UniProtKB/Swiss-Prot Q9Y2R2: Variant p.Arg620Trp

Tyrosine-protein phosphatase non-receptor type 22
Gene: PTPN22
Chromosomal location: 1p13.2
Variant information

Variant position:  620
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 have been found in patients and disease-association is reported in literature. However, this classification is not a definitive assessment of variant pathogenicity.
  • Polymorphism: No disease-association has been reported.
  • Unclassified: Variants have been found in patients but disease-association remains unclear.

Residue change:  From Arginine (R) to Tryptophan (W) at position 620 (R620W, p.Arg620Trp).
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 large size and aromatic (W)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
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:  Confers susceptibility to systemic lupus erythematosus and type 1 diabetes mellitus; affects CSK kinase binding.
Any additional useful information about the variant.

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



Sequence information

Variant position:  620
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:   SAVLATAPRIDDEIPPPLPV  R TPESFIVVEEAGEFSPNVPK
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                         SAVLATAPRIDDEIPPPLPVRTPESFIVVEEAGEFSPNVPK

Mouse                         TAVEAPSRRTDDEIPPPLPERTPESFIVVEEAGEPSPRVTE

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
Modified residue 635 – 635 Phosphoserine
Alternative sequence 204 – 807 Missing. In isoform 5.


Literature citations

Human protein tyrosine phosphatase (70zpep) homolog.
Liu T.; Zhang J.; Fu G.; Zhang Q.; Ye M.; Zhou J.; Wu J.; Shen Y.; Yu M.; Chen S.; Mao M.; Chen Z.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANT TRP-620;

Identification of a Variant Form of Tyrosine Phosphatase LYP.
Wang S.; Dong H.; Han J.; Ho W.T.; Fu X.; Zhao Z.J.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4); VARIANT TRP-620;

The DNA sequence and biological annotation of human chromosome 1.
Gregory S.G.; Barlow K.F.; McLay K.E.; Kaul R.; Swarbreck D.; Dunham A.; Scott C.E.; Howe K.L.; Woodfine K.; Spencer C.C.A.; Jones M.C.; Gillson C.; Searle S.; Zhou Y.; Kokocinski F.; McDonald L.; Evans R.; Phillips K.; Atkinson A.; Cooper R.; Jones C.; Hall R.E.; Andrews T.D.; Lloyd C.; Ainscough R.; Almeida J.P.; Ambrose K.D.; Anderson F.; Andrew R.W.; Ashwell R.I.S.; Aubin K.; Babbage A.K.; Bagguley C.L.; Bailey J.; Beasley H.; Bethel G.; Bird C.P.; Bray-Allen S.; Brown J.Y.; Brown A.J.; Buckley D.; Burton J.; Bye J.; Carder C.; Chapman J.C.; Clark S.Y.; Clarke G.; Clee C.; Cobley V.; Collier R.E.; Corby N.; Coville G.J.; Davies J.; Deadman R.; Dunn M.; Earthrowl M.; Ellington A.G.; Errington H.; Frankish A.; Frankland J.; French L.; Garner P.; Garnett J.; Gay L.; Ghori M.R.J.; Gibson R.; Gilby L.M.; Gillett W.; Glithero R.J.; Grafham D.V.; Griffiths C.; Griffiths-Jones S.; Grocock R.; Hammond S.; Harrison E.S.I.; Hart E.; Haugen E.; Heath P.D.; Holmes S.; Holt K.; Howden P.J.; Hunt A.R.; Hunt S.E.; Hunter G.; Isherwood J.; James R.; Johnson C.; Johnson D.; Joy A.; Kay M.; Kershaw J.K.; Kibukawa M.; Kimberley A.M.; King A.; Knights A.J.; Lad H.; Laird G.; Lawlor S.; Leongamornlert D.A.; Lloyd D.M.; Loveland J.; Lovell J.; Lush M.J.; Lyne R.; Martin S.; Mashreghi-Mohammadi M.; Matthews L.; Matthews N.S.W.; McLaren S.; Milne S.; Mistry S.; Moore M.J.F.; Nickerson T.; O'Dell C.N.; Oliver K.; Palmeiri A.; Palmer S.A.; Parker A.; Patel D.; Pearce A.V.; Peck A.I.; Pelan S.; Phelps K.; Phillimore B.J.; Plumb R.; Rajan J.; Raymond C.; Rouse G.; Saenphimmachak C.; Sehra H.K.; Sheridan E.; Shownkeen R.; Sims S.; Skuce C.D.; Smith M.; Steward C.; Subramanian S.; Sycamore N.; Tracey A.; Tromans A.; Van Helmond Z.; Wall M.; Wallis J.M.; White S.; Whitehead S.L.; Wilkinson J.E.; Willey D.L.; Williams H.; Wilming L.; Wray P.W.; Wu Z.; Coulson A.; Vaudin M.; Sulston J.E.; Durbin R.M.; Hubbard T.; Wooster R.; Dunham I.; Carter N.P.; McVean G.; Ross M.T.; Harrow J.; Olson M.V.; Beck S.; Rogers J.; Bentley D.R.;
Nature 441:315-321(2006)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT TRP-620;

Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT TRP-620;

Genetic association of the R620W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE.
Kyogoku C.; Langefeld C.D.; Ortmann W.A.; Lee A.; Selby S.; Carlton V.E.H.; Chang M.; Ramos P.; Baechler E.C.; Batliwalla F.M.; Novitzke J.; Williams A.H.; Gillett C.; Rodine P.; Graham R.R.; Ardlie K.G.; Gaffney P.M.; Moser K.L.; Petri M.; Begovich A.B.; Gregersen P.K.; Behrens T.W.;
Am. J. Hum. Genet. 75:504-507(2004)
Cited for: VARIANT TRP-620; INVOLVEMENT IN SLE;

A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes.
Bottini N.; Musumeci L.; Alonso A.; Rahmouni S.; Nika K.; Rostamkhani M.; MacMurray J.; Meloni G.F.; Lucarelli P.; Pellecchia M.; Eisenbarth G.S.; Comings D.; Mustelin T.;
Nat. Genet. 36:337-338(2004)
Cited for: VARIANT TRP-620; CHARACTERIZATION OF VARIANT TRP-620;

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.