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UniProtKB/Swiss-Prot Q9Y2R2: Variant p.Arg263Gln

Tyrosine-protein phosphatase non-receptor type 22
Gene: PTPN22
Variant information

Variant position:  263
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Polymorphism
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Arginine (R) to Glutamine (Q) at position 263 (R263Q, p.Arg263Gln).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from large size and basic (R) to medium size and polar (Q)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  1
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  Polymorphism; reduces risk of SLE and RA but not IDDM; associated with reduced risk of ulcerative colitis but not of Crohn disease; severely reduces phosphatase activity.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  263
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  807
The length of the canonical sequence.

Location on the sequence:   TWMLLKDGIIPENFSVFSLI  R EMRTQRPSLVQTQEQYELVY
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         TWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVY

Mouse                         TWMLLKDGIIPKNFSVFNLIQEMRTQRPSLVQTQEQYELVY

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 1 – 807 Tyrosine-protein phosphatase non-receptor type 22
Domain 24 – 289 Tyrosine-protein phosphatase
Binding site 274 – 274 Substrate
Alternative sequence 204 – 807 Missing. In isoform 5.
Alternative sequence 251 – 305 Missing. In isoform 3.
Helix 258 – 266


Literature citations

A loss-of-function variant of PTPN22 is associated with reduced risk of systemic lupus erythematosus.
Orru V.; Tsai S.J.; Rueda B.; Fiorillo E.; Stanford S.M.; Dasgupta J.; Hartiala J.; Zhao L.; Ortego-Centeno N.; D'Alfonso S.; Arnett F.C.; Wu H.; Gonzalez-Gay M.A.; Tsao B.P.; Pons-Estel B.; Alarcon-Riquelme M.E.; He Y.; Zhang Z.Y.; Allayee H.; Chen X.S.; Martin J.; Bottini N.; Danieli M.G.; Galeazzi M.; Sabbadini M.G.; Migliaresi S.; Sebastiani G.D.;
Hum. Mol. Genet. 18:569-579(2009)
Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 2-309 OF WILD TYPE AND VARIANT GLN-263; VARIANT GLN-263; CATALYTIC ACTIVITY; CHARACTERIZATION OF VARIANT GLN-263;

Differential association of two PTPN22 coding variants with Crohn's disease and ulcerative colitis.
Diaz-Gallo L.M.; Espino-Paisan L.; Fransen K.; Gomez-Garcia M.; van Sommeren S.; Cardena C.; Rodrigo L.; Mendoza J.L.; Taxonera C.; Nieto A.; Alcain G.; Cueto I.; Lopez-Nevot M.A.; Bottini N.; Barclay M.L.; Crusius J.B.; van Bodegraven A.A.; Wijmenga C.; Ponsioen C.Y.; Gearry R.B.; Roberts R.L.; Weersma R.K.; Urcelay E.; Merriman T.R.; Alizadeh B.Z.; Martin J.;
Inflamm. Bowel Dis. 17:2287-2294(2011)
Cited for: VARIANTS GLN-263 AND TRP-620; CHARACTERIZATION OF VARIANTS GLN-263 AND TRP-620;

Biochemical and functional studies of lymphoid-specific tyrosine phosphatase (Lyp) variants S201F and R266W.
Liu J.; Chen M.; Li R.; Yang F.; Shi X.; Zhu L.; Wang H.M.; Yao W.; Liu Q.; Meng F.G.; Sun J.P.; Pang Q.; Yu X.;
PLoS ONE 7:E43631-E43631(2012)
Cited for: VARIANTS PHE-201; GLN-263 AND TRP-266; CHARACTERIZATION OF VARIANTS PHE-201; GLN-263 AND TRP-266;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.