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Gene

ATM

ATM serine/threonine kinase

Summary

Cytogenetic location
11q22.3
Coordinates
Chromosome 11: 108,223,067–108,369,102 (GRCh38)
Exons
63 exons across 146 kb
Protein
3,056 amino acids, 350.7 kDa
Also known as
TEL1, TELO1
Previous symbols
ATA, ATDC, ATC, ATD
MANE Select transcript
ENST00000675843.1NM_000051.4
Locus type
Protein-coding

Curated reports relevant to this gene

  • Ataxia-Telangiectasia

    • Autosomal recessive

      Progressive cerebellar ataxia, telangiectasia, immunodeficiency and cancer predisposition caused by biallelic ATM changes.

      • ClinGen rates the link definitive
      • 8 GenCC submitters rate it definitive or strong
      Actionability

      Diagnosis guides infection prevention and immunoglobulin replacement, minimising exposure to ionising radiation, cancer and lung monitoring, and carrier testing in relatives.

  • Female Infertility

    • Diminished or absent ability of a female to achieve conception.

      • ClinGen rates the link definitive
      • 8 GenCC submitters rate it definitive or strong

  • Breast and Ovarian Cancer Genes Beyond BRCA1/2

    • ATM-related cancer predispositionAutosomal dominant

      A single variant in ATM moderately raises the risk of breast cancer and is linked to pancreatic and prostate cancer.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong
      Actionability

      Enhanced breast screening is generally recommended; carriers with a partner who also carries an ATM variant may wish to know the risk of ataxia-telangiectasia in their children.

    • Hereditary breast cancerAutosomal dominant

      Inherited susceptibility to breast cancer caused by variants in one of several genes.

      • 2 GenCC submitters rate it definitive or strong
      Actionability

      Earlier and more intensive breast screening, including MRI, may be recommended depending on the gene.

Broader groupings

  • Other Inborn Errors of Immunity

    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • ClinGen rates the link definitive
      • 8 GenCC submitters rate it definitive or strong
      Actionability

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

  • Inherited Neurodegenerative Disorders

    • KIF5A-Related Neurodegenerative DisorderAutosomal dominant

      One of 372 genes linked to it

      Caused by changes in one copy of KIF5A, which encodes a motor protein with a cargo-binding tail. Different types of change lead to different conditions: hereditary spastic paraplegia type 10, an axonal form of Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis (ALS).

      • ClinGen rates the link definitive
      • 8 GenCC submitters rate it definitive or strong
      Actionability

      Care is symptomatic and depends on the presentation, including physiotherapy, antispasticity medicines and multidisciplinary ALS care. Each child of an affected person has a 1 in 2 chance of inheriting the change; genetic counselling helps families understand this.

