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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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BRCA1 - ENST00000357654
Ensembl | RefSeq | UniProt
|Location||GRCh38 17:43044295-43125483 Ensembl UCSC|
|Description||BRCA1, DNA repair associated
E3 ubiquitin-protein ligase that specifically mediates the formation of 'Lys-6'-linked polyubiquitin chains and plays a central role in DNA repair by facilitating cellular responses to DNA damage. It is unclear whether it also mediates the formation of other types of polyubiquitin chains. The E3 ubiquitin-protein ligase activity is required for its tumor suppressor function. The BRCA1-BARD1 heterodimer coordinates a diverse range of cellular pathways such as DNA damage repair, ubiquitination and transcriptional regulation to maintain genomic stability. Regulates centrosomal microtubule nucleation. Required for normal cell cycle progression from G2 to mitosis. Required for appropriate cell cycle arrests after ionizing irradiation in both the S-phase and the G2 phase of the cell cycle. Involved in transcriptional regulation of P21 in response to DNA damage. Required for FANCD2 targeting to sites of DNA damage. May function as a transcriptional regulator. Inhibits lipid synthesis by binding to inactive phosphorylated ACACA and preventing its dephosphorylation. Contributes to homologous recombination repair (HRR) via its direct interaction with PALB2, fine-tunes recombinational repair partly through its modulatory role in the PALB2-dependent loading of BRCA2-RAD51 repair machinery at DNA breaks. Component of the BRCA1-RBBP8 complex which regulates CHEK1 activation and controls cell cycle G2/M checkpoints on DNA damage via BRCA1-mediated ubiquitination of RBBP8. Acts as a transcriptional activator
|PDB and PDB position||4y2g ~> 1720 (Explore)|
Exome Allele Frequency: 0.00017531
Genome Allele Frequency: 0.0001273723
|Pathogenicity||benign according to|
|Literature for Thr1720 in BRCA1||Not present|
|Literature for similar variants in homologous proteins||Not present|
Literature for Thr1720Ala in BRCA1
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
Classification: benign according to
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
The Thr1720Ala mutation in the protein has been classified as benign by our ensemble classifier system, with high confidence. There is a 83% agreement between all subclassifiers.
Data quality for this region is considered good. This means that enhanced, deep alignments are present and there is a variety of data for the algorithm to predict from.
External models have estimated which sets of features contributed primarily to the classification. These sets of features are listed here.
Primary contributing factors
Position features point towards pathogenic
Protein evolutionary pressure points towards pathogenic
Residue differences point towards benign
Gene vulnerability points towards pathogenic
The wildtype was observed in 43.89% of the 998 sequences analyzed. The variant type was observed in 1.10% of observed sequences.
This residue is involved in 2 Hydrogen Bonds, 3 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.