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UniProtKB/Swiss-Prot P02458: Variant p.Gly1305Asp

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

Variant position:  1305
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 Glycine (G) to Aspartate (D) at position 1305 (G1305D, p.Gly1305Asp).
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 glycine (G) to medium size and acidic (D)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -1
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 vitreoretinopathy; with phalangeal epiphyseal dysplasia.
Any additional useful information about the variant.

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

Sequence information

Variant position:  1305
The position of the amino-acid change on the UniProtKB canonical protein sequence.

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

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.







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.

Chain 1242 – 1487 Chondrocalcin
Domain 1253 – 1487 Fibrillar collagen NC1
Metal binding 1301 – 1301 Calcium
Metal binding 1303 – 1303 Calcium
Metal binding 1304 – 1304 Calcium; via carbonyl oxygen
Metal binding 1306 – 1306 Calcium; via carbonyl oxygen
Metal binding 1309 – 1309 Calcium
Disulfide bond 1283 – 1315
Disulfide bond 1289 – 1289 Interchain (with C-1306)
Disulfide bond 1306 – 1306 Interchain (with C-1289)

Literature citations

Vitreoretinopathy with phalangeal epiphyseal dysplasia, a type II collagenopathy resulting from a novel mutation in the C-propeptide region of the molecule.
Richards A.J.; Morgan J.; Bearcroft P.W.P.; Pickering E.; Owen M.J.; Holmans P.; Williams N.; Tysoe C.; Pope F.M.; Snead M.P.; Hughes H.;
J. Med. Genet. 39:661-665(2002)

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.