Schema for OMIM Genes - OMIM Gene Phenotypes - Dark Green Can Be Disease-causing
Database: hg38 Primary Table: omimGene2 Row Count: 18,574   Data last updated: 2020-08-05 Format description: Browser extensible data Note: genome-wide queries are not available for this table.
hg38.omim2gene.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hg38.omimAv.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hg38.omimGeneMap.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hg38.omimGeneMap2.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hg38.omimGeneSymbol.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hg38.omimPhenotype.omimId (via omimGene2.name) Note: genome-wide queries are not available for this table.
hgFixed.refLink.omimId (via omimGene2.name)
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
OMIM Genes (omimGene2) Track Description
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 Alleles Variants in the OMIM database that have associated
dbSNP identifiers. This track is currently unavailable on the hg38 assembly,
as it depends on dbSNP data that has not been released yet.
OMIM Genes The genomic positions of gene entries in the OMIM
database. The coloring indicates the associated OMIM phenotype map key.
OMIM Phenotypes - Gene Unknown 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
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.
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
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.
Since 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.
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 following options are selected:
group: Phenotype and Literature, track: OMIM Genes, table: omimGene2.
Enter coordinates or a gene symbol into the "Position" textbox, such as
chr1:11,106,535-11,262,551 or MTOR.
Change the "Output format" dropdown to "selected fields from primary
and related Tables" and click . Instead of returning
the standard formatted dataset from the omimGene2 table, this
bring 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.
Click on the will bring you to the results page:
chr1 11106534 11262551 MTOR 601231, Smith-Kingsmore syndrome,Focal cortical dysplasia, type II, somatic, 3, Autosomal dominant