## 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.

#### Terms and Conditions of Use

## 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:

- Androgen Receptor Gene Mutations Database (ARdb) - mutations in the AR gene.
- Blood Group Antigen Gene Mutation Database (BGMUT) - mutations in many genes.
- Cystic Fibrosis Mutation Database (CFMDB) - mutations in the CFTR gene.
- PEX Gene Database (dbPEX) - mutations in the PEX genes.
- HbVar database (HbVar) - variants and thalassemia mutations in the globin loci.
- Databases for immunodeficiency-causing mutations (IDbases) - mutations in many genes.
- Inherited Peripheral Neuropathies Mutation Database (IPNMDB) - mutations in many genes.
- Leiden Muscular Dystrophy pages (LMDp) - mutations in many genes
- PAHdb - mutations in the phenylalanine hydroxylase (PAH) gene.
- RettBASE (RettBASE) - mutations in the MECP2 gene.
- SRD5A2 - mutations in the steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2) gene.
- UniProt (Swiss-Prot/TrEMBL) (SP) - genome-wide variants within coding regions of UCSC Known Genes.

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