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UniProtKB/Swiss-Prot P02458: Variant p.Arg565Cys

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

Variant position:  565
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Arginine (R) to Cysteine (C) at position 565 (R565C, p.Arg565Cys).
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

Variant description:  In STL1.
Any additional useful information about the variant.

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



Sequence information

Variant position:  565
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:   NGDPGRPGEPGLPGARGLTG  R PGDAGPQGKVGPSGAPGEDG
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                         NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDG

Mouse                         NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDG

Rat                           NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDG

Bovine                        NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDG

Xenopus laevis                NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGASGEDG

Xenopus tropicalis            NGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGASGEDG

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 182 – 1241 Collagen alpha-1(II) chain
Region 97 – 1237 Disordered
Region 201 – 1214 Triple-helical region
Alternative sequence 1 – 1219 Missing. In isoform 3.


Literature citations

Variation in the vitreous phenotype of Stickler syndrome can be caused by different amino acid substitutions in the X position of the type II collagen Gly-X-Y triple helix.
Richards A.J.; Baguley D.M.; Yates J.R.W.; Lane C.; Nicol M.; Harper P.S.; Scott J.D.; Snead M.P.;
Am. J. Hum. Genet. 67:1083-1094(2000)
Cited for: VARIANT STL1 CYS-565; VARIANT DRRD PHE-667;

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.