How ATM is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 11, with a bracket where ATM sits. ATM and 9 genes near it on chromosome 11, from 107,796,085 to 108,796,084.Chromosome 1111q22.3p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q25107.8 Mb108 Mb108.2 Mb108.4 Mb108.6 MbSLC35F2: 107,790,455–107,928,293, reverse strandSLC35F2RAB39A: 107,928,448–107,968,143, forward strandRAB39ACUL5: 108,008,821–108,107,781, forward strandCUL5ACAT1: 108,116,695–108,148,957, forward strandACAT1NPAT: 108,155,267–108,222,659, reverse strandNPATATM: 108,223,067–108,369,102, forward strandATMC11orf65: 108,308,519–108,467,536, reverse strandC11orf65POGLUT3: 108,472,106–108,498,603, reverse strandPOGLUT3EXPH5: 108,505,435–108,593,780, reverse strandEXPH5DDX10: 108,665,053–108,940,999, forward strandDDX10Diagram of ATM: 63 exons on the forward strand of chromosome 11Exon 2: 19 known disease-causing sitesExon 3: 28 known disease-causing sitesExon 4: 36 known disease-causing sitesExon 5: 50 known disease-causing sitesExon 6: 41 known disease-causing sitesExon 7: 71 known disease-causing sitesExon 8: 54 known disease-causing sitesExon 9: 49 known disease-causing sitesExon 10: 102 known disease-causing sitesExon 11: 54 known disease-causing sitesExon 12: 20 known disease-causing sitesExon 13: 66 known disease-causing sitesExon 14: 38 known disease-causing sitesExon 15: 31 known disease-causing sitesExon 16: 20 known disease-causing sitesExon 17: 48 known disease-causing sitesExon 18: 45 known disease-causing sitesExon 19: 20 known disease-causing sitesExon 20: 46 known disease-causing sitesExon 21: 18 known disease-causing sitesExon 22: 34 known disease-causing sitesExon 23: 37 known disease-causing sitesExon 24: 55 known disease-causing sitesExon 25: 57 known disease-causing sitesExon 26: 65 known disease-causing sitesExon 27: 32 known disease-causing sitesExon 28: 33 known disease-causing sitesExon 29: 53 known disease-causing sitesExon 30: 48 known disease-causing sitesExon 31: 39 known disease-causing sitesExon 32: 35 known disease-causing sitesExon 33: 22 known disease-causing sitesExon 34: 32 known disease-causing sitesExon 35: 42 known disease-causing sitesExon 36: 48 known disease-causing sitesExon 37: 41 known disease-causing sitesExon 38: 25 known disease-causing sitesExon 39: 46 known disease-causing sitesExon 40: 24 known disease-causing sitesExon 41: 26 known disease-causing sitesExon 42: 38 known disease-causing sitesExon 43: 42 known disease-causing sitesExon 44: 38 known disease-causing sitesExon 45: 26 known disease-causing sitesExon 46: 79 known disease-causing sitesExon 47: 48 known disease-causing sitesExon 48: 40 known disease-causing sitesExon 49: 59 known disease-causing sitesExon 50: 51 known disease-causing sitesExon 51: 30 known disease-causing sitesExon 52: 44 known disease-causing sitesExon 53: 39 known disease-causing sitesExon 54: 24 known disease-causing sitesExon 55: 47 known disease-causing sitesExon 56: 38 known disease-causing sitesExon 57: 49 known disease-causing sitesExon 58: 50 known disease-causing sitesExon 59: 25 known disease-causing sitesExon 60: 36 known disease-causing sitesExon 61: 19 known disease-causing sitesExon 62: 33 known disease-causing sitesExon 63: 53 known disease-causing sitesExon 1: 108,223,067–108,223,186, 120 basesExon 2: 108,227,595–108,227,696, 102 bases. 11 variants with a page in exon 2. List themExon 3: 108,227,776–108,227,888, 113 bases. 8 variants with a page in exon 3. List themExon 4: 108,229,178–108,229,323, 146 bases. 7 variants with a page in exon 4. List themExon 5: 108,235,670–108,235,834, 165 bases. 17 variants with a page in exon 5. List themExon 6: 108,243,953–108,244,118, 166 bases. 8 variants with a page in exon 6. List themExon 7: 108,244,788–108,245,026, 239 bases. 20 variants with a page in exon 7. List themExon 8: 108,246,964–108,247,127, 164 bases. 14 variants with a page in exon 8. List themExon 9: 108,248,933–108,249,102, 170 bases. 17 variants with a page in exon 9. List themExon 10: 108,250,701–108,251,072, 372 bases. 27 variants with a page in exon 10. List themExon 11: 108,251,837–108,252,031, 195 bases. 12 variants with a page in exon 11. List themExon 12: 108,252,817–108,252,912, 96 bases. 5 variants with a page in exon 12. List themExon 13: 108,253,814–108,254,039, 226 bases. 14 variants with a page in exon 13. List themExon 14: 108,256,215–108,256,340, 126 bases. 7 variants with a page in exon 14. List themExon 15: 108,257,481–108,257,606, 126 bases. 