ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.7915A>T (p.Lys2639Ter)

dbSNP: rs2136572656
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001917093 SCV002187626 pathogenic Ataxia-telangiectasia syndrome 2022-10-04 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1421780). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys2639*) in the ATM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872).
Myriad Genetics, Inc. RCV004044127 SCV004932251 pathogenic Familial cancer of breast 2024-02-01 criteria provided, single submitter clinical testing This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Ambry Genetics RCV004044128 SCV005020286 pathogenic Hereditary cancer-predisposing syndrome 2023-11-13 criteria provided, single submitter clinical testing The p.K2639* pathogenic mutation (also known as c.7915A>T), located in coding exon 52 of the ATM gene, results from an A to T substitution at nucleotide position 7915. This changes the amino acid from a lysine to a stop codon within coding exon 52. This variant has been detected in conjunction with an ATM pathogenic variant in at least one individual diagnosed with clinical features of ataxia-telangiectasia; however, the phase of the two variants is unknown (Kim J et al. Nature, 2023 Jul;619:828-836; Hoche F et al. Cerebellum, 2019 Apr;18:225-244). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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