Human Gene ATM (uc001pkg.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 chr11:108,167,701-108,204,695 Size: 36,995 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr11:108,168,034-108,204,695 Size: 36,662 Coding Exon Count: 22 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:108,167,701-108,204,695)mRNA (may differ from genome)Protein (1027 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.00333-0.186 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015519 - ATM/Tel1
IPR003151 - PIK-rel_kinase_FAT
IPR014009 - PIK_FAT

Pfam Domains:
PF02259 - FAT domain

ModBase Predicted Comparative 3D Structure on Q68DE6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004674 protein serine/threonine kinase activity

Biological Process:
GO:0000077 DNA damage checkpoint
GO:0000723 telomere maintenance
GO:0006281 DNA repair
GO:0010212 response to ionizing radiation
GO:0016572 histone phosphorylation
GO:0090399 replicative senescence


-  Descriptions from all associated GenBank mRNAs
  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.
U26455 - Human phosphatidylinositol 3-kinase homolog (ATM) mRNA, complete cds.
BC137169 - Homo sapiens ataxia telangiectasia mutated, mRNA (cDNA clone MGC:168789 IMAGE:9021166), complete cds.
CR749436 - Homo sapiens mRNA; cDNA DKFZp781A0353 (from clone DKFZp781A0353).
Y08455 - H.sapiens mRNA for ataxia telangiectasia protein, exon skipped allele.
AK299843 - Homo sapiens cDNA FLJ57034 complete cds, highly similar to Serine-protein kinase ATM (EC 2.7.11.1).
LF377045 - JP 2014500723-A/184548: Polycomb-Associated Non-Coding RNAs.
LF377043 - JP 2014500723-A/184546: Polycomb-Associated Non-Coding RNAs.
MA612622 - JP 2018138019-A/184548: Polycomb-Associated Non-Coding RNAs.
MA612620 - JP 2018138019-A/184546: Polycomb-Associated Non-Coding RNAs.

-  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: CR749436, DKFZp781A0353, NM_000051, NP_000042, Q68DE6, Q68DE6_HUMAN
UCSC ID: uc001pkg.1
RefSeq Accession: NM_000051
Protein: Q68DE6

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

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: CR749436.1
exon count: 22CDS single in 3' UTR: no RNA size: 4559
ORF size: 3081CDS single in intron: no Alignment % ID: 99.85
txCdsPredict score: 6266.50frame shift in genome: no % Coverage: 73.52
has start codon: yes 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: 313# 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.