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UniProtKB/Swiss-Prot P02458: Variant p.Arg1459Cys

Collagen alpha-1(II) chain
Gene: COL2A1
Variant information

Variant position:  1459
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 Arginine (R) to Cysteine (C) at position 1459 (R1459C, p.Arg1459Cys).
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 medium size and polar (C)
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

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



Sequence information

Variant position:  1459
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1487
The length of the canonical sequence.

Location on the sequence:   TKHTGKWGKTVIEYRSQKTS  R LPIIDIAPMDIGGPEQEFGV
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                         TKHTGKWGKTVIEYRSQKTSRLPIIDIAPMDIGGPEQEFGV

Mouse                         TKHTGKWGKTVIEYRSQKTSRLPIIDIAPMDIGGAEQEFGV

Rat                           TKHTGKWGKTIIEYRSQKTSRLPIVDIAPMDIGGPDQEFGV

Bovine                        TKHTGKWGKTMIEYRSQKTSRLPIIDIAPMDIGGPEQEFGV

Xenopus laevis                KKHTGKWSKTVIEYRTQKTSRLPIVDIAPMDIGGADQEFGV

Xenopus tropicalis            KKHTGKWSKTVIEYRTQKTSRLPIVDIAPMDIGGADQEFGV

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 1242 – 1487 Chondrocalcin
Domain 1253 – 1487 Fibrillar collagen NC1
Disulfide bond 1323 – 1485


Literature citations

Mutations in KARS cause early-onset hearing loss and leukoencephalopathy: Potential pathogenic mechanism.
Zhou X.L.; He L.X.; Yu L.J.; Wang Y.; Wang X.J.; Wang E.D.; Yang T.;
Hum. Mutat. 38:1740-1750(2017)
Cited for: VARIANT CYS-1459;

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.