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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q06124: Variant p.Arg498Trp

Tyrosine-protein phosphatase non-receptor type 11
Gene: PTPN11
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Variant information Variant position: help 498 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance
Residue change: help From Arginine (R) to Tryptophan (W) at position 498 (R498W, p.Arg498Trp). 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: help 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: help -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: help In LPRD1; reduced phosphatase activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 498 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 593 The length of the canonical sequence.
Location on the sequence: help IIREKGVDCDIDVPKTIQMV R SQRSGMVQTEAQYRFIYMAV 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Mouse                         IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Rat                           IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Chicken                       IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV
Sequence annotation in neighborhood: help 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 2 – 593 Tyrosine-protein phosphatase non-receptor type 11
Domain 247 – 517 Tyrosine-protein phosphatase
Binding site 506 – 506
Alternative sequence 461 – 593 Missing. In isoform 3.
Helix 490 – 498



Literature citations
Clinical and molecular analysis of 30 patients with multiple lentigines LEOPARD syndrome.
Sarkozy A.; Conti E.; Digilio M.C.; Marino B.; Morini E.; Pacileo G.; Wilson M.; Calabro R.; Pizzuti A.; Dallapiccola B.;
J. Med. Genet. 41:E68-E68(2004)
Cited for: VARIANTS LPRD1 CYS-279; SER-279; ALA-464; MET-468; TRP-498; LEU-498 AND PRO-506; A PTPN11 allele encoding a catalytically impaired SHP2 protein in a patient with a Noonan syndrome phenotype.
Edwards J.J.; Martinelli S.; Pannone L.; Lo I.F.; Shi L.; Edelmann L.; Tartaglia M.; Luk H.M.; Gelb B.D.;
Am. J. Med. Genet. A 164:2351-2355(2014)
Cited for: VARIANT NS1 SER-491; VARIANT LPRD1 TRP-498; CHARACTERIZATION OF VARIANTS NS1 SER-491; CHARACTERIZATION OF VARIANT LPRD1 TRP-498;
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.