Description

This track shows the genomic positions of natural and artifical amino acid variants in the UniProt/SwissProt database. The data has been curated from scientific publications by the UniProt staff.

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt variants are labeled with the amino acid change at a given position and, if known, the abbreviated disease name. A "?" is used if there is no disease annotated at this location, but the protein is described as being linked to only a single disease in UniProt.

Mouse over a mutation to see the UniProt comments.

Artificially introduced mutations are colored green and naturally occurring variants are colored red. For full information about a particular variant, click the "UniProt variant" linkout. The "UniProt record" linkout lists all variants of a particular protein sequence. The "Source articles" linkout lists the articles in PubMed that originally described the variant(s) and were used as evidence by the UniProt curators.

Methods

UniProt sequences were aligned to RefSeq sequences first with BLAT, then lifted to genome positions with pslMap. UniProt variants were parsed from the UniProt XML file. The variants were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the LS-SNP pipeline by Mark Diekhans. The complete script is part of the kent source tree and is located in src/hg/utils/uniprotMutations.

Credits

This track was created by Maximilian Haeussler, with advice from Mark Diekhans and Brian Raney.

References

UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8. PMID: 24253303; PMC: PMC3965022

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278