How to: Find human variations associated with a phenotype or disease (clinical association)

Starting with a disease or phenotype in...

PubMed

  1. On the PubMed homepage, search with a disease or phenotype name and additional terms to find variations that have been identified as being associated with or causative for the phenotype, for example: humans[MeSH terms] AND asthma AND (causative OR associated OR association) AND (variation OR variant OR mutant).
  2. Alternatively, on the PubMed Clinical Queries page you can search for medical genetics publications. Perform a search on this page and link to "See all" records at the bottom of the Medical Genetics column (on the right).

ClinVar

  1. On the ClinVar homepage, enter a gene, HGVS expresssion, identifier from dbSNP or dbVar, MIM number, MedGen Concept ID, or phenotype name by typing in the search box.
  2. Click the Search button.
  3. Filter the results using the Filter Sidebar at the left.
  4. The result set will provide summary data of the submitted clinical interpretation(s), with details of interpretations from each submitter available from the details section.

dbVar

  1. On the dbVar homepage, enter a disease or phenotype name by typing in the search box.
  2. Click Limits under the search bar.
  3. In the “Clinical interpretation" section, select "Pathogenic" and "Uncertain Significance: likely pathogenic" by clicking the check boxes.
  4. Click the Search button.
  5. Click the “Variant” filter at the upper right (to exclude the report of the study registered in dbVar).
  6. Click any nsv identifier for more information and links to other NCBI resources.

PheGenI

  1. On the PheGenI homepage, select a Category or Trait name in the "Phenotype Selection" section. Selecting the "Category" first will limit the list of Traits to those available for the particular MeSH Category.
  2. To limit the retrieval of data by P-Value of the association report, enter the exponent in the box.
  3. Click the Search button.
  4. Click "Association Results" in the Search results section to review the data in the Association Results table to evaluate the evidence for the association between a variation and the measured trait.  For more and related information, click links to the "Gene", "PubMed", or "Source" databases.
  5. Alternatively, click "Genes" in the Search results section to review the genes associated with the phenotype selection.  Click a Location link to see an interactive graphical sequence viewer display for the selected gene.

Gene and linking to ClinVar

  1. On the Gene database homepage, enter a disease or phenotype name in search box and click "Search".
  2. If you want to review results for multiple genes as a group:
    • Complete the check box for the records of interest
    • Go to the "Find related data" section in the column at the right
    • Pick ClinVar from the menu
    • Press Find items
    • The result set will provide summary data of the submitted clinical interpretation(s) for the selected gene(s), with details of interpretations from each submitter available from the details section.
  3. If you want to review results for only one gene:
    • Display the gene of interest by clicking on the title
    • Click on Variation in the Table of contents at the top of the column at the right
    • Follow the links to ClinVar
    • The result set will provide summary data of the submitted clinical interpretation(s) for the selected gene, with details of interpretations from each submitter available from the details section.
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