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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 variants cause ataxia-telangiectasia and cancer predisposition. This Pathogenic frameshift removes ~53% of the protein, including the entire kinase domain, so the variant is expected to abolish ATM function — consistent with a disease-causing allele in this gene.
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.4231del
GRCh38
chr11:108289094 CA>C
GRCh37
chr11:108159821 CA>C
Pathogenic: PVS1 very strong plus PM2 and PM5 supporting satisfy VCEP Rule4 (one very strong with two supporting), with no benign criteria met.
Classification rationale
PVS1PM2PM5Pathogenic
ATM c.4231delframeshift
PVS1 (Very Strong): out-of-frame deletion creating premature stop p.(Ser1411AlafsTer40), predicted to trigger nonsense-mediated decay. PM2 (Supporting): absent from gnomAD v4.1 (AF=0), below the VCEP <=0.001% threshold. PM5 (Supporting): premature stop at residue ~1450, upstream of the p.Arg3047 truncation cutoff. Final: Pathogenic, via VCEP Rule4 — PVS1 very strong combined with PM2 and PM5 supporting.
PVS1 + PM2 + PM5→Pathogenic
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
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 · 10 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: out-of-frame deletion creating premature stop p.(Ser1411AlafsTer40), predicted to trigger nonsense-mediated decay.
vcep_atm_pvs1_1_5: ClinGen HBOP ATM VCEP v1.5 PVS1 decision guide - defines null variants (incl. frameshift), LOF mechanism, constitutive exons, p.R3047 as most C-terminal pathogenic residue, FATKIN/HEAT domain notes for NMD-escaping variants.cspec: ATM VCEP v1.5 CSPEC ruleset - PVS1 default Very Strong, 'Use ATM PVS1 Decision Tree'.pvs1_generic_framework: ClinGen SVI PVS1 recommendations (Abou Tayoun et al. 2018, PMID 30192042; PMC6185798) - NMD criterion applied here: a PTC more than ~50-55 nt upstream of the final exon-exon junction is predicted to trigger NMD; this PTC (codon 1450, exon 29 of 63) satisfies that rule.
Met at Supporting: completely absent from gnomAD v4.1 (AF=0), below the VCEP <=0.001% frequency threshold.
gnomAD v4.1 direct variant lookup for chr11-108289094-CA-C (dataset gnomad_r4) returned absent -> AF 0, satisfies VCEP frequency <=0.001%gnomAD v2.1 direct variant lookup for 11-108159821-CA-C (dataset gnomad_r2_1) returned absent (corroborating rarity)gnomAD-Canada v1.0 lookup for 11-108289094-CA-C returned absent (corroborating rarity)
Met at Supporting: premature stop at residue ~1450, upstream of the p.Arg3047 truncation cutoff for pathogenic ATM variants.
cspec: ATM VCEP v1.5 PM5 entry — Supporting rule 'Apply to frameshifting or truncating variants with premature termination codons upstream of p.Arg3047'; instructions 'Use as PM5_Supporting (not moderate)', 'Do not use for missense changes'; PVS1 entry — 'The most 3'/C-Terminal residue considered to be pathogenic is p.R3047'pvs1_variant_assessment: variant consequence scaffold — consequence_class 'frameshift', protein NP_000042.3:p.(S1411Afs*40), confirming the frameshift class used for the rulepm5_candidates: pipeline candidate-collection artifact confirming PM5 mode 'truncation_cutoff_gene_specific' and zero same-residue (classic missense) comparator candidates; the PM5 call itself is grounded in the CSPEC rule text and variant consequence, not in this artifact's 'not_applicable' recommendation (which refers to classic same-residue missense PM5 search)
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
23807571 ↗Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients.
25614872 ↗Ten new ATM alterations in Polish patients with ataxia-telangiectasia.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
27413114 ↗ATM Mutations in Cancer: Therapeutic Implications.ONCOKB
30348496 ↗Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype.ONCOKB
30553448 ↗Loss of ATM positively regulates Rac1 activity and cellular migration through oxidative stress.ONCOKB