ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.478_482del (p.Ser160fs) (rs587780624)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164941 SCV000215630 pathogenic Hereditary cancer-predisposing syndrome 2016-09-15 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 RCV000164941 SCV000682221 pathogenic Hereditary cancer-predisposing syndrome 2016-09-19 criteria provided, single submitter clinical testing
Counsyl RCV000122852 SCV000678112 likely pathogenic Ataxia-telangiectasia syndrome 2015-05-12 criteria provided, single submitter clinical testing
GeneDx RCV000484842 SCV000564607 pathogenic not provided 2016-10-17 criteria provided, single submitter clinical testing This deletion of 5 nucleotides in ATM is denoted c.478_482delTCTCA at the cDNA level and p.Ser160AlafsX23 (S160AfsX23) at the protein level. The normal sequence, with the bases that are deleted in brackets, is AATA[delTCTCA]GCAA. The deletion causes a frameshift, which changes a Serine to an Alanine at codon 160, and creates a premature stop codon at position 23 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature as a germline variant, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. We consider this variant to be pathogenic.
Invitae RCV000122852 SCV000166110 pathogenic Ataxia-telangiectasia syndrome 2018-12-14 criteria provided, single submitter clinical testing This sequence change deletes 5 nucleotides from exon 5 of the ATM mRNA (c.478_482delTCTCA), causing a frameshift at codon 160. This creates a premature translational stop signal (p.Ser160Alafs*23) and 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 individual(s) with personal and/or family history of breast and/or ovarian cancer (PMID: 26270727). ClinVar contains an entry for this variant (Variation ID: 185501). Loss-of-function variants in ATM are known to be pathogenic (PMID: 25614872, 23807571). For these reasons, this variant has been classified as Pathogenic.

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