Disclaimer
PhenCode is intended for research purposes only. Although the data are freely
available to all, users should treat the reported mutations with extreme
caution in clinical settings or for any diagnostic or population screening
purpose. This information requires expertise to interpret properly; clinical
diagnosis and/or treatment recommendations should be made only by medical
professionals.
Description
This track is a result of the PhenCode project. It consolidates variants
from several curated locus-specific databases and one genome-wide database.
Rich genotype and phenotype information is provided. This version includes
entries from the databases listed in the Methods section below. Work is in
progress to add more locus-specific databases.
Display Conventions and Configuration
This track is color-coded by the mutation type or phenotype association.
The default colors for mutation type are:
-
substitution = purple
-
insertion = green
-
duplication = orange
-
deletion = blue
-
complex = brown
-
unknown = black
The default colors for phenotype association are:
-
phenotype-associated = red
-
not phenotype-associated = green
-
phenotype association unknown = gray
The color choices are configurable using the drop-down menus on the Track
Settings page.
By default, items are labeled with the Human Genome Variation Society (HGVS)
name. Additionally, the Browser can be configured to display the common name
(if available) or both labels using the Label checkboxes at the
top of the Track Settings page.
All mutation types, locations, and data sources, except for the UniProt
(Swiss-Prot/TrEMBL) data source, are included in the default
display. To filter the display based on one or more of these characteristics,
check the appropriate boxes in the exclusion lists on the
Track Settings page.
Variants with phenotype associations that have been determined by a database
curator are listed as phenotype-associated or not
phenotype-associated. Variants with phenotype associations that have not
been determined by a curator are classified as unknown, and no
disease association is listed.
Methods
The data shown in this track were obtained from the following variant sources:
The HGVS-style name
was pulled directly or indirectly from the source
data. The information in this name, in combination with alignments of the
reference sequence against
the genome sequence, was used to position the variants. The source may have
additional variants that could not be mapped to the genome. Additional
attributes displayed for each variant depend on the information available
from the different source databases. If the source has web-accessible entries
for the variants, links are provided back to the source.
Credits
PhenCode developers
- Belinda Giardine, Ross Hardison, Webb Miller, Cathy Riemer
- Center for Comparative Genomics and Bioinformatics, Penn State University,
University Park, Pennsylvania
- Fan Hsu, Jim Kent, Andrew Kern, Robert Kuhn, Heather Trumbower
- Center for Biomolecular Science and Engineering, University of California,
Santa Cruz, California
- Richard Gibbons, Doug Higgs, Jim Hughes
- Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
- Garry Cutting, Andrew P. Feinberg
- Johns Hopkins University School of Medicine, Baltimore, Maryland
Cooperating databases
- ARdb:
- Bruce Gottlieb,
Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish
General Hospital, Montreal, Quebec, Canada
- BGMUT:
- Olga O. Blumenfeld and Santosh K. Patnaik,
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New
York
-
CFMDB:
- Julian Zielenski and Richard Sang,
The Hospital for Sick Children, Genetics and Genomic Biology, Toronto,
Ontario, Canada
-
dbPEX:
- Nancy Braverman, Institute of Genetic Medicine and Dept. of Pediatrics,
Johns Hopkins Medical Center, Baltimore, MD
Steven Steinberg, Dept.of Neurology,
Johns Hopkins University School of Medicine, Baltimore, MD
- HbVar:
- George Patrinos, Erasmus University, Rotterdam, Netherlands
Henri Wajcman, Hospital Henri Mondor, Creteil, France
David H.K. Chui, Boston University, Boston, Massachusetts
Nicholas Anagnou, University of Athens and IIBEAA, Athens, Greece
Georgi D. Efremov, Macedonian Academy of Sciences and Arts, RCGEB, Skopje,
Macedonia
- IDbases:
- Anne Durandy,
Michael Hershfield,
Laszlo Marodi,
Luigi D. Notarangelo,
Claudio Pignata,
Jose R. Regueiro,
Dirk Roos,
C.I.Edvard Smith,
Jouni Valiaho,
Mauno Vihinen,
Anna Villa,
Institute of Medical Technology, University of Tampere, Tampere, Finland
- IPNMDB:
- Eva Nelis, VIB - Department of Molecular Genetics, University of Antwerp, Antwerpen, Belgium
- LMDp:
- Johan T. den Dunnen,
Leiden University Medical Center, Leiden, Nederland
See also the database tool LOVD
- PAHdb:
- Charles R. Scriver, McGill University, Montreal Children's Hospital
Research Institute, Montreal, Quebec, Canada
- RettBASE:
- John Christodoulou,
Gladys Ho,
Andrew Grimm (previous database coordinator),
Children's Hospital at Westmead, Sydney and
University of Sydney, Australia
- Gene srd5a2:
- Juergen Reichardt, University of Sydney, Sydney, Australia
Nick Makridakis, University of Southern California, Los Angeles, California
- UniProt (Swiss-Prot/TrEMBL):
- Swiss Institute of Bioinformatics, Geneva, Switzerland