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UniProtKB/Swiss-Prot P21583: Variant p.Thr54Ala

Kit ligand
Gene: KITLG
Variant information

Variant position:  54
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LB/B
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:  From Threonine (T) to Alanine (A) at position 54 (T54A, p.Thr54Ala).
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 polar (T) 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

Polymorphism:  Genetic variants in KITLG define the skin/hair/eye pigmentation variation locus 7 (SHEP7) [MIM:611664]. Hair, eye and skin pigmentation are among the most visible examples of human phenotypic variation, with a broad normal range that is subject to substantial geographic stratification. In the case of skin, individuals tend to have lighter pigmentation with increasing distance from the equator. By contrast, the majority of variation in human eye and hair color is found among individuals of European ancestry, with most other human populations fixed for brown eyes and black hair.A non-coding SNP (dbSNP:rs12821256) has been shown to be associated with classic blond hair color in Europeans. This SNP is located 350 kb upstream from KITLG, in an enhancer specifically active in the hair follicle environment. It alters a LEF1 binding site, reducing LEF1 responsiveness in cultured keratinocytes. This SNP is not associated with eye pigmentation. It is most prevalent in Northern Europe (PubMed:24880339). -
Additional information on the polymorphism described.

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



Sequence information

Variant position:  54
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  273
The length of the canonical sequence.

Location on the sequence:   TNNVKDVTKLVANLPKDYMI  T LKYVPGMDVLPSHCWISEMV
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                         TNNVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMV

                              TDDVKDVTKLVANLPKDYKIALKYVPGMDVLPSHCWISVMV

Mouse                         TDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMV

Rat                           TDNVKDITKLVANLPNDYMITLNYVAGMDVLPSHCWLRDMV

Pig                           TDDVKDVTKLVANLPKDYKITLKYVPGMDVLPSHCWISEMV

Bovine                        TDDVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMV

Goat                          TDDVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMV

Cat                           TDDVKDVTKLVANLPKDYKIALKYVPGMDVLPSHCWISVMV

Horse                         TDDVKDVTKLVANLPKDYKITLKYVPGMDVLPSHCWISEMV

Chicken                       TDDVNDIAKLVGNLPNDYLITLKYVPKMDSLPNHCWLHLMV

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 – 273 Kit ligand
Chain 26 – 190 Soluble KIT ligand
Topological domain 26 – 214 Extracellular
Disulfide bond 29 – 114
Beta strand 53 – 56


Literature citations

No reference for the current variant in UniProtKB/Swiss-Prot.

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.