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
This truncating ATM variant is relevant to a tumor-suppressor gene in which loss of function causes ataxia-telangiectasia when biallelic and contributes to inherited cancer predisposition when heterozygous.
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8735_8751del
GRCh38
chr11:108353828 AGAGATATTGTGGATGGC>A
GRCh37
chr11:108224555 AGAGATATTGTGGATGGC>A
Pathogenic: ATM VCEP Rule4 is met by PVS1 (very strong) plus PM2 and PM5 (supporting).
Classification rationale
PVS1PM2PM5Pathogenic
ATM c.8735_8751delframeshift · exon 60
Pathogenic: PVS1 very strong supports a loss-of-function ATM truncation upstream of the VCEP pathogenic boundary. Pathogenic: PM2 supporting reflects the variant's absence from gnomAD v2.1 and v4.1. Pathogenic: PM5 supporting applies because the truncation ends upstream of ATM p.Leu3048 with PVS1 very strong.
PVS1 + PM2 + PM5→Pathogenic
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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
Protein
Location
Classification
Link
Applied criteria · 3 applied · 9 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 at very strong: the 17-nucleotide deletion causes p.Arg2912AsnfsTer7, truncating ATM 139 residues before its 3057-residue normal length and upstream of the VCEP p.Arg3047 boundary.
The case normalization identifies NM_000051.4:c.8735_8751del as NP_000042.3:p.(Arg2912AsnfsTer7) / p.(R2912Nfs*7), a frameshift with predicted protein position 2918 and normal protein length 3057.The ATM HBOP VCEP PVS1 guide defines frameshift variants as null-variant candidates, states that all exons of the default NM_000051.3 transcript can be considered constitutive, and identifies loss of function as an established disease mechanism in the ATM framework.The ATM VCEP guide states that the most 3-prime/C-terminal residue considered pathogenic is p.Arg3047; this truncation terminates at p.2918, upstream of that boundary.
Met, supporting: the variant is absent from gnomAD v2.1 and v4.1, with observed frequency 0 versus the ATM VCEP PM2 threshold of <=0.001%.
ATM HBOP VCEP version 1.6 specifies PM2 Supporting at frequency <=0.001% in the gnomAD subpopulation with the highest frequency, with a single-observation exception.The variant is reported absent from gnomAD v2.1 and v4.1, and also absent from the available gnomAD v2.1 non-cancer and v3.1 non-cancer records; the observed allele frequency is therefore 0.The VCEP does not require a non-cancer or exome-only source for PM2, so the default all-comers gnomAD entries were used for the primary assessment.
Met at supporting strength: the truncating product ends at approximately p.Asn2918, upstream of the ATM VCEP PM5 cutoff p.Leu3048, with PVS1 provisionally very strong.
ATM VCEP v1.6 PM5 rule: DNA variants must be NMD-prone, truncating, receive PVS1 at Very Strong strength, and have a premature termination codon upstream of p.Leu3048; the assigned strength is Supporting.The normalized protein consequence is p.(R2912Nfs*7), which predicts termination at approximately p.Asn2918 and therefore before p.Leu3048.The gene-level PVS1 context identifies ATM loss of function as an established disease mechanism, and the variant-level assessment supplies a suggested default PVS1 strength of Very Strong.
Assessed · not applied
· 4 not met · 5 not assessed
Pathogenic
PS3Not assessed: no variant-specific result was found in the approved ATM functional assays, and the 17-base deletion is absent from the SNV functional table.
PS4Not met: no qualifying case-control p-value, effect estimate, confidence interval, or validated proband-count evidence was reported for this exact deletion.
PM3Not assessed: no affected A-T proband, pathogenic variant in trans, phase information, or qualifying homozygous observation is documented for this variant.
PP1Not assessed: zero affected relatives with documented segregation are available, below the ATM VCEP threshold of one affected relative for PP1 Supporting.
PP5Not met: ClinVar contains no exact-variant expert-panel Pathogenic or Likely pathogenic classification for NM_000051.4:c.8735_8751del.
Benign
BA1Not met: the variant is absent from gnomAD v2.1 and v4.1, far below the ATM VCEP BA1 threshold of >0.5%.
BS1Not met: the variant is absent from gnomAD v2.1 and v4.1, below the ATM VCEP BS1 threshold of >0.05%.
BS3Not assessed: no variant-specific benign functional result was found in the approved ATM assays, and the 17-base deletion is absent from the SNV functional table.
BP2Not assessed: no unaffected adult carrier with a pathogenic or likely pathogenic ATM variant in trans, phase, or setting is documented.