Schema for UniProt Variants - UniProt/SwissProt Amino Acid Substitutions
  Database: dm6    Primary Table: spMut Data last updated: 2017-10-10
Big Bed File: /gbdb/dm6/bbi/uniprot/
Item Count: 2,561
Format description: Browser extensible data (12 fields) plus information about uniProt mutation
chromchr2LChromosome (or contig, scaffold, etc.)
chromStart16045891Start position in chromosome
chromEnd16045894End position in chromosome
nameG296RName of item
score1000Score from 0-1000
strand++ or -
thickStart16045891Start of where display should be thick (start codon)
thickEnd16045894End 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
mutationposition 296, Gly changed to ArgCoding seq. mutation
commentsIn allele RU-35; bicaudal phenotype; lowers RNA-bindingComment
variationIdUniProt variant
uniProtIdQ24009UniProt record
pmids9671494Source articles

Sample Rows
chr2L1604589116045894G296R1000+16045891160458940130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 296, Gly changed to ArgIn allele RU-35; bicaudal phenotype; lowers RNA-bindingQ240099671494
chr2L1617375716173760C629Y1000+16173757161737600130Manually reviewed (Swiss-Prot)Experimental mutation of amino acidsposition 629, Cys changed to TyrIn AR66; slower channel activation and reduction of peak currentQ242709502794,9539432
chr2L1644534916445352I8L1000+16445349164453520130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB15b,MB25aposition 8, Ile changed to Leustrain: MB15b,MB25a;Q8MM24
chr2L1644545716445460N44S1000+16445457164454600130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB13a, MB15b, MB25a, MB34a, MB37a,MB63aposition 44, Asn changed to Serstrain: MB13a, MB15b, MB25a, MB34a, MB37a,MB63a;Q8MM24
chr2L1644562516445628S100G1000+16445625164456280130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB01a,MB33aposition 100, Ser changed to Glystrain: MB01a,MB33a;Q8MM24
chr2L1644567316445676V116I1000+16445673164456760130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB08b, MB29b, MB36a, MB40b, MB47a, MB48b, MB52b,MB58bposition 116, Val changed to Ilestrain: MB08b, MB29b, MB36a, MB40b, MB47a, MB48b, MB52b,MB58b;Q8MM24
chr2L1644588316445886E186Q1000+16445883164458860130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB08b, MB29b, MB40b, MB45b, MB47a, MB48b, MB52b,MB80bposition 186, Glu changed to Glnstrain: MB08b, MB29b, MB40b, MB45b, MB47a, MB48b, MB52b,MB80b;Q8MM24
chr2L1644631116446314G305E1000+16446311164463140130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB01a, MB08b, MB29b, MB36a, MB45b, MB47a, MB48b,MB52b,MB80bposition 305, Gly changed to Glustrain: MB01a, MB08b, MB29b, MB36a, MB45b, MB47a, MB48b,MB52b,MB80b;Q8MM24
chr2L1644633516446338I313V1000+16446335164463380130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB48b,MB52bposition 313, Ile changed to Valstrain: MB48b,MB52b;Q8MM24
chr2L1644659316446596V399E1000+16446593164465960130Manually reviewed (Swiss-Prot)Naturally occurring sequence variantstrain: MB34a,MB39bposition 399, Val changed to Glustrain: MB34a,MB39b;Q8MM24

UniProt Variants (spMut) Track Description


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.


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 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 -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.


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


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