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 many curated locus-specific databases. Rich genotype and phenotype information is provided. This version includes entries from the databases listed in the Methods section below. This covers approximately 1/3 of the loci listed on the HGVS database listing. The coverage of the genome can be viewed using Genome Graphs. Work is in progress to add more locus-specific databases.

Display Conventions and Configuration

This track is color-coded by the mutation type.

The colors for mutation type are:

• substitution = purple
• insertion = green
• duplication = orange
• deletion = blue
• complex = brown
• unknown = black

Items are labeled with the Human Genome Variation Society (HGVS) name.

Methods

The data shown in this track were obtained from the following variant sources:

• Alzheimer Disease & Frontotemporal Dementia Mutation Database (AD&FTDMD) - mutations in several genes.
• ALPL gene mutations database (ALPL) - mutations in the ALPL gene.
• Androgen Receptor Gene Mutations Database (ARdb) - mutations in the AR gene.
• Blood Group Antigen Gene Mutation Database (BGMUT) - mutations in many genes.
• Osteopetrosis with renal tubular acidosis (CA2base) - mutations in the CA2 gene.
• Calcium Sensing Receptor Database (CASRdb) - mutations in the CASR gene.
• CBS Mutation Database (CBS) - mutations in the CBS gene.
• Cystic Fibrosis Mutation Database (CFMDB) - mutations in the CFTR gene.
• Autosomal dominant osteopetrosis, type 2 (CLCN7base) - mutations in the CLCN7 gene.
• PEX Gene Database (dbPEX) - mutations in the PEX genes.
• A database of retrotransposon insertion polymorphisms in humans (dbRIP)
• Hereditary angioedema type III (F12base) - mutations in the F12 gene.
• Fanconi Anemia Mutation Database (Fanconi) - mutations in Fanconi anemia genes.
• FHC Mutation Database (FHCDB) - mutations in various genes known to cause familial hypertrophic cardiomyopathy.
• HbVar database (HbVar) - variants and thalassemia mutations in the globin loci.
• Human Intermediate Filament Database (HIFD) - database of intermediate filament variants.
• IARC TP53 Mutation Database - mutations in the TP53 gene.
• Databases for immunodeficiency-causing mutations (IDbases) - mutations in many genes.
• Inherited Peripheral Neuropathies Mutation Database (IPNMDB) - mutations in many genes.
• ISTH SSC von Willebrand Factor Database(ISTH SSC VWF) - mutations found in the gene for human von Willebrand Factor.
• Kinase mutation database (KinMutBase) - mutations in protein kinase domains.
• Leiden Muscular Dystrophy pages (LMDp) - mutations in many genes
• Long QT Syndrome Database (LQTSdb) - mutations associated with Long QT syndrome.
• Mismatch Repair Genes Variant Database (MMR) - mutations in the mismatch repair genes
• Autosomal recessive osteopetrosis (OSTM1base) - mutations in the OSTM1 gene.
• PAHdb - mutations in the phenylalanine hydroxylase (PAH) gene.
• RettBASE (RettBASE) - mutations in the MECP2 gene.
• RISN Mutation Database(RISN) - mutations in genes underlying retinal disorders.
• RPGR Database(RPGR) - mutations in the RPGR gene.
• SRD5A2 - mutations in the steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2) gene.
• X-linked Adrenoleukodystrophy Database (X-ALD) - mutations in the ABCD1 gene.

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

AD&FTD Mutation Database:

Marc Cruts, Flanders Institute for Biotechnology and University of Antwerp, Belgium

ALPL:

Etienne Mornet, Centre Hospitalier de Versailles, Le Chesnay, France

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

CA2base:

Mauno Vihinen, Institute of Medical Technology, University of Tampere, Tampere, Finland

CASRdb:

Geoffrey Hendy and David Cole, McGill University, Montreal, Quebec, Canada

CBS:

Jan P. Kraus and Miroslav Janosik, University of Colorado School of Medicine, Aurora, Colorado
Viktor Kozich, Institute of Inherited Metabolic Diseases, Charles University in Prague, First Faculty of Medicine, Czech Republic

CFMDB:

Julian Zielenski and Richard Sang, The Hospital for Sick Children, Genetics and Genomic Biology, Toronto, Ontario, Canada

CLCN7base:

Mauno Vihinen, Institute of Medical Technology, University of Tampere, Tampere, Finland

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

dbRIP:

Ping Liang, Roswell Park Cancer Institute, Buffalo, New York
Mark Batzer, Louisiana State University, Baton Rouge, LA

F12base:

Mauno Vihinen, Institute of Medical Technology, University of Tampere, Tampere, Finland

Fanconi:

Arleen D. Auerbach, Francis Lach, The Rockefeller University, New York, NY

FHC Mutation Database, version 1.1:

This project is a collaborative effort among the Department of Molecular and Clinical Genetics and Department of Cardiology at the Royal Prince Alfred Hospital, and the Australian National Genomic Information Services. The curators are:
Dr. Bing Yu, Department of Molecular Genetics, C39 - Royal Prince Alfred Hospital, The University of Sydney, NSW 2006 Australia
Professor R. Trent, Department of Molecular Genetics, K25 - Medical Foundation Building, The University of Sydney, NSW 2006 Australia

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

HIFD:

Lim Yun Ping, Centre for Molecular Medicine and the Bioinformatics Institute, Singapore

IARC TP53:

Magali Olivier, Pierre Hainaut, Group of Molecular Carcinogenesis and Biomarkers, France

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

ISTH SSC VWF:

Dan Hampshire, Anne Goodeve, Nick Beauchamp, David Lillicrap, Ross MacLachlan, The University of Sheffield, United Kingdom

KinMutBase:

C. Ortutay, Jouni Valiaho, K. Stenberg, Mauno Vihinen, Institute of Medical Technology, University of Tampere, Tampere, Finland

LMDp:

Johan T. den Dunnen, Leiden University Medical Center, Leiden, Nederland
See also the database tool LOVD

LQTSdb:

Michael Christiansen, Lars Allan Larsen, and Paal Skytt Andersen, Molecular Cardiology Group, Statens Serum Institut, Denmark

MMR:

Michael O. Woods, Faculty of Medicine, HSC, Memorial University of Newfoundland, St. John's, NL, Canada

OSTM1base:

Mauno Vihinen, Institute of Medical Technology, University of Tampere, Tampere, Finland

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

RISN:

Markus Preising, Molecular Genetics Laboratory, University of Regensburg, Bavaria, Germany

RPGR:

Xinhua Shu and Alan Wright

SRD5A2:

Juergen Reichardt, University of Sydney, Sydney, Australia
Nick Makridakis, University of Southern California, Los Angeles, California

X-ALD:

Stephan Kemp, Academic Medical Center/Emma Children's Hospital, Amsterdam, The Netherlands