UniProtKB/Swiss-Prot P10721: Variant p.Val559Ala

Mast/stem cell growth factor receptor Kit
Gene: KIT
Chromosomal location: 4q11-q12
Variant information

Variant position:  559
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 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 Valine (V) to Alanine (A) at position 559 (V559A, p.Val559Ala).
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 medium size and hydrophobic (V) to small size and hydrophobic (A)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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:  In GIST.
Any additional useful information about the variant.



Sequence information

Variant position:  559
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  976
The length of the canonical sequence.

Location on the sequence:   IVMILTYKYLQKPMYEVQWK  V VEEINGNNYVYIDPTQLPYD
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                         IVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Mouse                         IVMVLTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Pig                           IVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Bovine                        FVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Goat                          FVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Cat                           IVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Dog                           IVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYD

Chicken                       IVMILVYIYLQKPKYEVQWKVVEEINGNNYVYIDPTQLPYD

Xenopus laevis                AVAVLMYKYLQKPKYEIQWKVVEEINGNNYVYIDPTQLPYD

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 26 – 976 Mast/stem cell growth factor receptor Kit
Topological domain 546 – 976 Cytoplasmic
Metal binding 568 – 568 Magnesium
Modified residue 547 – 547 Phosphotyrosine; by autocatalysis
Modified residue 553 – 553 Phosphotyrosine; by autocatalysis
Modified residue 568 – 568 Phosphotyrosine; by autocatalysis
Modified residue 570 – 570 Phosphotyrosine; by autocatalysis
Alternative sequence 414 – 976 Missing. In isoform 3.
Mutagenesis 571 – 571 I -> A. Reduction in SH2B2/APS binding. Abolishes SH2B2/APS binding; when associated with A-939.
Beta strand 558 – 564


Literature citations

Germline mutation in the juxtamembrane domain of the kit gene in a family with gastrointestinal stromal tumors and urticaria pigmentosa.
Beghini A.; Tibiletti M.G.; Roversi G.; Chiaravalli A.M.; Serio G.; Capella C.; Larizza L.;
Cancer 92:657-662(2001)
Cited for: VARIANT GIST ALA-559;

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.