ClinVar Miner

Submissions for variant NM_001351834.2(ATM):c.5511_5512del (p.Phe1837fs) (rs1555107263)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000550809 SCV000622597 pathogenic Ataxia-telangiectasia syndrome 2017-04-24 criteria provided, single submitter clinical testing This sequence change deletes 2 nucleotides from exon 37 of the ATM mRNA (c.5511_5512delTT), causing a frameshift at codon 1837. This creates a premature translational stop signal (p.Phe1837Leufs*11) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, loss-of-function variants in ATM are known to be pathogenic (PMID: 25614872, 23807571). For these reasons, this variant has been classified as Pathogenic.
Color Health, Inc RCV000777221 SCV000912912 pathogenic Hereditary cancer-predisposing syndrome 2020-04-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV000777221 SCV001186185 pathogenic Hereditary cancer-predisposing syndrome 2019-02-09 criteria provided, single submitter clinical testing The c.5511_5512delTT pathogenic mutation, located in coding exon 36 of the ATM gene, results from a deletion of two nucleotides at nucleotide positions 5511 to 5512, causing a translational frameshift with a predicted alternate stop codon (p.F1837Lfs*11). 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.
Cancer Genomics Group,Japanese Foundation For Cancer Research RCV001030598 SCV001193483 likely pathogenic Hereditary breast and ovarian cancer syndrome 2019-05-01 criteria provided, single submitter research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000550809 SCV001360468 likely pathogenic Ataxia-telangiectasia syndrome 2019-04-26 criteria provided, single submitter clinical testing Variant summary: ATM c.5511_5512delTT (p.Phe1837LeufsX11) 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 (e.g. c.5712dupA (p.Ser1905fsX25), c.5908C>T (p.Gln1970X), c.6404_6405insTT (p.Arg2136fsX1)). The variant was absent in 250904 control chromosomes (gnomAD). To our knowledge, no occurrence of c.5511_5512delTT in individuals affected with Ataxia-Telangiectasia and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has provided clinical-significance assessments for this variant in ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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