclear whether ATM Gln1098Arg is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Invitae RCV000476634 SCV000546813 uncertain significance Ataxia-telangiectasia syndrome 2018-02-27 criteria provided, single submitter clinical testing This sequence change replaces glutamine with arginine at codon 1098 of the ATM protein (p.Gln1098Arg). The glutamine residue is moderately conserved and there is a small physicochemical difference between glutamine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ATM-related disease. ClinVar contains an entry for this variant (Variation ID: 407540). 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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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