MGI Alleles and Phenotypes

The Phenotypes, Alleles & Disease Models project in MGI enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.

This hub contains 33 Allele/Phenotype tracks. Alleles are broken down into 4 separate tracks by allele type; Induced, Spontaneous, Targeted, and Transgenic. Phenotype tracks are based on the 29 top level MP terms, any phenotype annotated with a child term of a specific top level term will be found in that track.

This track data is updated weekly every Monday.


A primary objective for MGI is the maintenance of a complete catalog of phenotypic mutations in the laboratory mouse. These include spontaneous, induced, and genetically engineered mutations (targeted knockouts and conditionals, transgenics, Cre-constructs, targeted reporters, gene traps, transposon-induced mutations, etc.).

MGI serves as the international authoritative source for nomenclature for mouse alleles, and maintains a complete list of allele symbols, names, and synonyms, each with a unique accession ID. Researchers are encouraged to submit new alleles to reserve symbols and obtain accession IDs prior to publication.

A complete listing of alleles can be downloaded from the ftp site (


Phenotypes are the manifestation of an individual's genotype in its environment. In the most straightforward case, phenotypic effects of allelic mutations are observed in relation to a control strain background; and the environment within the observing laboratory is considered constant.

Complications quickly expand when considering complex, multi-genic mutations, conditional and tissue-specific allele ablation, the combination of mutations in multiple genes in a single animal, the use of multiple strain backgrounds on which mutations are created and/or transferred, and the experimental application of additional environmental variables that can heighten or lessen phenotypic outcome. To maximize the usefulness of these complex data, phenotypes in MGI are associated with specific genotypes (combinations of allelic mutations on specific genetic backgrounds).

Phenotypes are described in MGI using the Mammalian Phenotype Ontology, a structured vocabulary that allows consistent annotation of mouse genotypes with standard phenotype terminology and associates each piece of phenotypic data with its source (e.g., published literature, large-scale mutagenesis centers, individual research laboratories).


QTL are quantitative trait loci, defined by the association of phenotypic characteristics with chromosomal regions. Generally many such loci contribute to quantitative characters, such as body metrics (e.g., length, adiposity), substance preference/aversion (e.g., to alcohol, cocaine), autoimmunity and susceptibility to infection, etc. Recently some QTL have been identified with their underlying genes. MGI captures information on strain-specific QTL variants, including genome location, descriptions of mapping analysis and significance scores, and descriptions of phenotypes using Mammalian Phenotype Ontology terms. QTL can be searched in the same way as other phenotypic alleles.


All data and analysis is provided by MGI. This information is also available on or for a complete data download please see

Hub data is maintained by Paul Hale( Please email with any questions over this hub or the data herein.


Blake JA, Eppig JT, Kadin JA, Richardson JE, Smith CL, Bult CJ, and the Mouse Genome Database Group. 2017. Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. Nucl. Acids Res. 2017 Jan. 4;45 (D1): D723-D729.