ClinVar Miner

Submissions for variant NM_001184.4(ATR):c.1439G>T (p.Ser480Ile)

gnomAD frequency: 0.00001  dbSNP: rs750056135
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001146905 SCV001307669 uncertain significance Seckel syndrome 1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV001304856 SCV001494157 uncertain significance not provided 2021-08-27 criteria provided, single submitter clinical testing This sequence change replaces serine with isoleucine at codon 480 of the ATR protein (p.Ser480Ile). The serine residue is weakly conserved and there is a large physicochemical difference between serine and isoleucine. This variant is present in population databases (rs750056135, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with ATR-related conditions. ClinVar contains an entry for this variant (Variation ID: 901183). 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.
Ambry Genetics RCV002393368 SCV002701419 uncertain significance Inborn genetic diseases 2021-09-30 criteria provided, single submitter clinical testing The p.S480I variant (also known as c.1439G>T), located in coding exon 6 of the ATR gene, results from a G to T substitution at nucleotide position 1439. The serine at codon 480 is replaced by isoleucine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV001146905 SCV003801876 uncertain significance Seckel syndrome 1 2023-02-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003127647 SCV003801877 uncertain significance Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome 2023-02-08 criteria provided, single submitter clinical testing

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