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PhenCode specifications


Unique identifier OMICS_00279
Name PhenCode
Alternative name Phenotypes for ENCODE
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Ross C. Hardison

Publication for Phenotypes for ENCODE

PhenCode citations


Proxy Molecular Diagnosis from Whole Exome Sequencing Reveals Papillon Lefevre Syndrome Caused by a Missense Mutation in CTSC

PLoS One
PMCID: 4370501
PMID: 25799584
DOI: 10.1371/journal.pone.0121351

[…] t the variant showed that it was previously identified in a homozygous state by Zhang et al in a single Saudi Arabian proband [] and the variant was present in HGMD (Public version, ID: CM002939) and PhenCode (ID: CTSCbase_D0022:g.44271G>A) []. This provided strong evidence that this was the likely causal variant in the two PLS siblings. Thus the region containing the variant was amplified and seq […]


Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci

Cancer Inform
PMCID: 4179605
PMID: 25288875
DOI: 10.4137/CIN.S13789

[…] t the coding sequence of tumor suppressor genes, DNA repair genes, or oncogenes. In protein-coding regions, there are many annotation resources for assigning functional information. For example, PMD, PhenCode, and HumDiv/HumVar/Polyphen2 are catalogs constructed from one or more variant databases or from the literature with the intent of annotating specific variants for functional effect. Similarl […]


A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene

PMCID: 4156994
PMID: 25215231
DOI: 10.1155/2014/639751

[…] s mutations affecting protein tolerance including a neutral set of mutations comprising 17393 human coding nsSNPs and a pathogenic set of 14610 missense mutations obtained by manual curation from the PhenCode database.Prediction accuracy accomplished by MutPred and PolyPhen2 depends on their specific criterion. Twelve structural and six sequence-based properties were used in this study (). About 2 […]


VariVis: a visualisation toolkit for variation databases

BMC Bioinformatics
PMCID: 2375904
PMID: 18430251
DOI: 10.1186/1471-2105-9-206

[…] However, these tools are of limited use to LSDB curators as they do not enable them to easily utilise their own data sets, which are often more complete than the published literature [], although the PhenCode project has gone some way to mitigate the difficulty in loading an LSDB into the UCSC Browser []. However, the requirement of directing users away from the website of a locus specific databas […]

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PhenCode institution(s)
Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania; National Human Genome Research Institute, Bethesda, Maryland; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California; Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatrics, Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland; Erasmus Medical Center, Faculty of Medicine, Department of Cell Biology and Genetics, Rotterdam, Netherlands; Weatherall Institute of Molecular Medicine, Oxford, UK; Department of Medicine, Boston University, Boston, Massachusetts; Montreal Children's Hospital Research Institute, Montreal, QC, Canada; Department of Chemistry, Albert Einstein College of Medicine, Bronx, New York; Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC, Canada; Institute of Medical Technology, University of Tampere, Tampere, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania

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