ATM-related cancer predisposition

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Summary

ATM-related cancer predisposition (MONDO:0700270) is a cancer caused by ATM (GenCC Definitive), with 2 cohort genes (1 CIViC-evidence somatic driver; 288 ClinVar predisposition records).

At a glance

  • Classification: Cancer
  • Causal gene: ATM (GenCC Definitive)
  • Cohort genes: 2
  • ClinVar variants: 288

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameATM-related cancer predisposition
Mondo IDMONDO:0700270
GARD0026410
Is cancer (heuristic)yes

Data availability: 288 ClinVar variants · 136 ClinGen variant curations · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseasehereditary neoplastic syndromeATM-related cancer predisposition

Related subtypes (116): mosaic variegated aneuploidy syndrome, tuberous sclerosis, hereditary breast ovarian cancer syndrome, hereditary multiple osteochondromas, nevoid basal cell carcinoma syndrome, leukemia, chronic lymphocytic, susceptibility to, 2, blue rubber bleb nevus, cherubism, Beckwith-Wiedemann syndrome, multiple self-healing squamous epithelioma, erythroleukemia, familial, susceptibility to, goiter, multinodular 1, with or without Sertoli-Leydig cell tumors, hyperparathyroidism 2 with jaw tumors, Kaposi sarcoma, susceptibility to, hereditary leiomyomatosis and renal cell cancer, susceptibility to uveal melanoma, melanoma and neural system tumor syndrome, nasopharyngeal carcinoma, susceptibility to, 2, WAGR syndrome, neuroblastoma, susceptibility to, 1, Rothmund-Thomson syndrome, mismatch repair cancer syndrome 1, Wiskott-Aldrich syndrome, N syndrome, hereditary thrombocytopenia and hematologic cancer predisposition syndrome, prostate cancer/brain cancer susceptibility, Brooke-Spiegler syndrome, pancreatic cancer, susceptibility to, 1, Carney-Stratakis syndrome, nasopharyngeal carcinoma, susceptibility to, 1, ovarian cancer, susceptibility to, 1, colorectal cancer, susceptibility to, 1, lung cancer susceptibility 1, leukemia, chronic lymphocytic, susceptibility to, 1, Kostmann syndrome, colorectal cancer, susceptibility to, 2, colorectal cancer, susceptibility to, 3, colorectal cancer, susceptibility to, 5, colorectal cancer, susceptibility to, 6, colorectal cancer, susceptibility to, 7, leukemia, chronic lymphocytic, susceptibility to, 3, leukemia, chronic lymphocytic, susceptibility to, 4, leukemia, chronic lymphocytic, susceptibility to, 5, lung cancer susceptibility 3, colorectal cancer, susceptibility to, 8, colorectal cancer, susceptibility to, 9, colorectal cancer, susceptibility to, 10, colorectal cancer, susceptibility to, 11, lung cancer susceptibility 4, neuroblastoma, susceptibility to, 3, neuroblastoma, susceptibility to, 4, neuroblastoma, susceptibility to, 5, neuroblastoma, susceptibility to, 6, leukemia, acute lymphocytic, susceptibility to, 1, leukemia, acute lymphocytic, susceptibility to, 2, lung cancer susceptibility 5, BAP1-related tumor predisposition syndrome, familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome, Maffucci syndrome, basal cell carcinoma, susceptibility to, 7, colorectal cancer, susceptibility to, 12, leukemia, acute lymphoblastic, susceptibility to, 3, cholangiocarcinoma, susceptibility to, progeroid features-hepatocellular carcinoma predisposition syndrome, neuroblastoma, susceptibility to, 7, DDX41-related hematologic malignancy predisposition syndrome, nasopharyngeal carcinoma, susceptibility to, 3, familial isolated hyperparathyroidism, intestinal polyposis syndrome, dyskeratosis congenita, familial rhabdoid tumor, multiple endocrine neoplasia, hereditary pheochromocytoma-paraganglioma, PTEN hamartoma tumor syndrome, familial multiple fibrofolliculoma, hereditary retinoblastoma, familial atypical multiple mole melanoma syndrome, hereditary nonpolyposis colon cancer, Li-Fraumeni syndrome, Cobb syndrome, neurofibromatosis, susceptibility to familial cutaneous melanoma, pancreatic cancer, susceptibility to, 5, leukemia, acute myeloid, susceptibility to, diffuse gastric and lobular breast cancer syndrome with or without cleft lip and/or palate, glioma susceptibility, hemangioma, capillary infantile, susceptibility to, CDH1-related diffuse gastric and lobular breast cancer syndrome, NTHL1-deficiency tumor predisposition syndrome, SAMD9-related spectrum and myeloid neoplasm risk, neuroblastoma, susceptibility to, 2, BARD1-related cancer predisposition, BRCA1-related cancer predisposition, BRCA2-related cancer predisposition, CHEK2-related cancer predisposition, PALB2-related cancer predisposition, RAD51C-related cancer predisposition, RAD51D-related cancer predisposition, Li-fraumeni-like syndrome, breast cancer, familial, susceptibility to, 1, breast cancer, familial, susceptibility to, 2, breast cancer, familial, susceptibility to, 3, colorectal cancer, susceptibility to, 4, colorectal cancer, susceptibility to, on chromosome 15, ovarian cancer, familial, susceptibility to, 1, ovarian cancer, familial, susceptibility to, 2, ovarian cancer, familial, susceptibility to, 3, inherited hematologic cancer-predisposing syndrome, mosaic neurofibromatosis/schwannomatosis, tumor predisposition syndrome 2, prostate cancer, hereditary, X-linked 3, follicular lymphoma, susceptibility to, GPR161-related medulloblastoma predisposition, SAMD9L-related spectrum and myeloid neoplasm risk, HAVCR2-related cancer predisposition, EGLN1-related erythrocytosis and pheochromocytoma/paraganglioma predisposition

