ATM encodes a kinase that acts as a master controller of the cellular DNA damage response: it detects double-strand breaks and coordinates DNA repair, cell cycle arrest, or apoptosis through downstream targets including p53, BRCA1, and CHK2. Loss-of-function mutations in both copies of ATM cause ataxia telangiectasia, an autosomal recessive disorder characterized by neurological problems, immune deficiency, and cancer predisposition. ATM functions as a tumor suppressor: individuals with ataxia telangiectasia are prone to childhood lymphomas, leukemias, and breast cancer, while carriers of a single altered copy have increased risk of breast, pancreatic, prostate, and other cancers. Somatic ATM mutations also occur in lymphoid malignancies and solid tumors, and ATM-deficient cancers are often especially sensitive to DNA-damaging treatments.
This variant
ATM is a tumor suppressor whose loss-of-function mutations cause ataxia telangiectasia when biallelic and increase cancer risk in single-copy carriers. This Pathogenic frameshift truncates the ATM kinase and is predicted to trigger nonsense-mediated decay, so it is expected to abolish ATM function and carry clinical significance for cancer risk in this individual and family.
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7628dup
GRCh38
chr11:108331554 T>TA
GRCh37
chr11:108202281 T>TA
BasisPathogenic: ATM VCEP v1.5 Rule4 is met by one very strong criterion (PVS1) and two supporting criteria (PM2, PM5).▾
Pathogenic: ATM VCEP v1.5 Rule4 is met by one very strong criterion (PVS1) and two supporting criteria (PM2, PM5).
Classification rationale
PVS1PM2PM5Pathogenic
ATM c.7628dupframeshift · exon 51
PVS1 (Very Strong): one-base frameshift p.(Asn2543LysfsTer5) predicted to trigger nonsense-mediated decay, truncating about 510 residues. PM2 (Supporting): absent from gnomAD v4.1, below the <=0.001% population frequency threshold. PM5 (Supporting): premature termination upstream of the p.Arg3047 ATM truncation cutoff. Pathogenic: ATM VCEP v1.5 Rule4, combining 1 very strong and 2 supporting criteria.
PVS1 + PM2 + PM5→Pathogenic
Gene diagram
· NM_000051.4 · variants mapped to exon structure
ATMNM_000051.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in ATM—click a row to locate it on the plot · use the link column to open its page
Variant ↕
Protein
Location
Classification
Link
Applied criteria · 3 applied · 8 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 3
Strength Supporting Moderate Strong Very strong
✓
PVS1very strongPathogenic
Met: one-base frameshift creates premature stop codon p.(Asn2543LysfsTer5) predicted to trigger nonsense-mediated decay, truncating about 510 residues.
Case normalization identifies NM_000051.4:c.7628dup as NP_000042.3:p.(Asn2543LysfsTer5), with the reference protein ending at residue 3057 and the predicted frameshift product ending at residue 2547 before the stop.Transcript exon coordinates place c.7628 in exon 51; multiple coding exons remain downstream, supporting nonsense-mediated decay of the premature-termination transcript.The ATM VCEP v1.5 PVS1 guide defines frameshift variants as null-variant candidates in ATM, states that loss of function is a known disease mechanism, and considers all exons of its default transcript constitutive; its caution concerns only loss-of-function variants at the extreme 3′ end or splice variants with in-frame exon skipping, neither of which describes this variant.
Met (supporting): absent from gnomAD v4.1, below the <=0.001% frequency threshold.
The ClinGen HBOP ATM VCEP version 1.5 PM2 rule applies at supporting strength when frequency is <=0.001% in gnomAD v4; n=1 in a single subpopulation is also sufficient for PM2_Supporting.gnomAD v4.1 reports the variant as absent.The variant is additionally reported absent from gnomAD v2.1 and gnomAD-Canada v1.0; no homozygote or ancestry-specific frequency is reported.
Met (supporting): the premature stop at approximately p.2547 lies upstream of the p.Arg3047 ATM truncation cutoff.
ClinGen HBOP ATM VCEP v1.5 PM5 rule: apply to frameshifting or truncating variants with premature termination codons upstream of p.Arg3047; the rule lists Supporting as the applicable strength.Case normalization identifies NM_000051.4:c.7628dup as NP_000042.3:p.(Asn2543LysfsTer5), placing the premature termination before p.Arg3047.pm5_candidates.json identifies the governing ATM PM5 mode as truncation_cutoff_gene_specific and states that classic same-residue missense searching is not eligible for this non-missense variant.