UniProtKB/Swiss-Prot Q06124: Variant p.Tyr63Cys

Tyrosine-protein phosphatase non-receptor type 11
Gene: PTPN11
Chromosomal location: 12q24.1
Variant information

Variant position:  63
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
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 Tyrosine (Y) to Cysteine (C) at position 63 (Y63C, p.Tyr63Cys).
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 aromatic (Y) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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

Involvement in disease:  Noonan syndrome 1 (NS1) [MIM:163950]: A form of Noonan syndrome, a disease characterized by short stature, facial dysmorphic features such as hypertelorism, a downward eyeslant and low-set posteriorly rotated ears, and a high incidence of congenital heart defects and hypertrophic cardiomyopathy. Other features can include a short neck with webbing or redundancy of skin, deafness, motor delay, variable intellectual deficits, multiple skeletal defects, cryptorchidism, and bleeding diathesis. Individuals with Noonan syndrome are at risk of juvenile myelomonocytic leukemia, a myeloproliferative disorder characterized by excessive production of myelomonocytic cells. Some patients with NS1 develop multiple giant cell lesions of the jaw or other bony or soft tissues, which are classified as pigmented villonodular synovitis (PVNS) when occurring in the jaw or joints. {ECO:0000269|PubMed:11704759, ECO:0000269|PubMed:11992261, ECO:0000269|PubMed:12161469, ECO:0000269|PubMed:12325025, ECO:0000269|PubMed:12529711, ECO:0000269|PubMed:12634870, ECO:0000269|PubMed:12717436, ECO:0000269|PubMed:12739139, ECO:0000269|PubMed:12960218, ECO:0000269|PubMed:15384080, ECO:0000269|PubMed:15889278, ECO:0000269|PubMed:15948193, ECO:0000269|PubMed:19020799, ECO:0000269|PubMed:24891296, ECO:0000269|PubMed:28074573}. Note=The disease is caused by mutations affecting the gene represented in this entry. Mutations in PTPN11 account for more than 50% of the cases.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In NS1.
Any additional useful information about the variant.

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



Sequence information

Variant position:  63
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  597
The length of the canonical sequence.

Location on the sequence:   LSVRRNGAVTHIKIQNTGDY  Y DLYGGEKFATLAELVQYYME
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                         LSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYME

Mouse                         LSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYME

Rat                           LSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYME

Chicken                       LSVRRTGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYME

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 2 – 597 Tyrosine-protein phosphatase non-receptor type 11
Domain 6 – 102 SH2 1
Modified residue 62 – 62 Phosphotyrosine
Modified residue 66 – 66 Phosphotyrosine
Beta strand 63 – 65


Literature citations

Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome.
Tartaglia M.; Mehler E.L.; Goldberg R.; Zampino G.; Brunner H.G.; Kremer H.; van der Burgt I.; Crosby A.H.; Ion A.; Jeffery S.; Kalidas K.; Patton M.A.; Kucherlapati R.S.; Gelb B.D.;
Nat. Genet. 29:465-468(2001)
Cited for: VARIANTS NS1 GLY-61; CYS-63; GLY-72; SER-72; ASP-76; ARG-79; VAL-282; ASP-308 AND VAL-508;

PTPN11 mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity.
Tartaglia M.; Kalidas K.; Shaw A.; Song X.; Musat D.L.; van der Burgt I.; Brunner H.G.; Bertola D.R.; Crosby A.H.; Ion A.; Kucherlapati R.S.; Jeffery S.; Patton M.A.; Gelb B.D.;
Am. J. Hum. Genet. 70:1555-1563(2002)
Cited for: VARIANTS NS1 ALA-42; ALA-60; ASN-61; GLY-61; ASP-62; CYS-63; GLY-72; ILE-73; ASP-76; ARG-79; ALA-106; ASP-139; CYS-279; VAL-282; LEU-285; SER-285; ASP-308; SER-308; VAL-309; LYS-505 AND VAL-508;

PTPN11 mutations in Noonan syndrome type I: detection of recurrent mutations in exons 3 and 13.
Maheshwari M.; Belmont J.; Fernbach S.; Ho T.; Molinari L.; Yakub I.; Yu F.; Combes A.; Towbin J.A.; Craigen W.J.; Gibbs R.A.;
Hum. Mutat. 20:298-304(2002)
Cited for: VARIANTS NS1 ASP-62; CYS-63 AND THR-506;

PTPN11 (protein-tyrosine phosphatase, nonreceptor-type 11) mutations in seven Japanese patients with Noonan syndrome.
Kosaki K.; Suzuki T.; Muroya K.; Hasegawa T.; Sato S.; Matsuo N.; Kosaki R.; Nagai T.; Hasegawa Y.; Ogata T.;
J. Clin. Endocrinol. Metab. 87:3529-3533(2002)
Cited for: VARIANTS NS1 GLY-61; CYS-63; SER-72; ILE-73; SER-285 AND ASP-308;

Spectrum of mutations in PTPN11 and genotype-phenotype correlation in 96 patients with Noonan syndrome and five patients with cardio-facio-cutaneous syndrome.
Musante L.; Kehl H.G.; Majewski F.; Meinecke P.; Schweiger S.; Gillessen-Kaesbach G.; Wieczorek D.; Hinkel G.K.; Tinschert S.; Hoeltzenbein M.; Ropers H.-H.; Kalscheuer V.M.;
Eur. J. Hum. Genet. 11:201-206(2003)
Cited for: VARIANTS NS1 LYS-58; ASN-61; GLY-61; CYS-63; GLN-69; LEU-71; SER-72; ILE-73; ASP-76; ARG-79; ASP-139; ARG-256; VAL-282 AND ASP-308;

Correlation between PTPN11 gene mutations and congenital heart defects in Noonan and LEOPARD syndromes.
Sarkozy A.; Conti E.; Seripa D.; Digilio M.C.; Grifone N.; Tandoi C.; Fazio V.M.; Di Ciommo V.; Marino B.; Pizzuti A.; Dallapiccola B.;
J. Med. Genet. 40:704-708(2003)
Cited for: VARIANTS NS1 ILE-2; ALA-42; ASP-62; CYS-63; GLY-72; PRO-79; ALA-106; CYS-279; ASP-308; SER-308; MET-472; ARG-507; VAL-508 AND PHE-564;

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.