Description

OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM).

The OMIM data are separated into three separate tracks:

OMIM Alellic Variant Phenotypes (OMIM Alleles)
    Variants in the OMIM database that have associated dbSNP identifiers.

OMIM Gene Phenotypes (OMIM Genes)
    The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key.

OMIM Cytogenetic Loci Phenotypes - Gene Unknown (OMIM Cyto Loci)
    Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes.

This track shows the cytogenetic locations of phenotype entries in the Online Mendelian Inheritance in Man (OMIM) database for which the gene is unknown.

Display Conventions and Configuration

Cytogenetic locations of OMIM entries are displayed as solid blocks. The entries are colored according to the OMIM phenotype map key of associated disorders:

• Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.
• Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found.
• Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene.
• Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.

Gene symbols and disease information, when available, are displayed on the details pages.

The descriptions of 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

This track was constructed as follows:

• The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
• Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field.
• The cytogenetic location data (from the location column in omimGeneMap) were parsed and converted into genomic start and end positions based on the cytoBand table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the omimLocation table.
• All entries with no associated phenotype map key and all OMIM gene entries as reported in the "OMIM Genes" track were then excluded from the omimLocation table.

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.

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. PMID: 18842627; PMC: PMC2686440

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. PMID: 15608251; PMC: PMC539987