OMIM Genes Track Settings
 
OMIM Genes - Dark Green Can Be Disease-causing   (All Phenotype and Literature tracks)

Display mode:   
Label: OMIM ID    gene symbol   

Include Entries of:
  • Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.   
  • Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.   
  • Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.   
  • Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.   
  • Others: no associated OMIM phenotype map key info available.   
View table schema
Data last updated: 2020-01-15

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 Alleles
    Variants in the OMIM database that have associated dbSNP identifiers.

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 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. 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 disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. PMID: 15608251; PMC: PMC539987