ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.5908C>T (p.Gln1970Ter) (rs587781722)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000129909 SCV000184727 pathogenic Hereditary cancer-predisposing syndrome 2016-12-12 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Alterations resulting in premature truncation (e.g.reading frame shift, nonsense)
Color RCV000129909 SCV000911668 pathogenic Hereditary cancer-predisposing syndrome 2018-05-08 criteria provided, single submitter clinical testing
Counsyl RCV000200350 SCV000485172 pathogenic Ataxia-telangiectasia syndrome 2016-03-08 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000762823 SCV000893181 pathogenic Familial cancer of breast; Ataxia-telangiectasia syndrome 2018-10-31 criteria provided, single submitter clinical testing
GeneDx RCV000235704 SCV000293233 pathogenic not provided 2018-03-23 criteria provided, single submitter clinical testing This pathogenic variant is denoted ATM c.5908C>T at the cDNA level and p.Gln1970Ter (Q1970X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAA>TAA), is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. ATM Gln1970Ter has been reported in both the homozygous and compound heterozygous state in several individuals with Ataxia-telangiectasia and is considered to be the most common pathogenic ATM variant in Costa Rica (Telatar 1998, Mitui 2003, Mitui 2009, Termsarasab 2015). This variant is considered pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000200350 SCV000694305 pathogenic Ataxia-telangiectasia syndrome 2016-12-09 criteria provided, single submitter clinical testing Variant summary: The ATM c.5908C>T (p.Gln1970X) variant results in a premature termination codon, predicted to cause a truncated or absent ATM protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest was not observed in controls (ExAC, 1000 Gs, or ESP). The variant of interest has been reported in multiple affected individuals via publications and has been implicated to be a Costa Rican founder mutation. In addition, multiple clinical diagnostic laboratories cite the variant as "pathogenic." Therefore, the variant of interest has been classified as "Pathogenic."
Invitae RCV000200350 SCV000253741 pathogenic Ataxia-telangiectasia syndrome 2018-12-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln1970*) in the ATM gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in the literature in individuals affected with ataxia-telangiectasia. It is a common disease-causing allele in the Costa Rican population (PMID: 9443866, 12815592). ClinVar contains an entry for this variant (Variation ID: 141404). Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). For these reasons, this variant has been classified as Pathogenic.

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