ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.3935_3936GA[2] (p.Glu1313fs) (rs1555093684)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667702 SCV000792195 likely pathogenic Ataxia-telangiectasia syndrome 2017-06-09 criteria provided, single submitter clinical testing
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine RCV000709712 SCV000839887 likely pathogenic Familial cancer of breast 2017-12-24 criteria provided, single submitter clinical testing This c.3939_3940delGA (p.Glu1313Aspfs*7) variant in the ATM gene is predicted to introduce a premature translation termination codon. This variant has been observed in a patient with pancreatic cancer (PMID 27449771). Mono-allelic variants in the ATM gene have been associated with susceptibility to breast cancer (OMIM 114480) whereas bi-allelic variants in this gene are associated with Ataxia-telangiectasia (OMIM 208900). This frameshift variant in the ATM gene is classified as likely pathogenic.
Invitae RCV000667702 SCV001217006 pathogenic Ataxia-telangiectasia syndrome 2019-12-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu1313Aspfs*7) 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 observed in an individual affected with pancreatic cancer (PMID: 27449771). ClinVar contains an entry for this variant (Variation ID: 552442). Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). For these reasons, this variant has been classified as Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000709712 SCV001339139 likely pathogenic Familial cancer of breast 2020-03-26 criteria provided, single submitter clinical testing Variant summary: ATM c.3939_3940delGA (p.Glu1313AspfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251244 control chromosomes (gnomAD). c.3939_3940delGA has been reported in the literature in an individual affected with pancreatic cancer (Yang_2016). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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