3 variants with a page in exon 15. List themExon 16: 108,258,986–108,259,075, 90 bases. 7 variants with a page in exon 16. List themExon 17: 108,267,171–108,267,342, 172 bases. 12 variants with a page in exon 17. List themExon 18: 108,268,410–108,268,609, 200 bases. 8 variants with a page in exon 18. List themExon 19: 108,271,064–108,271,146, 83 bases. 2 variants with a page in exon 19. List themExon 20: 108,271,251–108,271,406, 156 bases. 8 variants with a page in exon 20. List themExon 21: 108,272,532–108,272,607, 76 bases. 5 variants with a page in exon 21. List themExon 22: 108,272,722–108,272,852, 131 bases. 16 variants with a page in exon 22. List themExon 23: 108,279,491–108,279,608, 118 bases. 9 variants with a page in exon 23. List themExon 24: 108,280,995–108,281,168, 174 bases. 16 variants with a page in exon 24. List themExon 25: 108,282,710–108,282,879, 170 bases. 6 variants with a page in exon 25. List themExon 26: 108,284,227–108,284,473, 247 bases. 23 variants with a page in exon 26. List themExon 27: 108,287,600–108,287,715, 116 bases. 6 variants with a page in exon 27. List themExon 28: 108,288,977–108,289,103, 127 bases. 7 variants with a page in exon 28. List themExon 29: 108,289,602–108,289,801, 200 bases. 11 variants with a page in exon 29. List themExon 30: 108,292,619–108,292,793, 175 bases. 6 variants with a page in exon 30. List themExon 31: 108,293,313–108,293,477, 165 bases. 12 variants with a page in exon 31. List themExon 32: 108,294,927–108,295,059, 133 bases. 6 variants with a page in exon 32. List themExon 33: 108,297,287–108,297,382, 96 bases. 4 variants with a page in exon 33. List themExon 34: 108,299,714–108,299,885, 172 bases. 5 variants with a page in exon 34. List themExon 35: 108,301,648–108,301,789, 142 bases. 11 variants with a page in exon 35. List themExon 36: 108,302,853–108,303,029, 177 bases. 11 variants with a page in exon 36. List themExon 37: 108,304,675–108,304,852, 178 bases. 9 variants with a page in exon 37. List themExon 38: 108,307,897–108,307,984, 88 bases. 6 variants with a page in exon 38. List themExon 39: 108,310,160–108,310,315, 156 bases. 11 variants with a page in exon 39. List themExon 40: 108,312,411–108,312,498, 88 bases. 6 variants with a page in exon 40. List themExon 41: 108,315,823–108,315,911, 89 bases. 7 variants with a page in exon 41. List themExon 42: 108,316,011–108,316,113, 103 bases. 9 variants with a page in exon 42. List themExon 43: 108,317,373–108,317,521, 149 bases. 14 variants with a page in exon 43. List themExon 44: 108,319,954–108,320,058, 105 bases. 11 variants with a page in exon 44. List themExon 45: 108,321,301–108,321,420, 120 bases. 5 variants with a page in exon 45. List themExon 46: 108,325,310–108,325,544, 235 bases. 15 variants with a page in exon 46. List themExon 47: 108,326,058–108,326,225, 168 bases. 12 variants with a page in exon 47. List themExon 48: 108,327,645–108,327,758, 114 bases. 9 variants with a page in exon 48. List themExon 49: 108,329,021–108,329,238, 218 bases. 14 variants with a page in exon 49. List themExon 50: 108,330,214–108,330,421, 208 bases. 9 variants with a page in exon 50. List themExon 51: 108,331,444–108,331,557, 114 bases. 5 variants with a page in exon 51. List themExon 52: 108,331,879–108,332,037, 159 bases. 10 variants with a page in exon 52. List themExon 53: 108,332,762–108,332,900, 139 bases. 14 variants with a page in exon 53. List themExon 54: 108,333,886–108,333,968, 83 bases. 5 variants with a page in exon 54. List themExon 55: 108,334,969–108,335,109, 141 bases. 15 variants with a page in exon 55. List themExon 56: 108,335,845–108,335,961, 117 bases. 12 variants with a page in exon 56. List themExon 57: 108,343,222–108,343,371, 150 bases. 21 variants with a page in exon 57. List themExon 58: 108,345,743–108,345,908, 166 bases. 21 variants with a page in exon 58. List themExon 59: 108,347,279–108,347,365, 87 bases. 5 variants with a page in exon 59. List themExon 60: 108,353,766–108,353,880, 115 bases. 8 variants with a page in exon 60. List themExon 61: 108,354,811–108,354,874, 64 bases. 7 variants with a page in exon 61. List themExon 62: 108,365,082–108,365,218, 137 bases. 11 variants with a page in exon 62. List themExon 63: 108,365,325–108,369,102, 3,778 bases. 17 variants with a page in exon 63. List them151015202530354045505560635′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 12.9 kb of the gene's 146 kb; 9,171 of those bases code for the protein.