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

288 retrieved; paginated sample, class counts are floors:

89 pathogenic, 66 uncertain significance, 40 conflicting classifications of pathogenicity, 27 likely pathogenic, 23 benign/likely benign, 22 pathogenic/likely pathogenic, 12 benign, 9 likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1676606Single allelePathogenicreviewed by expert panel
127337NM_000051.4(ATM):c.1339C>T (p.Arg447Ter)ATMPathogeniccriteria provided, multiple submitters, no conflicts
127340NM_000051.4(ATM):c.1564_1565del (p.Glu522fs)ATMPathogenicreviewed by expert panel
127374NM_000051.4(ATM):c.3802del (p.Glu1267_Val1268insTer)ATMPathogenicreviewed by expert panel
127403NM_000051.4(ATM):c.5228C>T (p.Thr1743Ile)ATMPathogenicreviewed by expert panel
127405NM_000051.4(ATM):c.5290del (p.Leu1764fs)ATMPathogenicreviewed by expert panel
127463NM_000051.4(ATM):c.8786+1G>AATMPathogenicreviewed by expert panel
1332151NM_000051.4(ATM):c.3662G>A (p.Trp1221Ter)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
135780NM_000051.4(ATM):c.8266A>T (p.Lys2756Ter)ATMPathogenicreviewed by expert panel
140818NM_000051.4(ATM):c.6997dupATMPathogenicreviewed by expert panel
140889NM_000051.4(ATM):c.1402_1403del (p.Lys468fs)ATMPathogenicreviewed by expert panel
140897NM_000051.4(ATM):c.8565_8566delinsAA (p.Ser2855_Val2856delinsArgIle)ATMPathogenicreviewed by expert panel
140907NM_000051.4(ATM):c.8473C>T (p.Gln2825Ter)ATMPathogenicreviewed by expert panel
141037NM_000051.4(ATM):c.378del (p.Asp126fs)ATMPathogeniccriteria provided, multiple submitters, no conflicts
141325NM_000051.4(ATM):c.2284_2285del (p.Leu762fs)ATMPathogenicreviewed by expert panel
141404NM_000051.4(ATM):c.5908C>T (p.Gln1970Ter)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
141474NM_000051.4(ATM):c.1355del (p.Thr452fs)ATMPathogenicreviewed by expert panel
141647NM_000051.4(ATM):c.7517_7520delATMPathogeniccriteria provided, multiple submitters, no conflicts
141742NM_000051.4(ATM):c.790del (p.Tyr264fs)ATMPathogenicreviewed by expert panel
141887NM_000051.4(ATM):c.1158del (p.Lys387fs)ATMPathogenicreviewed by expert panel
142355NM_000051.4(ATM):c.6976-2A>CATMPathogenicreviewed by expert panel
142700NM_000051.4(ATM):c.8147T>C (p.Val2716Ala)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1713223NM_000051.4(ATM):c.6372C>G (p.Tyr2124Ter)ATMPathogenicreviewed by expert panel
1733279NM_000051.4(ATM):c.3617T>A (p.Leu1206Ter)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
181865NM_000051.4(ATM):c.8264_8268del (p.Tyr2755fs)ATMPathogeniccriteria provided, multiple submitters, no conflicts
181874NM_000051.4(ATM):c.237del (p.Lys79fs)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
181974NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys)ATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
185137NM_000051.4(ATM):c.3349C>T (p.Gln1117Ter)ATMPathogenicreviewed by expert panel
185405NM_000051.4(ATM):c.2839-3_2839delinsGATACTAATMPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
186242NM_000051.4(ATM):c.8395_8404del (p.Phe2799fs)ATMPathogenicreviewed by expert panel

