Schema for OMIM Alleles - OMIM Allelic Variant Phenotypes
  Database: hg38    Primary Table: omimAvSnp    Row Count: 25,879   Data last updated: 2020-08-05
Format description: Browser extensible data
Note: genome-wide queries are not available for this table.
fieldexampleSQL type info description
bin 592smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 1014142int(10) unsigned range Start position in chromosome
chromEnd 1014143int(10) unsigned range End position in chromosome
name 147571.0003varchar(255) values Name of item

Connected Tables and Joining Fields
        hg38.omimAv.avId (via omimAvSnp.name) Note: genome-wide queries are not available for this table.

Sample Rows
 
binchromchromStartchromEndname
592chr110141421014143147571.0003
592chr110143191014319147571.0002
592chr110143581014359147571.0001
592chr110415811041582103320.0003
593chr110505741050575103320.0001
593chr110507621050763103320.0002
594chr112137371213738600315.0001
594chr112322781232279615291.0001
594chr112322931232294615291.0010
594chr112324701232471615291.0005

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

OMIM Alleles (omimAvSnp) Track Description
 

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.

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