ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.3088A>G (p.Lys1030Glu)

dbSNP: rs863224561
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000197182 SCV000254080 uncertain significance Ataxia-telangiectasia syndrome 2023-05-18 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: 216200). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 1030 of the ATM protein (p.Lys1030Glu).
Color Diagnostics, LLC DBA Color Health RCV000777897 SCV000913916 uncertain significance Hereditary cancer-predisposing syndrome 2019-12-11 criteria provided, single submitter clinical testing This missense variant replaces lysine with glutamic acid at codon 1030 of the ATM protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/251222 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000777897 SCV001179787 uncertain significance Hereditary cancer-predisposing syndrome 2019-10-07 criteria provided, single submitter clinical testing The p.K1030E variant (also known as c.3088A>G), located in coding exon 20 of the ATM gene, results from an A to G substitution at nucleotide position 3088. The lysine at codon 1030 is replaced by glutamic acid, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Baylor Genetics RCV004567414 SCV005055922 uncertain significance Familial cancer of breast 2024-03-22 criteria provided, single submitter clinical testing

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