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ATM ATM serine/threonine kinase [ Homo sapiens (human) ]

Gene ID: 472, updated on 22-Feb-2020

Summary

Official Symbol
ATMprovided by HGNC
Official Full Name
ATM serine/threonine kinaseprovided by HGNC
Primary source
HGNC:HGNC:795
See related
Ensembl:ENSG00000149311 MIM:607585
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AT1; ATA; ATC; ATD; ATE; ATDC; TEL1; TELO1
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 15.4), spleen (RPKM 9.5) and 25 other tissues See more
Orthologs

Genomic context

See ATM in Genome Data Viewer
Location:
11q22.3
Exon count:
69
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (108222484..108369102)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (108093559..108239829)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene cullin 5 Neighboring gene acetyl-CoA acetyltransferase 1 Neighboring gene nuclear protein, coactivator of histone transcription Neighboring gene chromosome 11 open reading frame 65 Neighboring gene uncharacterized LOC112267909 Neighboring gene protein O-glucosyltransferase 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes.
NHGRI GWA Catalog
Does metformin work for everyone? A genome-wide association study for metformin response.
NHGRI GWA Catalog
Genome-wide association study identifies three new melanoma susceptibility loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env PML, TopBP1, NBS1 or ATM-induced activation of phosphorylation of Chk2 participates in the DNA damage-elicited pro-apoptotic cascade that leads to the demise of Env-elicited syncytia PubMed
env Interactions between tumor suppressor protein PML, TopBP1 and ATM exhibit in HIV-1 Env-elicited syncytia PubMed
env Tumor suppressor protein PML is required for the activating phosphorylation of ATM, p38 MAPK, and p53 in HIV-1 Env-elicited syncytia PubMed
Rev rev Ataxia-telangiectasia-mutated (ATM) kinase enhances HIV-1 replication by stimulating the action of the HIV-1 Rev viral posttranscriptional regulator PubMed
Tat tat HIV-1 Tat upregulates ATM expression in Tat-infected Jurkat T cells PubMed
Vif vif A3G upregulates NKG2D ligands through an ATM pathway and in which HIV-1 Vif counteracts this upregulation by decreasing A3G expression PubMed
Vpr vpr HIV-1 Vpr activates ATM, a DNA double-strand break kinase that is required for cell response to DNA damage and for genome stability PubMed
integrase gag-pol DNA double-strand breaks enhance integration of HIV-1 into macrophages in an IN D64A mutant, which has defective integrase catalytic activity. This IN-D64A-independent viral transduction is blocked by an inhibitor of ATM PubMed
gag-pol ATM is proposed to play a role in the prevention of HIV-1 Integrase mediated cell killing PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC74674, DKFZp781A0353

Gene Ontology Provided by GOA

Function Evidence Code Pubs
1-phosphatidylinositol-3-kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent protein kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein N-terminus binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein dimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA damage checkpoint IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA damage induced protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest TAS
Traceable Author Statement
more info
 
DNA double-strand break processing TAS
Traceable Author Statement
more info
 
DNA replication TAS
Traceable Author Statement
more info
 
V(D)J recombination IEA
Inferred from Electronic Annotation
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
cell cycle arrest IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to X-ray IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to gamma radiation IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to nitrosative stress IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to retinoic acid ISS
Inferred from Sequence or Structural Similarity
more info
 
determination of adult lifespan IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair via homologous recombination IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair via nonhomologous end joining TAS
Traceable Author Statement
more info
 
establishment of RNA localization to telomere IMP
Inferred from Mutant Phenotype
more info
PubMed 
establishment of protein-containing complex localization to telomere IC
Inferred by Curator
more info
PubMed 
female meiotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
histone mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
histone phosphorylation IEA
Inferred from Electronic Annotation
more info
 
immunoglobulin production IEA
Inferred from Electronic Annotation
more info
 
intrinsic apoptotic signaling pathway in response to DNA damage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipoprotein catabolic process IEA
Inferred from Electronic Annotation
more info
 
male meiotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
meiotic telomere clustering IEA
Inferred from Electronic Annotation
more info
 
mitotic spindle assembly checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of B cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of TORC1 signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of TORC1 signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of telomere capping IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
oocyte development IEA
Inferred from Electronic Annotation
more info
 
ovarian follicle development IEA
Inferred from Electronic Annotation
more info
 
peptidyl-serine autophosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-serine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-3-phosphate biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA catabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA damage response, signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone phosphorylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of telomerase catalytic core complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of telomere maintenance via telomerase ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of telomere maintenance via telomere lengthening IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
pre-B cell allelic exclusion ISS
Inferred from Sequence or Structural Similarity
more info
 
protein autophosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
protein autophosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
reciprocal meiotic recombination TAS
Traceable Author Statement
more info
PubMed 
regulation of apoptotic process TAS
Traceable Author Statement
more info
 
regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cellular response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
regulation of cellular response to heat TAS
Traceable Author Statement
more info
 
regulation of microglial cell activation IEA
Inferred from Electronic Annotation
more info
 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
NOT regulation of telomerase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of telomere maintenance via telomerase IGI
Inferred from Genetic Interaction
more info
PubMed 
replicative senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to ionizing radiation IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
signal transduction involved in mitotic G2 DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
somitogenesis IEA
Inferred from Electronic Annotation
more info
 
telomere maintenance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thymus development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
DNA repair complex IDA
Inferred from Direct Assay
more info
PubMed 
cell IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
colocalizes_with nuclear chromosome, telomeric region IC
Inferred by Curator
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spindle IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
serine-protein kinase ATM
Names
A-T mutated
AT mutated
TEL1, telomere maintenance 1, homolog
ataxia telangiectasia mutated
NP_000042.3
NP_001338763.1
NP_001338764.1
NP_001338765.1
XP_005271619.2
XP_006718906.1
XP_006718908.1
XP_011541142.1
XP_011541144.1
XP_011541145.1
XP_011541146.1
XP_011541147.1
XP_016873278.1
XP_016873279.1
XP_016873280.1
XP_016873281.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009830.1 RefSeqGene