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 14 · Orphanet: 8 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
ATMLoFBLCA,BRCA,CCRCC,CHOL,CLLSLL,COAD,COADREAD,ESCA,HCC,LUAD,LUSC,MEL,NSCLC,PAAD,PANCREAS,PANET,PCM,PLMESO,PRAD,PROSTATE,STAD,UCEC,UTUC,WDTCCIViC #69

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
ATMDefinitiveAutosomal dominantATM-related cancer predisposition14

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ATMOrphanet:100Ataxia-telangiectasia
ATMOrphanet:1331Familial prostate cancer
ATMOrphanet:145Hereditary breast and/or ovarian cancer syndrome
ATMOrphanet:227535Hereditary breast cancer
ATMOrphanet:370109Ataxia-telangiectasia variant
ATMOrphanet:440437Familial colorectal cancer Type X
ATMOrphanet:52416Mantle cell lymphoma
ATMOrphanet:67038B-cell chronic lymphocytic leukemia

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ATMHGNC:795ENSG00000149311Q13315Serine-protein kinase ATMgencc,clinvar
C11orf65HGNC:28519ENSG00000166323Q8NCR3Protein MFIclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ATMSerine-protein kinase ATMSerine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor.
C11orf65Protein MFIActs as an inhibitor of mitochondrial fission.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.5

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Kinase113.9×0.142
Other/Unknown10.9×0.805

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ATMKinaseyes2.7.11.1PI3/4_kinase_cat_dom, PIK-rel_kinase_FAT, FATC_dom
C11orf65Other/Unknownno

Expression context

Cohort genes with no expression data: 0.

2 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)2
unknown0

Top tissues across cohort

TissueCohort genes
calcaneal tendon1
colonic epithelium1
corpus callosum1
left testis1
right testis1
sperm1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ATM286ubiquitousmarkercalcaneal tendon, colonic epithelium, corpus callosum
C11orf65163ubiquitousmarkersperm, left testis, right testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ATM7,383
C11orf65312

Structural data

PDB: 1 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ATMQ1331514

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
C11orf65Q8NCR374.69

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 61. Enrichment computed across 2 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Sensing of DNA Double Strand Breaks11903.3×0.007ATM
TP53 Regulates Transcription of Caspase Activators and Caspases1951.7×0.007ATM
Pexophagy1951.7×0.007ATM
Defective homologous recombination repair (HRR) due to PALB2 loss of function1951.7×0.007ATM
Diseases of DNA Double-Strand Break Repair1815.7×0.007ATM
Defective homologous recombination repair (HRR) due to BRCA2 loss of function1815.7×0.007ATM
Stabilization of p531761.3×0.007ATM
p53-Dependent G1 DNA Damage Response1713.8×0.007ATM
p53-Dependent G1/S DNA damage checkpoint1713.8×0.007ATM
G1/S DNA Damage Checkpoints1671.8×0.007ATM
Resolution of D-Loop Structures1634.4×0.007ATM
Diseases of DNA repair1571.0×0.007ATM
TP53 Regulates Transcription of Cell Death Genes1543.8×0.007ATM
TP53 Regulates Transcription of Genes Involved in Cytochrome C Release1543.8×0.007ATM
Regulation of TP53 Activity through Methylation1543.8×0.007ATM
Regulation of TP53 Expression and Degradation1519.1×0.007ATM
DNA Double Strand Break Response1475.8×0.007ATM
Impaired BRCA2 binding to PALB21456.8×0.007ATM
Defective homologous recombination repair (HRR) due to BRCA1 loss of function1423.0×0.007ATM
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function1423.0×0.007ATM
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function1423.0×0.007ATM
Cellular response to heat stress1393.8×0.007ATM
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)1393.8×0.007ATM
Homologous DNA Pairing and Strand Exchange1380.7×0.007ATM
Homology Directed Repair1308.6×0.007ATM
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)1308.6×0.007ATM
Impaired BRCA2 binding to RAD511308.6×0.007ATM
Resolution of D-loop Structures through Holliday Junction Intermediates1300.5×0.007ATM
HDR through Single Strand Annealing (SSA)1292.8×0.007ATM
Regulation of TP53 Degradation1292.8×0.007ATM

