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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.
Here you can download scenes for different molecular viewers, so you can analyze the structure in more detail.
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ATM
ENST00000278616 | p.Met1040Val
Summary
ATM - ENST00000278616
| Gene | ATM -
ENSG00000149311
| ENSP00000278616
| ENST00000278616 Ensembl | RefSeq | UniProt |
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| 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}.; |
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| Condition(s) |
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| Sequence |
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| PDB and PDB position | 5np1 1040 (Explore) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| gnomAD |
Exome Allele Frequency: 0.003072148 Genome Allele Frequency: 0.01136725 gnomAD |
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| Pathogenicity | benign according to VKGL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Older predictions |
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Literature
Helix classification
Classification: benign according to VKGL
This variant was found in the VKGL dataset. According to this authoritative source this variant is classified as benign. A prediction is available for this variant, but this source takes precedence in our classification.
Helix prediction details
Prediction: benign 1%
The Met1040Val mutation in the protein has been classified as benign by our ensemble classifier system, with very high confidence. There is a 97% agreement between all subclassifiers.
Data quality
Data quality for this region is considered good. This means that structural data is present, alignments are deep and the species in those alignments are diverse.
Assistant summary
This is an automatically generated assessment, it is not reviewed by humans and only has partial access to the information contained in the report. Generating this may take some time.
Evolutionary pressure
Conservation
The wildtype was observed in 52.98% of the 168 sequences analyzed. The variant type was observed in 21.43% of observed sequences.
This residue is involved in 2 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.