Schema for OMIM Genes - OMIM-Associated Genes

Database: hg19 Primary Table: omimGene Row Count: 16,067
Format description: Browser extensible data

field	example	SQL type	info	description
`bin`	591	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	879583	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	894679	`int(10) unsigned`	range	End position in chromosome
`name`	610770	`varchar(255)`	values	Name of item

      hg19.omimGeneMap.omimId (via omimGene.name)
      hg19.omimMorbidMap.omimId (via omimGene.name)
      hg19.omimToKnownCanonical.omimId (via omimGene.name)
      hg19.refLink.omimId (via omimGene.name)

bin	chrom	chromStart	chromEnd	name
591	chr1	879583	894679	610770
592	chr1	934341	935552	608060
592	chr1	948846	949915	147571
592	chr1	955502	991492	103320
593	chr1	1138888	1142089	603905
593	chr1	1146706	1149512	600315
594	chr1	1217488	1227409	601328
594	chr1	1246964	1260046	611354
594	chr1	1266725	1269843	605865
594	chr1	1270658	1284492	601365

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Description

NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.

Because the UCSC Genes mappings are based on associations from RefSeq and UniProt, they are dependent on any interpretations from those sources. Furthermore, because many OMIM records refer to multiple gene names, or syndromes not tightly mapped to individual genes, the associations in this track should be treated with skepticism and any conclusions based on them should be carefully scrutinized using independent resources.

This track shows the positions of canonical UCSC genes that have been associated with identifiers in the Online Mendelian Inheritance in Man (OMIM) database. The associations were obtained from RefSeq and UniProt annotations. To simplify the track, annotations on splice variants have been collapsed so that only canonical UCSC splice variants are displayed.

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).

Display Conventions and Configuration

Positions of OMIM-associated canonical UCSC genes are displayed as solid blocks. The color of the block depends on the classification assigned by OMIM.

If the OMIM identifier is listed in the OMIM Morbid Map, the item is colored red.
If there is no Morbid Map annotation , the item is colored blue.

Where relevant, disease information from the Morbid Map "disorder" column is displayed on the details page for an item. If the canonical UCSC gene represents a cluster of more than one gene, the other genes are listed on the track details page.

By default, items are labeled with the OMIM identifier. The label can be changed to the OMIM gene/syndrome or the UCSC gene symbol on the track configuration page.

Methods

This annotation was constructed as follows:

A set of UCSC genes was compiled that have cross-references to RefSeq genes with associated OMIM IDs, as defined in the Genome Browser database refLink table.
A second set of UCSC genes was compiled in which the corresponding UniProt proteins have external links to OMIM, based on data in the spXref2 table in the UCSC proteome database.
The two gene sets were combined and duplicates removed, resulting in a subset of UCSC genes that have associated OMIM IDs.
Each of the genes in the combined set was replaced with its associated canonical gene, based on the UCSC canonical gene set defined by the knownIsoforms and knownCanonical tables.
Duplicates were removed from the canonical set, and the data were sorted and loaded into the omimGene table.

In addition, data from the OMIM genemap and morbidmap files were loaded into the omimGeneMap and omimMorbidMap tables in the Genome Browser database.

Credits

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

References

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.

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.