Human Gene ATM (uc009yxs.1)
  Description: Homo sapiens ataxia telangiectasia mutated (ATM), mRNA.
RefSeq Summary (NM_000051): The protein encoded by this gene belongs to the PI3/PI4-kinase family. This protein is an important cell cycle checkpoint kinase that phosphorylates; thus, it functions as a regulator of a wide variety of downstream proteins, including tumor suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1. This protein and the closely related kinase ATR are thought to be master controllers of cell cycle checkpoint signaling pathways that are required for cell response to DNA damage and for genome stability. Mutations in this gene are associated with ataxia telangiectasia, an autosomal recessive disorder. [provided by RefSeq, Aug 2010].
Transcript (Including UTRs)
   Position: hg19 chr11:108,139,137-108,142,133 Size: 2,997 Total Exon Count: 2 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsPathwaysOther Names
GeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:108,139,137-108,142,133)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerGeneNetworkHGNCLynx
MalacardsPubMedWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATM
CDC HuGE Published Literature: ATM
Positive Disease Associations: ataxia-telangiectasia , breast cancer , diffuse large B-cell lymphoma , endometrial cancer , fibrosis, subcutaneous , Hodgkin's disease , Melanoma , prostate cancer , radiotherapy response
Related Studies:
  1. ataxia-telangiectasia
    McConville CM et al. 1996, Mutations associated with variant phenotypes in ataxia-telangiectasia., American journal of human genetics. 1996 Aug;59(2):320-30. [PubMed 8755918]
  2. breast cancer
    Dork, T. et al. 2001, Spectrum of ATM gene mutations in a hospital-based series of unselected breast cancer patients., Cancer research. 2001 Oct;61(20):7608-15. [PubMed 11606401]
    We conclude that a large variety of distinct ATM mutations and variants exist among breast cancer patients, some of which can contribute to the etiology and progression of the malignancy. Screening for frequent A-T mutations such as the 1066-6-->G splice site substitution can be effective to prospectively identify A-T heterozygotes in an unselected cancer patient population.
  3. breast cancer
    Iannuzzi, C. M. et al. 2002, ATM mutations in female breast cancer patients predict for an increase in radiation-induced late effects., International journal of radiation oncology, biology, physics. 2002 Mar;52(3):606-13. [PubMed 11849780]
    Possession of an ATM mutation, particularly when 2 are present, may be predictive of an increase in subcutaneous late tissue effects after RT for breast cancer and may subsequently prove to be a relative contraindication to standard management. These patients may be better served with reduced doses of radiation. Equivalent local control remains to be tested, but this germline alteration may radiosensitize normal tissues, as well as the tumor itself. DHPLC is effective in the identification of these patients. A larger study is required to confirm these findings.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ATM
Diseases sorted by gene-association score: ataxia-telangiectasia* (1798), mantle cell lymphoma* (813), ataxia* (494), t-cell prolymphocytic leukemia* (443), primary immunodeficiency disease* (412), breast cancer* (367), chronic lymphocytic leukemia* (301), brca1 hereditary breast and ovarian cancer syndrome* (301), kidney cancer* (285), brca2 hereditary breast and ovarian cancer syndrome* (245), cerebellar ataxia* (245), ataxia-oculomotor apraxia 3* (179), ataxia and polyneuropathy, adult-onset* (179), renal cell carcinoma* (141), prolymphocytic leukemia (54), leukemia, b-cell, chronic (19), nijmegen breakage syndrome (19), bilateral breast cancer (18), lymphoma (17), telangiectasis (15), synchronous bilateral breast carcinoma (14), cll/sll (13), cerebellar disease (10), apraxia (9), bloom syndrome (9), richter's syndrome (9), adhesive otitis media (8), cerebellar degeneration (8), leukemia (8), sporadic breast cancer (8), xeroderma pigmentosum, group a (8), li-fraumeni syndrome (7), swayback (6), female breast cancer (6), lig4 syndrome (5), urethra adenocarcinoma (5), urethra clear cell adenocarcinoma (5), autosomal recessive cerebellar ataxia (5), fanconi anemia, complementation group a (5), urethral benign neoplasm (5), lymphoblastic leukemia (4), myxosarcoma (4), radiation cystitis (4), dyskinetic cerebral palsy (4), nodular malignant melanoma (4), spinal chordoma (4), lung cancer (2), colorectal cancer (2), asphyxiating thoracic dystrophy (2), lymphoma, non-hodgkin (1), nervous system disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.48 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 244.54 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  X91196 - H.sapiens mRNA for E14 and A-T proteins.
LF208492 - JP 2014500723-A/15995: Polycomb-Associated Non-Coding RNAs.
LF213954 - JP 2014500723-A/21457: Polycomb-Associated Non-Coding RNAs.
U33841 - Human ataxia telangiectasia (ATM) mRNA, complete cds.
MA449531 - JP 2018138019-A/21457: Polycomb-Associated Non-Coding RNAs.
MA444069 - JP 2018138019-A/15995: Polycomb-Associated Non-Coding RNAs.
AF035328 - Homo sapiens clone E21ACOR ATM (ATM) mRNA, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04110 - Cell cycle
hsa04115 - p53 signaling pathway
hsa04210 - Apoptosis

BioCarta from NCI Cancer Genome Anatomy Project
h_cdc25Pathway - cdc25 and chk1 Regulatory Pathway in response to DNA damage
h_rbPathway - RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage
h_atrbrcaPathway - Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility
h_p53Pathway - p53 Signaling Pathway
h_atmPathway - ATM Signaling Pathway
h_chemicalPathway - Apoptotic Signaling in Response to DNA Damage
h_g1Pathway - Cell Cycle: G1/S Check Point
h_p53hypoxiaPathway - Hypoxia and p53 in the Cardiovascular system
h_g2Pathway - Cell Cycle: G2/M Checkpoint
h_plk3Pathway - Regulation of cell cycle progression by Plk3

-  Other Names for This Gene
  Alternate Gene Symbols: AF035328
UCSC ID: uc009yxs.1
RefSeq Accession: NM_000051

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ATM:
ataxia-telangiectas (Ataxia-Telangiectasia)
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: no RNA accession: AF035328.1
exon count: 2CDS single in 3' UTR: no RNA size: 307
ORF size: 0CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 536.00frame shift in genome: no % Coverage: 98.37
has start codon: no stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.