Interpreting a Phenotypic Allele Summary
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This document answers the following questions about the allele summary report:

See also:

When does an allele summary appear?

The Phenotypic Alleles Query Results -- Summary appears either when a query on the Phenotypes, Alleles, and Disease Models Query Form returns any alleles or when you select All alleles or specific allele types on a gene/marker detail report (see Alleles and Phenotypes for more information).

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What should show up in this report?

A search for alleles results in a summary listing of any "hits" with links to detail records. The You searched for... box at the top of the Phenotypic Alleles Query Results summary reiterates the search parameters that produced the report and contains items such as:

When you access the allele summary from a gene/marker detail report, the marker symbol, name and, MGI identifier appear in a box at the top of the page.

You'll also find a line of text near the top that reports the number of unique alleles matching your query. For example, if a query returns 122 different alleles, this line would read

Showing alleles 1 - 100 of 122

You can use the toggle to change the number of items displayed or page through the results.

Table columns summarize information about the alleles matching your query. The results appear in some or all of the following fields (depending on your query form choices).

FieldDescription
Allele Symbol
Gene; Allele Name
[Camera icon]
Official symbol for the allele, linked to its Phenotypic Allele Detail Report.
Name for the allele.
If a camera icon appears, images are associated with the allele. Click the icon to view any associated image(s).
ChrChromosome of the marker that the allele is associated with.
Synonyms Any synonyms (unofficial symbols and names) for the allele.
Category Specific allele type (e.g., knockout, targeted, gene trapped). Cell line (in parentheses) indicates that there is no information about the creation of a mouse line for the allele. Chimera (in parentheses) means that MGI has information only about the chimeric mouse.

Alleles that involve multiple genes display links to up to three of the affected genes in this section along with the option to View all the affected genes with their feature types, genome coordinates, associated references and curatorial notes.

Abnormal Phenotypes Reported in these SystemsHigh level terms from the Mammalian Phenotype (MP) Ontology annotated to the allele. See the Mammalian Phenotype Browser. These high level terms are also found in the Phenotype Selection List pop-up (when you click Anatomical Systems Affected by Phenotypes on the Phenotypes, Alleles, and Disease Models Query Form). Phenotypes that are only annotated to complex genotypes—those involving more than one genome feature—are not listed in this summary but can be found in the Phenotypic Allele Detail Report.
Human Disease ModelsHuman disease terms and OMIM IDs annotated to the allele. Diseases that are only annotated to complex genotypes—those involving more than one genome feature—are not listed in this summary but can be found in the Phenotypic Allele Detail Report. See the Human Disease Vocabulary Browser.

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How do I interpret an allele summary report?

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Why do some alleles have observed phenotypes and some do not?

The vocabulary is annotated at the genotype level. If an allele either does not yet have a genotype or has a genotype with no annotations, the Abnormal Phenotypes Reported in these Systems and Human Disease Models fields are blank. Also, phenotypes and human diseases that are only annotated to complex genotypes—those involving more than one genome feature—are not displayed in this summary but can be found in the Phenotypic Allele Detail Report.


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Can I edit my original options and requery?

Yes, you can.

Notes:

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Can I get my results as tab-delimited text or spreadsheet files?

Yes. In your search results click on the Text File or Excel File icon. Your web browser will download a file of the results.

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Can I sort my results?

Yes, you can.

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What if my query returns no results?

See What if my query returns no results? in Using the Phenotypes, Alleles, and Disease Models Query Form.

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