OMIM Alleles Track Settings
 
OMIM Allelic Variant Phenotypes   (All Phenotype and Literature tracks)

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Data last updated at UCSC: 2022-06-15

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 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 allelic variants in the Online Mendelian Inheritance in Man (OMIM) database that have associated dbSNP identifiers.

Display Conventions and Configuration

Genomic positions of OMIM allelic variants are marked by solid blocks, which appear as tick marks when zoomed out.

The details page for each variant displays the allelic variant description, the amino acid replacement, and the associated dbSNP and/or ClinVar identifiers with links to the variant's details at those resources.

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.

Methods

This track was constructed as follows:

  • The OMIM allelic variant data file mimAV.txt was obtained from OMIM and loaded into the MySQL table omimAv.
  • The genomic position for each allelic variant in omimAv with an associated dbSnp identifier was obtained from the snp151 table. The OMIM AV identifiers and their corresponding genomic positions from dbSNP were then loaded into the omimAvSnp table.

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.

Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information.

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