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ENTool Introduction and Background
RDDC Mutation Direct is an online tool specialized in the visualization and interpretation of genetic variant data, designed to provide researchers and clinicians with efficient variant information queries. The tool allows users to search by gene name, mutation site, or disease. Users can quickly retrieve essential details, including genomic location, mutation type, and functional impact, following standardized nomenclature. It also supports multi-transcript mutation display and in-depth variant analysis. With an intuitive and user-friendly interface, the tool enables effortless access to key mutation data, serving as a foundational resource for downstream genetic analysis. It is well-suited for routine research inquiries and the rapid interpretation of clinical genetic test reports.
Detailed Operating Steps
1、Enter the Tool Interface:
Open a browser and navigate to: https://rddc.tsinghua-gd.org/zh/tool/variant to access the Mutation Direct homepage.
2、Enter Search Criteria:
Enter gene name: Type the gene name into the search bar. For example, if you type "TP53," the system will dynamically suggest relevant genes. After clicking and selecting your target gene, it will appear as a tag in the search bar (e.g., [Gene:TP53])
Add Mutation Site or Disease Information: For more precise searches, you can continue to enter a mutation site (e.g., "c.743G>A") or a disease name (e.g., "Li-Fraumeni syndrome"). The system will generate new tags (e.g., [Mutation:c.743G>A]), allowing for multi-condition combined searches.
3、Execute Search and View Results
Initiate Search: Once the tags are confirmed, click the [Search] button to the right of the search bar to go to the results page.
Understand Search Results: The results page will display all entries related to your target mutation. Since a single gene might have multiple transcripts (e.g., TP53's NM_000546, NM_001126112, etc.), and a single mutation site might correspond to results under various transcripts, you'll need to select the target transcript based on your research needs (usually prioritizing mainstream transcripts, such as NM_000546.6).
4、In-Depth Mutation Detail Analysis
Access Mutation Details Page: Click on a mutation entry corresponding to a specific transcript to enter its details page. The target mutation will be highlighted in purple. Hovering your mouse over it will display coordinate information and the number of reported mutations.
In-Depth Mutation Query: Click the [Recorded mutations & Al-aided prediction] button to expand the following interactive content
Amino Acid Change Collection: For example, c.743G>A corresponds to p.R248Q (Arginine → Glutamine);
Clinical Significance Collection: Summarizes conclusions on the pathogenicity of the mutation from published literature (e.g., "possibly pathogenic," "benign," etc.);
AI Prediction Tool: Provides a one-click access to the Pathogenicity Predictor for pathogenicity prediction and RNA Splicer for splicing prediction.
Multi-Dimensional View Switching: Click the [Protein Mutation] button in the top left to switch to the amino acid sequence visualization view. The mutation site will be automatically highlighted. Hovering over the site will display real-time coordinate information and the number of reported mutations.
Sequence Function Switching: Click the green [Gene Sequence] button in the top right to view the DNA/RNA sequence details of the transcript. This supports precise localization of the mutation site within the sequence and provides sequence search and download functions.
Quick Location Function (Base/Amino Acid): In the [Mutation Site Search] input box in the top right corner of the page, enter the specific base or amino acid position (e.g., "c.547" or "p.Asn123"). The system will highlight the search result in purple.
Quick Location Function (Exon): In the [Search and Select Corresponding Exon] input box in the top right corner of the page, you can directly check the target exon number (e.g., "Exon 1") or click the exon shortcut buttons on the interface. The system will highlight the corresponding sequence region in green.
Precautions
Multi-Condition Combined Search: Supports entering multiple tags simultaneously, including multiple genes, mutation sites, or diseases, to narrow down the search scope.
Gene Name Standardization: Enter standard gene symbols (e.g., "TP53" instead of "p53"). You can confirm the correct name via NCBI Gene.
Mutation Site Format: Follow HGVS naming rules (e.g., "c.123A>T" for coding region mutations, "g.456C>G" for genomic mutations). Incorrect formats may lead to parsing failures.
Disease Name Format: Try to use the full English name for searching. Incorrect formats may lead to the disease not being found or tags not being generated.
Auxiliary Functions and Resources
Result Filtering and Sorting: At the top of the results page, you can quickly filter information using options like "Genes," "Nucleotide," and "Clinical Significance." Clicking the up/down arrows next to column names allows sorting by "Disease count," "Publications," etc. The show/hide columns button can help organize data, making the results more intuitive.
Codon Chart: A codon table is provided to help understand the effect of mutations on amino acid coding.
Tutorial: For a video tutorial, hover your mouse over the [Resource] button in the top navigation bar and select [Tutorials] from the menu. Alternatively, access assistance by clicking [step-by-step guide] below the search box.
Applications
Research: Quickly locate the genomic coordinates and types of gene variations reported in literature, providing essential data for functional studies (e.g., pinpointing cancer driver mutations or rare disease-associated variations).
Clinical: Power real-time parsing systems for standardized gene test reports, helping doctors accurately understand the molecular characteristics of variations (e.g., identifying mutation types in drug-metabolizing genes).
Education: Visually demonstrate the relationship between variant naming conventions and their actual genomic positions, ideal for teaching variant annotation in genetics courses.
Industry: Rapidly verify the standardized nomenclature of candidate gene variations, ensuring consistency in gene test product reports or database entries.
