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. Further, please be
sure to click through to omim.org for the very latest, as they are continually
NOTE ABOUT DOWNLOADS:
OMIM is the property
of Johns Hopkins University and is not available for download or mirroring
by any third party without their permission. Please see
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
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
- 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.
This track was constructed as follows:
- The data file genemap.txt from OMIM was loaded into the MySQL table
- 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
- 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.
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.
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.
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
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.
PMID: 15608251; PMC: PMC539987