Sequencing ATM

2Easy

How hard ATM is to sequence with short reads, out of 100

Almost all of ATM's exons sit where short reads map cleanly.

What adds to it: the share of ATM's exons in each kind of hard region

  • Mappability0.5%
  • Homology0%
  • Shared with chrY0%
  • Reference coverage0%
  • Repeats2.1%
  • GC content5.4%

A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scored

2,935

positions in ATM where ClinVar classes a change as pathogenic or likely pathogenic

11 of them (0.4%) fall in regions short reads find hard.

  • Low mappability (11 sites)

A whole genome covers all 146 kb of ATM, introns included, not only the 12.9 kb of exons.

Variants with a page (811)

The ATM variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A911Rfs*19c.2730_2731insAGExon 18108,268,501Pathogenic3 stars out of 4 reviewed by expert panel
c.2T>CExon 2108,227,626Pathogenic3 stars out of 4 reviewed by expert panel
c.332-1G>AIntron 4108,235,669Pathogenic3 stars out of 4 reviewed by expert panel
c.496+5G>AIntron 5108,235,839Pathogenic3 stars out of 4 reviewed by expert panel
c.1122_1123delExon 9108,248,987Pathogenic3 stars out of 4 reviewed by expert panel
c.1607+1G>TIntron 10108,251,073Pathogenic3 stars out of 4 reviewed by expert panel
c.2251-2A>TIntron 14108,257,479Pathogenic3 stars out of 4 reviewed by expert panel
c.2251-4A>GIntron 14108,257,477Likely pathogenic3 stars out of 4 reviewed by expert panel
c.2466+5G>CIntron 16108,259,080Likely pathogenic3 stars out of 4 reviewed by expert panel
c.2639-23_2639-21delIntron 17108,268,386Pathogenic3 stars out of 4 reviewed by expert panel

See all 811 ATM variants →

ClinVar pathogenic variants (3,833)

The ATM variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.

  • Pathogenic 2,826
  • Pathogenic/likely pathogenic 278
  • Likely pathogenic 729
VariantConditionsClinVar classificationReview status
NM_000051.4(ATM):c.2T>C (p.Met1Thr)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.67C>T (p.Arg23Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.217_218del (p.Glu73fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.332-1G>AATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.387del (p.Asp130fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.467G>A (p.Trp156Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.480_484del (p.Gln161fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.496+5G>AATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.748C>T (p.Arg250Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.790del (p.Tyr264fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.824del (p.Ser274_Leu275insTer)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1122_1123del (p.Glu376fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1158del (p.Lys387fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1355del (p.Thr452fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1396C>T (p.Gln466Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1402_1403del (p.Lys468fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1442T>G (p.Leu481Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1564_1565del (p.Glu522fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1607+1G>TATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.1782del (p.Val595fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.2152dup (p.Cys718fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.2251-2A>TATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.2284_2285del (p.Leu762fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.2413C>T (p.Arg805Ter)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel
NM_000051.4(ATM):c.2508dup (p.Ser837fs)ATM-related cancer predispositionPathogenic3 stars out of 4 reviewed by expert panel

See all 3,833 with every other ATM variant in ClinVar → (opens in a new tab)

Genes linked to the same conditions

Traits linked to ATM

The Human Phenotype Ontology lists these as features of the rare conditions ATM can cause. Each trait's page lists the other genes linked to it.

Abnormality of the nervous system

Show 29 more traits

External links

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-21: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.21-c791e85a.

Cite this page

APA

Dante Labs. (n.d.). ATM gene: ATM serine/threonine kinase. Retrieved 23 October 2026, from https://dantelabs.com/genes/atm

Vancouver

Dante Labs. ATM gene: ATM serine/threonine kinase [Internet]. [cited 23 October 2026]. Available from: https://dantelabs.com/genes/atm

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