## 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):

- 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.
- Light Gray for Others - no associated OMIM phenotype map key info available.

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:

- The data file `genemap.txt` from OMIM was loaded into the MySQL table `omimGeneMap`.
- The data file `mim2gene.txt` from OMIM was processed and loaded into the MySQL table `omim2gene`.
- Entries in `genemap.txt` having disorder info were parsed and loaded into the `omimPhenotype` table.
- For each OMIM gene in the `omim2gene` table, the Entrez Gene ID was used to get the corresponding RefSeq Gene ID via the `refLink` table, and the RefSeq ID was used to get the genomic location from the `refGene` table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into the `omimGene2` table, the primary table for this track.

*The locations in the `refGene` table are from alignments of RefSeq Genes to the reference genome using BLAT.

## 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.