    Range
    5001..151268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_135

mRNA and Protein(s)

  1. NM_000051.3NP_000042.3  serine-protein kinase ATM isoform a

    See identical proteins and their annotated locations for NP_000042.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AP001925, AP005718, U26455, U33841, X91196
    Consensus CDS
    CCDS31669.1
    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Related
    ENSP00000278616.4, ENST00000278616.8
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  2. NM_001351834.2NP_001338763.1  serine-protein kinase ATM isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform . Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AP001925, AP005718, U33841
    Consensus CDS
    CCDS31669.1
    Related
    ENSP00000388058.2, ENST00000452508.6
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  3. NM_001351835.1NP_001338764.1  serine-protein kinase ATM isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
    Source sequence(s)
    AI479273, AP001925
    Consensus CDS
    CCDS86245.1
    Related
    ENSP00000491585.1, ENST00000639240.1
    Conserved Domains (1) summary
    pfam11640
    Location:8110
    TAN; Telomere-length maintenance and DNA damage repair
  4. NM_001351836.1NP_001338765.1  serine-protein kinase ATM isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, 3' UTR, and 3' coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
    Source sequence(s)
    BC061584
    Consensus CDS
    CCDS86245.1
    Related
    ENSP00000480205.1, ENST00000526567.5
    Conserved Domains (1) summary
    pfam11640
    Location:8110
    TAN; Telomere-length maintenance and DNA damage repair

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    108222484..108369102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542843.2XP_011541145.1  serine-protein kinase ATM isoform X3

    Conserved Domains (3) summary
    cd05171
    Location:26832890
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam11640
    Location:11165
    TAN; Telomere-length maintenance and DNA damage repair
  2. XM_017017791.1XP_016873280.1  serine-protein kinase ATM isoform X6

  3. XM_017017792.2XP_016873281.1  serine-protein kinase ATM isoform X7

  4. XM_011542842.3XP_011541144.1  serine-protein kinase ATM isoform X2

    Conserved Domains (4) summary
    cd05171
    Location:26282907
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20422434
    FAT; FAT domain
    pfam02260
    Location:29713000
    FATC; FATC domain
    pfam11640
    Location:11112
    TAN; Telomere-length maintenance and DNA damage repair
  5. XM_011542844.3XP_011541146.1  serine-protein kinase ATM isoform X4

    Conserved Domains (3) summary
    cd05171
    Location:23352614
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:17492141
    FAT; FAT domain
    pfam02260
    Location:26782707
    FATC; FATC domain
  6. XM_005271562.5XP_005271619.2  serine-protein kinase ATM isoform X1

    See identical proteins and their annotated locations for XP_005271619.2

    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  7. XM_017017790.2XP_016873279.1  serine-protein kinase ATM isoform X1

    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  8. XM_017017789.2XP_016873278.1  serine-protein kinase ATM isoform X1

    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  9. XM_011542840.3XP_011541142.1  serine-protein kinase ATM isoform X1

    See identical proteins and their annotated locations for XP_011541142.1

    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  10. XM_006718843.4XP_006718906.1  serine-protein kinase ATM isoform X1

    See identical proteins and their annotated locations for XP_006718906.1

    UniProtKB/Swiss-Prot
    Q13315
    UniProtKB/TrEMBL
    A0A024R3C7
    Conserved Domains (4) summary
    cd05171
    Location:26832962
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:20972489
    FAT; FAT domain
    pfam02260
    Location:30263055
    FATC; FATC domain
    pfam11640
    Location:8165
    TAN; Telomere-length maintenance and DNA damage repair
  11. XM_011542845.2XP_011541147.1  serine-protein kinase ATM isoform X5

    Conserved Domains (3) summary
    cd05171
    Location:22472526
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:16612053
    FAT; FAT domain
    pfam02260
    Location:25902619
    FATC; FATC domain
  12. XM_006718845.2XP_006718908.1  serine-protein kinase ATM isoform X8

    See identical proteins and their annotated locations for XP_006718908.1

    UniProtKB/Swiss-Prot
    Q13315
    Conserved Domains (3) summary
    cd05171
    Location:13351614
    PIKKc_ATM; Catalytic domain of Ataxia Telangiectasia Mutated
    pfam02259
    Location:7491141
    FAT; FAT domain
    pfam02260
    Location:16781707
    FATC; FATC domain

RNA

  1. XR_002957150.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_138292.3: Suppressed sequence

    Description
    NM_138292.3: This RefSeq was permanently suppressed because the CDS was partial, and the transcript retained intronic sequence at its 5' end.
  2. NM_138293.1: Suppressed sequence

    Description
    NM_138293.1: This RefSeq was permanently suppressed because it represents a partial, incompletely processed transcript.
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