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Here you can see the gene and the variant being analyzed.

We summarize a large amount of clinical data on this gene here. Links are added where available to source information.

Prediction information is summarized here, the percentage shows the likelihood that the variant is pathogenic.

Agreement is a measure (out of 5 stars) of how much our predictors agree between each other. When predictors agree, the prediction is more likely to be correct.

Data quality is a measure (out of 5 stars) of how good the underlying data for this prediction is. This is an assessment of the depth of our alignments and the number of structures available, among other factors.

This table shows literature for this exact position and protein, if it is available.

This table shows literature for this position in homologous proteins, if it is available.

This is a description of our prediction.

This plot illustrates the agreement between different classifiers. If the prediction distributions align on one side it indicates increased certainty in the prediction.

This describes the data quality for this position.

Here are the four factors that contributed most to the prediction. Factors that contributed to a benign prediction are colored blue, pathogenic factors are colored red.

This plot shows all the factors for prediction. Factors that contributed to a benign prediction are colored blue, pathogenic factors are colored red.

This plot shows the conservation on this position.

Here the conservation statistics are described.

This is an interactive structure display. Feel free to play with it after the tour!

This is a list of interactions we found for this position.

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Summary

ATM - ENST00000278616

Gene ATM - ENSG00000149311 | ENSP00000278616 | ENST00000278616
Ensembl | RefSeq | UniProt
Location GRCh38 11:108222832-108369099 Ensembl UCSC
Description ATM serine/threonine kinase

Serine/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. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. After the introduction of DNA breaks by the RAG complex on one immunoglobulin allele, acts by mediating a repositioning of the second allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. Also involved in signal transduction and cell cycle control. May function as a tumor suppressor. Necessary for activation of ABL1 and SAPK. Phosphorylates DYRK2, CHEK2, p53/TP53, FANCD2, NFKBIA, BRCA1, CTIP, nibrin (NBN), TERF1, RAD9 and DCLRE1C. May play a role in vesicle and/or protein transport. Could play a role in T-cell development, gonad and neurological function. Plays a role in replication-dependent histone mRNA degradation. Binds DNA ends. Phosphorylation of DYRK2 in nucleus in response to genotoxic stress prevents its MDM2-mediated ubiquitination and subsequent proteasome degradation. Phosphorylates ATF2 which stimulates its function in DNA damage response. {ECO:0000269|PubMed:10973490, ECO:0000269|PubMed:12556884, ECO:0000269|PubMed:14871926, ECO:0000269|PubMed:15916964, ECO:0000269|PubMed:16086026, ECO:0000269|PubMed:16858402, ECO:0000269|PubMed:17923702, ECO:0000269|PubMed:19431188, ECO:0000269|PubMed:19965871}.;

Condition(s)
  • Ataxia telangiectasia (AT)

    A rare recessive disorder characterized by progressive cerebellar ataxia, dilation of the blood vessels in the conjunctiva and eyeballs, immunodeficiency, growth retardation and sexual immaturity. Patients have a strong predisposition to cancer; about 30% of patients develop tumors, particularly lymphomas and leukemias. Cells from affected individuals are highly sensitive to damage by ionizing radiation and resistant to inhibition of DNA synthesis following irradiation.
    The disease is caused by mutations affecting the gene represented in this entry. OMIM

    MedGen: C1458155 C0677776 C0017636 C0004135 C0950123 OrphaNet: 145 100 360 180250
PDB and PDB position 5np1 ~> 2227 (Explore)
gnomAD This variant is not present in gnomAD .
Pathogenicity pathogenic according to Clinvar
Literature for His201Tyr in HDAC8 Not present
Literature for similar variants in homologous proteins Not present

Literature

Literature for Arg2227Cys in ATM

There is no literature available for this specific variant

Literature for similar variants in homologous proteins

There is no literature available for variants in a homologous proteins

corona.ai classification

Classification: pathogenic according to Clinvar

This variant was found in the Clinvar dataset. According to this authoritative source this variant is classified as pathogenic. A prediction is available for this variant, but this source takes precedence in our classification.

corona.ai prediction details

Prediction: pathogenic 92%

The Arg2227Cys mutation in the protein has been classified as pathogenic by our ensemble classifier system, with high confidence. There is a 88% agreement between all subclassifiers.

Data quality

Data quality for this region is considered unknown. No assessment of data quality has been made for this region.

Prediction factors

External models have estimated which sets of features contributed primarily to the classification. These sets of features are listed here.

Primary contributing factors

  • Alignment depth features point towards pathogenic
  • Structural features point towards benign
  • Residue differences point towards pathogenic
  • Position features point towards pathogenic

Evolutionary pressure

Conservation

The wildtype was observed in 83.08% of the 1005 sequences analyzed. The variant type was observed in < 1% of observed sequences.


This residue is involved in 1 CationPi interaction, 2 Hydrogen Bonds and 7 Hydrophobic interactions.

Interaction statistics were calculated using advanced molecular optimization techniques and may not be visible in the plain PDB file. Please download the YASARA scene to explore the interactions in more detail.