Assembly: Human Feb. 2009 (GRCh37/hg19) Data last updated at UCSC: 2024-12-04
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. Further, please be
sure to click through to omim.org for the very latest, as they are continually
updating data.
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
for downloads.
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 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, phenotype, and inheritance 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 mousing over
each entry.
Mode of Inheritance
Abbreviation
Autosomal Dominant
AD
Autosomal Recessive
AR
Digenic Dominant
DD
Digenic Recessive
DR
Isolated Cases
IC
Mitochondrial
Mi
Multifactorial
Mu
Pseudoautosomal Dominant
PADom
Pseudoautosomal Recessive
PARec
Somatic Mosaicism
SomMos
Somatic Mutation
SMu
X-Linked
XL
X-Linked Dominant
XLD
X-Linked Recessive
XLR
Y-Linked
YL
Brackets, "[ ]", before the phenotype name indicate "nondiseases," mainly genetic variations that
lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal
hyperthyroxinemia).
Braces, "{ }", indicate mutations that contribute to susceptibility to multifactorial disorders
(e.g., diabetes, asthma) or to susceptibility to infection (e.g., malaria).
Question marks, "?", indicate that the relationship between the phenotype and gene is provisional.
More details about this relationship are provided in the comment field of the map and in the gene
and phenotype OMIM entries.
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.
Data Updates
This track is automatically updated once a week from OMIM data. The most recent update time is shown
at the top of the track documentation page.
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.
Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range
Go to Table Browser, make sure the right dataset is selected:
group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
Define region of interest by entering coordinates or a gene symbol into the "Position" textbox, such as
chr1:11,166,591-11,322,608 or MTOR, or upload a list.
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.
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.
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.
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