Description

This track shows the genomic positions of all gene entries in the Online Mendelian Inheritance in Man (OMIM) database.

Display Conventions and Configuration

Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored according to the associated OMIM phenotype map key (if any):

Gene symbol and disease information, when available, are displayed on the details page for an item, and links to related RefSeq Genes and UCSC Genes are given.

The descriptions of the OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items displayed can be filtered according to phenotype map key on the track controls page.

Methods

The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations:

Data Access

Because OMIM has only allowed Data queries within individual chromosomes, no download files are available from the Genome Browser. Full genome datasets can be downloaded directly from the OMIM Downloads page. All genome-wide downloads are freely available from OMIM after registration.

If you need the OMIM data in exactly the format of the UCSC Genome Browser, for example if you are running a UCSC Genome Browser local installation (a partial "mirror"), please create a user account on omim.org and contact OMIM via https://omim.org/contact. Send them your OMIM account name and request access to the UCSC Genome Browser "entitlement". They will then grant you access to a MySQL/MariaDB data dump that contains all UCSC Genome Browser OMIM tables.

UCSC offers queries within chromosomes from Table Browser that include a variety of filtering options and cross-referencing other datasets using our Data Integrator tool. UCSC also has an API that can be used to retrieve data in JSON format from a particular chromosome range.

Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information.

Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range

  1. Go to Table Browser, make sure the right dataset is selected: group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
  2. Define region of interest by entering coordinates or a gene symbol into the "Position" textbox, such as chr1:11,106,535-11,262,551 or MTOR, or upload a list.
  3. Format your data by setting the "Output format" dropdown to "selected fields from primary and related Tables" and click . This brings up the data field and linked table selection page.
  4. Select chrom, chromStart, chromEnd, and name from omimGene2 table. Then select the related tables omim2gene and omimPhenotype and click . This brings up the fields of the linked tables, where you can select approvedGeneSymbol, omimID, description, omimPhenotypeMapKey, and inhMode.
  5. Click on the to proceed to the results page:
    chr1	11106534	11262551	MTOR	601231,	Smith-Kingsmore syndrome,Focal cortical dysplasia, type II, somatic,	3,	Autosomal dominant

For a quick link to pre-fill these options, click this session link.

Credits

Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.

References

Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM®). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. Epub 2008 Oct 8.

Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.