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
establishment of RNA localization to telomere14213.0×0.005ATM
establishment of protein-containing complex localization to telomere14213.0×0.005ATM
positive regulation of telomerase catalytic core complex assembly14213.0×0.005ATM
pre-B cell allelic exclusion12808.7×0.005ATM
cellular response to nitrosative stress12808.7×0.005ATM
peptidyl-serine autophosphorylation11685.2×0.005ATM
negative regulation of mitochondrial fission11685.2×0.005C11orf65
negative regulation of telomere capping11685.2×0.005ATM
regulation of telomere maintenance via telomerase11404.3×0.005ATM
obsolete negative regulation of protein targeting to mitochondrion11404.3×0.005C11orf65
positive regulation of telomere maintenance via telomere lengthening11404.3×0.005ATM
lipoprotein catabolic process11203.7×0.005ATM
V(D)J recombination11053.2×0.005ATM
meiotic telomere clustering1936.2×0.005ATM
female meiotic nuclear division1842.6×0.005ATM
histone mRNA catabolic process1842.6×0.005ATM
cellular response to X-ray1842.6×0.005ATM
DNA double-strand break processing1766.0×0.005ATM
regulation of autophagosome assembly1561.7×0.006ATM
pexophagy1526.6×0.006ATM
regulation of cellular response to heat1526.6×0.006ATM
positive regulation of DNA damage response, signal transduction by p53 class mediator1495.6×0.006ATM
replicative senescence1495.6×0.006ATM
negative regulation of B cell proliferation1468.1×0.006ATM
oocyte development1468.1×0.006ATM
cellular response to stress1421.3×0.006ATM
signal transduction in response to DNA damage1401.2×0.006ATM
positive regulation of telomere maintenance via telomerase1366.4×0.007ATM
cellular response to gamma radiation1300.9×0.008ATM
mitotic spindle assembly checkpoint signaling1280.9×0.008ATM

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 1

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
ATMAMIODARONE HYDROCHLORIDE

Top cohort targets by molecule count

SymbolMoleculesMax phase
ATM354
C11orf6500

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
AMIODARONE HYDROCHLORIDE4ATM
FURAZOLIDONE4ATM
ESTRADIOL ACETATE4ATM
NAFTIFINE HYDROCHLORIDE4ATM
METHYSERGIDE MALEATE4ATM
AMITRIPTYLINE HYDROCHLORIDE4ATM
XYLOMETAZOLINE HYDROCHLORIDE4ATM
FLUVOXAMINE MALEATE4ATM
ESTRADIOL VALERATE4ATM
PERMETHRIN4ATM
MITOTANE4ATM
TICLOPIDINE HYDROCHLORIDE4ATM
ENOXIMONE4ATM
METHYLENE BLUE ANHYDROUS4ATM
DITHIAZANINE IODIDE4ATM
ETHACRYNIC ACID4ATM
SECNIDAZOLE4ATM
MENADIONE4ATM
FENOFIBRATE4ATM
DIPYRIDAMOLE4ATM
DACTOLISIB3ATM
STREPTONIGRIN2ATM
CALCIMYCIN2ATM
ENPIROLINE2ATM
OXACEPROL2ATM
TOLONIUM CHLORIDE2ATM
ESTRADIOL BENZOATE2ATM
BERZOSERTIB2ATM
LARTESERTIB2ATM
ALTHIAZIDE2ATM

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
ATM240Binding:233, Functional:5, ADMET:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ATM2.7.11.1non-specific serine/threonine protein kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
ATM240

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Drug repurposing candidates

30 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

CompoundMax phaseCohort target (bioactivity)
AMIODARONE HYDROCHLORIDE4ATM
FURAZOLIDONE4ATM
ESTRADIOL ACETATE4ATM
NAFTIFINE HYDROCHLORIDE4ATM
METHYSERGIDE MALEATE4ATM
AMITRIPTYLINE HYDROCHLORIDE4ATM
XYLOMETAZOLINE HYDROCHLORIDE4ATM
FLUVOXAMINE MALEATE4ATM
ESTRADIOL VALERATE4ATM
PERMETHRIN4ATM
MITOTANE4ATM
TICLOPIDINE HYDROCHLORIDE4ATM
ENOXIMONE4ATM
METHYLENE BLUE ANHYDROUS4ATM
DITHIAZANINE IODIDE4ATM
ETHACRYNIC ACID4ATM
SECNIDAZOLE4ATM
MENADIONE4ATM
FENOFIBRATE4ATM
DIPYRIDAMOLE4ATM
DACTOLISIB3ATM
STREPTONIGRIN2ATM
CALCIMYCIN2ATM
ENPIROLINE2ATM
OXACEPROL2ATM
TOLONIUM CHLORIDE2ATM
ESTRADIOL BENZOATE2ATM
BERZOSERTIB2ATM
LARTESERTIB2ATM
ALTHIAZIDE2ATM

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1ATM
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1C11orf65

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
C11orf650

Clinical trials & evidence

Clinical trials

Clinical trials: 0.