Schema for UniProt Variants - UniProt/SwissProt Amino Acid Substitutions
  Database: mm10    Primary Table: spMut Data last updated: 2021-06-24
Big Bed File: /gbdb/mm10/uniprot/unipMut.bb
Item Count: 8,290
Format description: Browser extensible data (12 fields) plus information about uniProt mutation
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart130814599Start position in chromosome
chromEnd130814602End position in chromosome
nameL519AName of item
score1000Score from 0-1000
strand++ or -
thickStart130814599Start of where display should be thick (start codon)
thickEnd130814602End of where display should be thick (stop codon)
reserved0Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes3Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
statusManually reviewed (Swiss-Prot)Status
varTypeExperimental mutation of amino acidsVariant Type
diseasesDiseases
mutationposition 519, Leu changed to AlaCoding seq. mutation
commentsPrevents receptor internalization.Comment
variationIdUniProt variant
dbSnpIddbSNP
uniProtIdQ2TB54UniProt record
pmids11062505Source articles

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsstatusvarTypediseasesmutationcommentsvariationIddbSnpIduniProtIdpmids
chr1130814599130814602L519A1000+1308145991308146020130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 519, Leu changed to AlaPrevents receptor internalization.Q2TB5411062505
chr1130814602130814605L520A1000+1308146021308146050130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 520, Leu changed to AlaPrevents receptor internalization.Q2TB5411062505
chr1131055770131055773W335A1000-1310557701310557730130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 335, Trp changed to AlaLeads to constitutive protein kinase activity.P491387592979
chr1131055788131055791K329R1000-1310557881310557910130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 329, Lys changed to ArgLeads to constitutive protein kinase activity.P491387592979
chr1131055815131055818T320E1000-1310558151310558180130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 320, Thr changed to GluMimicks phosphorylation state and constitutive protein kinase activity; when associated with E-208.P491387592979
chr1131055815131055818T320A1000-1310558151310558180130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 320, Thr changed to AlaStrong decrease in kinase activity; when associated with A-208.P491387592979
chr1131057518131057521T208E1000-1310575181310575210130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 208, Thr changed to GluMimicks phosphorylation state and constitutive protein kinase activity; when associated with E-320.P491387592979
chr1131057518131057521T208A1000-1310575181310575210130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 208, Thr changed to AlaStrong decrease in kinase activity; when associated with A-320.P491387592979
chr1131129330131129333Y368E1000-1311293301311293330130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 368, Tyr changed to GluMinimal loss of kinase activity; when associated with E-366.Q922Y012356771
chr1131129330131129333Y368A1000-1311293301311293330130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 368, Tyr changed to AlaLoss of kinase activity.Q922Y012356771

UniProt Variants (spMut) Track Description
 

Description

NOTE:
This track is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the genome browser database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.

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.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The underlying data file for this track is called spMut.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mm10/bbi/uniprot/spMut.bb -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

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

References

UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120

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